Polycyclic aromatic bridges for molecular electronic sensors.

Abstract

In various embodiments, synthetic bridge molecules that can be used in molecular electronic sensors are disclosed. In various aspects, the bridge molecules comprise polycyclic aromatic hydrocarbon structures that are fused rings in the shape of long, narrow ribbons, with terminal groups at the opposite short ends for selective binding to metal electrodes, one or more substituents near the midpoint of the long edge for binding to probe molecules, and one or more additional substituents for solubility or other effects. In various embodiments, the bridge molecules herein are conductive, and when bridged between gapped electrodes, they create a closed circuit in the sensor.

Description

[Technical field]

[0001] CROSS-REFERENCE TO RELATED APPLICATIONS This application claims priority to and the benefit of U.S. Provisional Patent Application No. 62 / 833,562, filed April 12, 2019, entitled “Polycyclic Aromatic Bridges for Molecular Electronic Sensors,” the entire disclosure of which is incorporated herein by reference.

[0002] Field The present disclosure relates generally to molecular electronic sensors, and more particularly to the design, synthesis and use of electronically conducting polycyclic aromatic molecules as components in molecular electronic sensors. [Background technology]

[0003] background The broad field of molecular electronics was introduced in the 1970s by Aviram and Ratner. The idea was that the smallest possible electrical circuits would incorporate single molecules as circuit components. Molecular circuit elements can achieve diverse functions and operations as switches, rectifiers, actuators or sensors, depending on the molecule. Such constructs can be applied as sensors, since molecular interactions can provide the basis for single-molecule sensing.

[0004] For example, one class of molecular elements that can be used in electronic circuits that has been extensively explored is carbon nanotubes (CNTs). Carbon nanotubes can be used to bridge between two electrodes, thereby forming a molecular wire. Of all the nanoscale circuit options, CNTs have been explored extensively because they are easily formed in bulk. For example, CNTs arise as a by-product of combustion at the molecular level and have good conductive properties. However, CNTs are not formed in precise, highly controlled reactions, and it is hardly possible to plan, formulate or design and control their dimensions, or modify them with atomic precision in terms of position and elemental composition.

[0005] Molecular sensors can include various biopolymers as bridges between two electrodes and may rely on at least some degree of molecular self-assembly in their manufacture. Despite recent advances in the field of molecular electronic sensors, novel macromolecules for such sensors that are not CNTs or biomolecules are desired to reduce costs, facilitate self-assembly binding of the macromolecules to other components, and improve the performance, durability and reliability of molecular sensors that include macromolecular circuit components. Summary of the Invention [Means for solving the problem]

[0006] overview In various embodiments, synthetic macromolecules are disclosed that can be used in a variety of molecular electronic sensors. In various aspects, the design and synthesis of polycyclic aromatic compounds is described, in addition to the use of the molecules herein as bridging molecules in molecular electronic sensor circuits.

[0007] In various embodiments, the polycyclic aromatic bridged molecules herein comprise molecular ribbons having a core structure consisting essentially of fused benzene and / or heteroaromatic rings, such that the ribbons, as a whole, comprise sp2 In various examples, the molecular ribbons are functionalized at specific positions to aid in the attachment of the molecular ribbons to other molecules, such as metal electrodes and probe molecules, and to optimize the desired solubility of the molecular ribbons in various solvents. [Brief description of the drawings]

[0008] [Figure 1] FIG. 1 illustrates the general concept of molecular electronics, in which a single molecular circuit element bridges between two spaced apart electrodes.

[0009] [Diagram 2] FIG. 2 illustrates an embodiment of a molecular electronic sensor and an example of its functioning.

[0010] [Diagram 3] FIG. 3 illustrates an embodiment of a self-assembly process in the fabrication of a molecular electronic sensor.

[0011] [Figure 4] FIG. 4 illustrates an embodiment of a molecular electronic sensor that can be used for DNA sequencing.

[0012] [Diagram 5] FIG. 5 illustrates an embodiment of a molecular sensor structure that includes a polymerase conjugated to a bridging molecule that spans the electrode gap, which can be used in DNA sequencing experiments.

[0013] [Figure 6] FIG. 6 illustrates an embodiment of an apparatus for electrical measurements on a molecular sensor.

[0014] [Figure 7] FIG. 7 illustrates an electron microscope (EM) image of spaced electrodes containing gold metal dot contacts for molecular cross-linking.

[0015] [Figure 8] FIG. 8 illustrates an example of a sequencing signal generated from an experimental molecular sensor in a DNA sequencing study.

[0016] [Figure 9] FIG. 9 illustrates the general structural scheme and design rationale for polycyclic aromatic ring-bridged molecules according to the present disclosure, represented by the polycyclic ribbon structure of compound (I).

[0017] [Figure 10] FIG. 10 illustrates the general structural scheme and design rationale for a variety of polycyclic aromatic ring-bridged molecules, represented by the polycyclic ribbon structure of compound (II).

[0018] [Figure 11] FIG. 11 illustrates a class of polycyclic aromatic hydrocarbon bridged molecules, compound (III), according to the present disclosure.

[0019] [Figure 12] FIG. 12 illustrates a 3D space-filling model of an embodiment of compound (IV), a polycyclic aromatic hydrocarbon (PAH) crosslinked molecule, containing PEG side chains to promote water solubility.

[0020] [Figure 13] FIG. 13 illustrates a 3D space-filling model of an embodiment of a bridge and probe molecule conjugate compound (V) comprising E. coli Klenow fragment polymerase linked to a bridge and a polycyclic aromatic hydrocarbon ("PAH") nanoribbon further comprising a PEG side chain.

[0021] [Figure 14] FIG. 14 illustrates embodiments representative of low molecular weight polycyclic aromatic hydrocarbons that can be used as building blocks or intermediates in the synthesis of the crosslinking molecules herein, or monomeric moieties or substructures within the crosslinking molecules disclosed herein.

[0022] [Figure 15] FIG. 15 illustrates embodiments representative of monocyclic carbon ring structures that can be used as building blocks for the polycyclic aromatic hydrocarbon bridge molecules herein, or monomeric moieties or substructures within the bridge molecules disclosed herein.

[0023] [Figure 16] FIG. 16 illustrates embodiments representative of heterocyclic ring structures that can be used as building blocks for the polycyclic aromatic hydrocarbon bridge molecules herein, or monomeric moieties or substructures within the bridge molecules disclosed herein.

[0024] [Figure 17] FIG. 17 illustrates the type of polycyclic aromatic hydrocarbon bridge represented by compound (III), with the functional regions of the molecule displayed below the chemical structure.

[0025] [Figure 18] FIG. 18 illustrates a class of polycyclic aromatic hydrocarbon bridged molecules represented by compound (VI), which includes a single continuous 13-atom wide polycyclic aromatic hydrocarbon conductor (herein, "13-APAH"), with the aromatic portion of the ribbon being approximately 1.4 nm wide.

[0026] [Figure 19] FIG. 19 illustrates a class of polycyclic aromatic hydrocarbon bridged molecules represented by compound (VII), which includes a single contiguous 9-atom wide polycyclic aromatic hydrocarbon conductor (herein, "9-APAH").

[0027] [Figure 20] FIG. 20 illustrates the type of polycyclic aromatic hydrocarbon bridged molecule represented by compound (VIII), which contains a 2-monoPEG-PAH structure.

[0028] [Figure 21]FIG. 21 illustrates a class of polycyclic aromatic hydrocarbon bridged molecules, represented by compound (XV), containing 2-monoPEG-PAH structures of various lengths based on the number of monomer units and with thiomethyl substituents at each end for electrode attachment.

[0029] [Figure 22] 22-30 illustrate embodiments of synthetic routes to the synthetic cross-linking molecule represented by compound (XV) of FIG. [Figure 23] 22-30 illustrate embodiments of synthetic routes to the synthetic cross-linking molecule represented by compound (XV) of FIG. [Figure 24] 22-30 illustrate embodiments of synthetic routes to the synthetic cross-linking molecule represented by compound (XV) of FIG. [Diagram 25] 22-30 illustrate embodiments of synthetic routes to the synthetic cross-linking molecule represented by compound (XV) of FIG. [Figure 26] 22-30 illustrate embodiments of synthetic routes to the synthetic cross-linking molecule represented by compound (XV) of FIG. [Figure 27] 22-30 illustrate embodiments of synthetic routes to the synthetic cross-linking molecule represented by compound (XV) of FIG. [Figure 28] 22-30 illustrate embodiments of synthetic routes to the synthetic cross-linking molecule represented by compound (XV) of FIG. [Figure 29] 22-30 illustrate embodiments of synthetic routes to the synthetic cross-linking molecule represented by compound (XV) of FIG. [Diagram 30] 22-30 illustrate embodiments of synthetic routes to the synthetic cross-linking molecule represented by compound (XV) of FIG.

[0030] [Figure 31a] 31a and 31b illustrate the 2D chemical structure and the corresponding 3D structural model of a synthetic bridge molecule comprising a single dendron-attached polyanthracene nanoribbon, respectively. [Figure 31b]31a and 31b illustrate the 2D chemical structure and the corresponding 3D structural model of a synthetic bridge molecule comprising a single dendron-attached polyanthracene nanoribbon, respectively.

[0031] [Diagram 32] FIG. 32 illustrates an embodiment of a molecular component for a sensor circuit in which the molecular component includes two PAH molecules that act as arms for wiring a sensor probe molecule into the circuit.

[0032] [Diagram 33] FIG. 33 illustrates an embodiment of a single PAH electrode bridge molecule that can be used in DNA sequencing.

[0033] [Diagram 34] FIG. 34 illustrates an embodiment of a single PAH electrode bridge molecule that can be used in DNA sequencing.

[0034] [Figure 35a] 35a and 35b illustrate the 2D chemical structure and the corresponding 3D structural model, respectively, of a synthetic crosslinking molecule containing a zigzag edge PAH crosslink, compound (XIII). [Figure 35b] 35a and 35b illustrate the 2D chemical structure and the corresponding 3D structural model, respectively, of a synthetic crosslinking molecule containing a zigzag edge PAH crosslink, compound (XIII).

[0035] [Diagram 36] 36-42 illustrate embodiments of synthetic routes to compound (VI) of FIG. [Figure 37] 36-42 illustrate embodiments of synthetic routes to compound (VI) of FIG. [Figure 38] 36-42 illustrate embodiments of synthetic routes to compound (VI) of FIG. [Figure 39] 36-42 illustrate embodiments of synthetic routes to compound (VI) of FIG. [Diagram 40] 36-42 illustrate embodiments of synthetic routes to compound (VI) of FIG. [Diagram 41] 36-42 illustrate embodiments of synthetic routes to compound (VI) of FIG. [Diagram 42] 36-42 illustrate embodiments of synthetic routes to compound (VI) of FIG.

[0036] [Diagram 43] FIG. 43 illustrates an embodiment of a polycyclic bridged molecule represented by compound (XII) that includes a phenyl-substituted 12-APAH ribbon structure with zigzag edges.

[0037] [Figure 44a] Figures 44a-44e illustrate embodiments of PAH cross-linked molecules; Figure 44a illustrates the 2D chemical structure of compound (XIX); Figure 44b shows a 3D model of compound (XIX); Figure 44c shows a diagram of a bulk sample and a TEM image of this compound; Figure 44d shows the mass spectrum of this compound; Figure 44e shows the 1H-NMR spectrum of this compound. [Figure 44b] Figures 44a-44e illustrate embodiments of PAH cross-linked molecules; Figure 44a illustrates the 2D chemical structure of compound (XIX); Figure 44b shows a 3D model of compound (XIX); Figure 44c shows a diagram of a bulk sample and a TEM image of this compound; Figure 44d shows the mass spectrum of this compound; Figure 44e shows the 1H-NMR spectrum of this compound. [Fig. 44c] Figures 44a-44e illustrate embodiments of PAH cross-linked molecules; Figure 44a illustrates the 2D chemical structure of compound (XIX); Figure 44b shows a 3D model of compound (XIX); Figure 44c shows a diagram of a bulk sample and a TEM image of this compound; Figure 44d shows the mass spectrum of this compound; Figure 44e shows the 1H-NMR spectrum of this compound. [Fig.44d]Figures 44a-44e illustrate embodiments of PAH cross-linked molecules; Figure 44a illustrates the 2D chemical structure of compound (XIX); Figure 44b shows a 3D model of compound (XIX); Figure 44c shows a diagram of a bulk sample and a TEM image of this compound; Figure 44d shows the mass spectrum of this compound; Figure 44e shows the 1H-NMR spectrum of this compound. [Figure 44e] Figures 44a-44e illustrate embodiments of PAH cross-linked molecules; Figure 44a illustrates the 2D chemical structure of compound (XIX); Figure 44b shows a 3D model of compound (XIX); Figure 44c shows a diagram of a bulk sample and a TEM image of this compound; Figure 44d shows the mass spectrum of this compound; Figure 44e shows the 1H-NMR spectrum of this compound. DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS

[0038] Detailed Description Molecular electronics refers to circuits that use single molecules or molecular assemblies as components of an electronic circuit. Figure 1 illustrates the general concept of molecular electronics, in which molecules participate as key elements in an electrical circuit. In the illustrated embodiment, molecules are used as conductive bridges that complete an electrical circuit between an anode and a cathode or between a source and a drain electrode. Such circuits can be detection circuits, in which a single molecular bridge constitutes a transducer that interacts with a test solution and generates an electrical signal related to the composition of the test solution. In particular, such a sensor complex may include a single conductive bridge molecule, and the signal is related to the modulation of the current flowing through the molecular conductor.

[0039] Figure 2 illustrates an embodiment of a molecular electronic sensor that includes a circuit that further includes a probe molecule in addition to a bridge molecule. In the upper part of the figure, the probe molecule is illustrated interacting with various target molecules in solution, where the probe molecule is linked to a molecular bridge molecule that is directly present in the circuit. The lower part of the figure shows the function of the sensor by monitoring the current flowing through the bridge molecule and the generation of individual current spikes that indicate various interactions of the probe molecule with various target molecules.

[0040] FIG. 3 illustrates the general concept of self-assembly in the manufacture of molecular sensors. In various aspects, molecular electronic sensors can self-assemble by chemical reactions, allowing for efficient manufacture on a commercial scale. FIG. 3 illustrates a bridge molecule with chemical groups L, R, and P that allow for self-assembly, whereby a probe molecule ("probe") is conjugated to the P functional group, the left electrode is conjugated to the L functional group, and the right electrode is conjugated to the R functional group. In various embodiments, L and R are chemically distinct substituents, such that the bridge molecule can self-assemble in a specific orientation relative to the electrodes. In other examples, L and R are the same group. It should be noted that "left" and "right" are used throughout this disclosure merely to simplify the discussion of the orientation of a molecule having two ends that can be attached to spaced apart electrodes, with one end of the molecule attached to one electrode and the other end of the molecule attached to the other electrode to bridge the gap between the two spaced apart electrodes. Depending on the spatial orientation of the viewer, the left electrode can be the source electrode and the right electrode can be the drain electrode, or vice versa. Similarly, a long and narrow molecule (e.g., a DNA oligomer, a polypeptide, or a polycyclic aromatic hydrocarbon nanoribbon) has a leftmost end and a rightmost end, such as the end of a single thread, or the short end of a rectangular strip or ribbon.

[0041] There is a great interest in molecular sensors designed for and applied to DNA sequencing. An embodiment of a molecular sensor for DNA sequencing is illustrated in Figures 4 and 5. In these examples, the electronic circuit includes a molecular complex further including an enzyme, such as a polymerase, conjugated to a bridge molecule. The enzyme binds processively to the DNA strand and causes an electrical perturbation in the molecular electronic circuit that can be detected by a highly sensitive current meter. The conductive bridge molecule may include a biopolymer, such as a double-stranded DNA molecule, and the probe molecule may include a DNA polymerase that can bind to a single-stranded DNA target to generate a sequence-related signal. The electrical signal may include current spikes over time, as shown. The current signal thus observed may contain individual spikes corresponding to specific DNA bases, allowing the DNA sequence to be determined.

[0042] FIG. 5 illustrates a detailed working sensor 200 embodiment used herein as a DNA reading device for a DNA sequencing system. The molecular sensor structure 200 comprises two electrodes 201 and 202, which include titanium (Ti), aluminum (Al), copper (Cu), ruthenium (Ru), platinum (Pt), palladium (Pd), chromium (Cr) or other metals. The electrodes 201 and 202 may include source and drain electrodes in a circuit. The electrodes 201 and 202 are separated by a nano-gap of about 10 nm. Other gap distances may be required to accommodate other lengths of biomolecular bridges and the relative sizes of the probe molecules conjugated thereto. In this example, the bridge molecule 203 comprises a double-stranded DNA oligomer molecule approximately 20 nm in length (e.g., 60 bases; 6 helical turns) with thiol groups 204 and 205 configured at both the 3' and 5' ends of the oligomer for coupling of the bridge molecule 203 to gold contact points 206 and 207 provided on each metal electrode 201 and 202. The bonds between both ends of the DNA oligomer and the gold contact points comprise sulfur-gold bonds available from the thiol group on the 5' end of the DNA bridge molecule that is bound to gold. The probe molecule in this sensor comprises the Klenow fragment of E. coli polymerase I molecule 210 chemically cross-linked to streptavidin protein 212 at covalent linker 211 using a biotinylation site on the polymerase, which in turn binds to binding site 214 via a biotinylated nucleotide in the synthetic DNA oligomer 203. In operation, the sensor 200 further includes a DNA strand 220 that is processed by a polymerase 210. Figure 5 approximates the relative sizes of the molecules and atoms. In accordance with the present disclosure, this exemplary double-stranded DNA bridging molecule 203 may be replaced by a synthetic bridging molecule, such as the fused polycyclic aromatic hydrocarbon ribbons described herein.

[0043] In various embodiments, the molecular sensor for DNA sequencing further comprises an array of nanoscale electrodes, such as electrodes arranged in a plurality of paired electrodes. The two electrodes in the paired electrodes may be spaced apart (gapped) by a nanoscale gap, referred to herein as a "nano gap". An example of a measurement system that can be used to generate a sensor signal corresponding to a DNA base is illustrated in FIG. 6.

[0044] As illustrated in FIG. 6, such nanoscale sensors can be post-processed and placed on the pixels of a CMOS sensor pixel array, which further includes all of the control circuitry required to support measurement, readout, and generate such signals from multiple sensors operating in parallel. FIG. 6 illustrates various electrical components and connections in a molecular sensor. In the upper portion of the figure, a cross-section of an electrode-substrate structure 300 is illustrated, including attachment to an analyzer 301 for applying a voltage to the sensor's bridge molecules and measuring the current flowing therethrough. In the lower portion of the figure, a perspective view of an electrode array 302 that can be used in a bridge circuit is illustrated. Each pair of electrodes includes a contact dot or island of a first metal (e.g., "metal-1") and a second metal (e.g., "metal-2") at the end of each electrode near the gap that separates the electrodes. In various examples, metal-1 and metal-2 may include the same metal or different metals. In other aspects, the contact dots are gold (Au) islands on metal electrodes that include different metals. In various experiments, the contact dots comprise gold (Au) beads or gold (Au) coated electrode tips that support the self-assembly of a single bridge molecule over each gap between a pair of electrodes, such as via thiol-gold or reactive carbene-gold bonds at each end of the bridge molecule.

[0045] FIG. 7 illustrates a reduction to implement an embodiment of a DNA sequencing sensor. The electron microscope image shows an electrode with gold metal dot contacts for cross-linking. In this example, the electrodes are disposed on a silicon substrate and were produced by e-beam lithography. A side-by-side electrode is shown on the left, in this case titanium with gold dot contacts. The image in the middle of the figure is a close-up showing the electrode gap of 7 nm and the gold dot contacts on the electrodes spaced about 15 nm apart. The image on the right is a close-up showing the about 10 nm gold dots at the tip of the electrode.

[0046] Measured signals obtained from DNA sequencing are shown in FIG. 8. These signals were obtained from a polymerase sensor processing a template having the sequence G4A8-G4A8-G4A8-G4A8. The signals show current versus time during the performance of the experiment. The inset from t=34 sec to 39 sec shows the electrical signal reflecting this base sequence. In various embodiments, such signal enhancement results in more accurate sequencing.

[0047] Bridging molecules in molecular electronic sensors such as the sensors discussed herein may include molecules other than DNA, and in some cases, these bridging molecules can be completely synthetic molecules, such as polycyclic aromatic compounds that contain fused aromatic rings.In various embodiments herein, a new class of bridging molecules is disclosed for use in molecular electronic sensors.Furthermore, the means for synthesizing these new molecules and their use in detecting DNA template-driven single molecule nucleotide (dNTP) incorporation events mediated by bound polymerase are disclosed herein, particularly for DNA sequencing.

[0048] In various aspects of the present disclosure, polycyclic aromatic molecules are disclosed. The synthetic molecules contain specific structures and various functional groups, forming a class of bridged molecules suitable for molecular sensor applications. One general class of such molecules disclosed herein is represented by compound (I), which is illustrated in FIG. 9. FIG. 9 illustrates the general structural scheme and design rationale for polycyclic aromatic ring bridged molecules according to the present disclosure. As shown in FIG. 9, the general class of molecules represented by compound (I) includes polymeric ribbon-like structures or nanoribbons that contain fused aromatic rings that provide the desired structure and conductive properties. The aromatic rings can be monocyclic (e.g., entirely carbocyclic) aromatic rings or heterocyclic (e.g., one or more heteroatoms in any of the aromatic rings in the ribbon) aromatic rings, or any combination of carbocyclic and heterocyclic aromatic rings that define a specific structure for the nanoribbon. As used herein, the acronym "PAH" refers to carbocyclic nanoribbon structures, or in other words, "polycyclic aromatic hydrocarbons" that contain fused aromatic rings. In various embodiments, all of the aromatic rings in the PAH are benzene rings and the entire ribbon contains delocalized electrons originating from π-orbitals.

[0049] As shown in compound (I) in FIG. 9, the left and right end groups (L and R groups, respectively) are provided at either position on the opposite edges of the ribbon. These functional groups are selected to support the self-assembly of the individual circuits onto a pair of electrodes, and when the nanoribbons are joined, thus bridging the pair of electrodes, electrical conductivity is ensured between the bridge and the electrodes. Depending on the nature of the functional groups L and R, if necessary, a nanoribbon such as compound (I) can be designed to spatially orient itself and specifically, i.e., to bind L to one electrode and R to the other electrode of a pair of spaced apart electrodes. Compound (I) also contains one or more binding groups P that support the self-assembly of the probe molecules onto the nanoribbons to form a probe-molecule complex. The P-functional group can be located anywhere along one of the parallel long edges of the molecular ribbon, such as at or near the midpoint of the length of the PAH ribbon. As further illustrated diagrammatically in Figure 9, compound (I) can also include one or more diverse functional side chains S1, S2, S3, etc., selected to promote enhanced solubility, sensor self-assembly, and signaling performance of the PAH ribbon. Figure 9 shows these side chains S1, S2, S3, etc., attached to any one of the two edges of nanoribbon compound (I) to achieve various solubility, structural conformational properties, and / or self-assembly properties. However, it is important to note that there can be any number of S1, S2, S3 side chains, etc., attached at any location along any of the four edges of the ribbon to achieve desired structural and functional properties in the ribbon.

[0050] The schematic structure of compound (I) is not intended to be limited to the illustrated ribbons of uniform width. For example, various embodiments of polycyclic bridged molecules may include repeating periodicities of width, such as intervals of 3-ring width and 5-ring width. These ribbons of non-uniform width are discussed in more detail herein.

[0051] Referring now to FIG. 10, the type of nanoribbon can be more clearly recognized by the structure of compound (II), which includes a rectangular-shaped PAH core ribbon structure made up entirely of fused benzene rings. As illustrated, compound (II) has a sheet-like structure with a width (w) and length (l) determined primarily by the number of fused rings in the core structure of the molecule. Indeed, the long extending functional groups attached to the ribbon may exaggerate the width and / or length of the molecular bridges and may even obscure the width and / or length of the core ribbon structure, but for simplicity, reference will be made herein to the dimensions w and l of the core ribbon structure. The sheet-like structure of compound (II), as illustrated, results in four edges to the ribbon, defined as edge 1, edge 2, edge 3, and edge 4. Edge 1 and edge 3 are referred to herein as the longer parallel edges, while edge 2 and edge 4 are referred to herein as the shorter parallel edges. The "ends" of the PAH ribbon are necessarily the edges, Edge 2 and Edge 4. As specified above for compound (I), the various substituents L, R, P and S 1 , S 2 , S 3 etc. can be located anywhere around the ribbon, but when bridging a gap between spaced apart electrodes, it is practical to have the L and R functionalities on edge 2 and edge 4, i.e., on the opposite shorter edges or "ends" of the ribbon. In various embodiments, for attachment to a probe molecule, the P functionality may be located along one of the longer edges, edge 1 or edge 3, somewhere near the midpoint of the length (l). There may be more than one P functionality configured to attach to a probe molecule. Various side chains S 1 , S 2 , S 3 It is important to understand that the number and position of the S, etc., are completely variable. For example, the S, which is very specifically bonded to a particular benzene ring in compound (II), 1 There can be exactly one group, S 2 Group or S 3 There is no group, or there are several or more different groups S attached to various individual sites.1 , S 2 , S 3 etc. The core PAH ribbon contains a fused aromatic system and therefore may contain one or more substituents S 1 , S 2 , S 3 etc. may only be attached to carbon atoms along the edges of the ribbon. In various embodiments, two or more S 1 , S 2 , S 3 Any combination of groups may form further aromatic or non-aromatic rings.

[0052] In various embodiments, the ribbon includes fused benzene rings, such that the ribbon is a complete carbocyclic ring, with sp 2 The cross-linking molecules synthesized herein with such nanoribbon cores are conductive due to electron delocalization. Depending on the spatial orientation of the fused benzene rings, a PAH ribbon containing a rectangular ribbon structure of constant width always has zigzag periodicity on two of its opposite parallel edges and tooth-like periodicity on the other two of its opposite parallel edges, but due to the hexagonal shape for each ring in the ribbon, not all four edges of the ribbon can be zigzag or tooth-like. Two parallel edges always have tooth-like periodicity, while the other two parallel edges always have zigzag periodicity. In the case of compound (II) in FIG. 10, the shorter edges, edges 2 and 4, contain zigzag periodicity, while the longer edges, edges 1 and 3, contain tooth-like periodicity. Ribbons stretched such that their width (w) is greater than their length (l) reverse this orientation, and the shorter edges of the PAH ribbons have a tooth-like periodicity. These strict rules are not followed when the core structure is just a linear thread of fused benzene rings (i.e., a ribbon the width of a single ring). These aspects become more evident as various subclasses and molecular species are discussed.

[0053] As used herein, "zigzag" nanoribbons refer to polycyclic aromatic hydrocarbon nanoribbons having fused benzene rings oriented such that the longer parallel edges contain a zigzag periodicity, while the shorter parallel edges contain a tooth-like periodicity (Figure 35a is an example of what is referred to herein as a "zigzag" nanoribbon structure).

[0054] As used herein, a "non-zigzag" nanoribbon refers to a polycyclic aromatic hydrocarbon nanoribbon having fused benzene rings oriented such that the longer parallel edges contain tooth-like periodicity while the shorter parallel edges contain zigzag periodicity. (Compound (II) in FIG. 10 is an example of what is referred to herein as a "non-zigzag" nanoribbon structure because the shorter parallel edges, edges 2 and 4, but not the longer parallel edges, have zigzag periodicity.)

[0055] In the case of zigzag nanoribbons (e.g., structures exemplified in Figures 35a, 35b, and 43), each fused benzene ring contributes 0.23 nm to the length of the nanoribbon and 0.46 nm to the width of the nanoribbon. In various embodiments, the length of the zigzag nanoribbon ranges from about 12 to about 434 benzene rings (about 3 nm to about 100 nm) and the width ranges from about 1 to about 50 benzene rings (about 0.46 nm to about 23 nm). In the case of non-zigzag nanoribbons (e.g., compound (I) in Figure 9 and compound (II) in Figure 10), the orientation of the benzene rings is reversed and each benzene ring contributes 0.46 nm to the length of the nanoribbon and 0.23 nm to the width of the nanoribbon. In various embodiments, non-zigzag nanoribbons such as Compound (II) have lengths ranging from about 6 to about 217 benzene rings (about 3 nm to about 100 nm) and widths ranging from about 1 to about 100 benzene rings (about 0.23 nm to about 23 nm).

[0056] In the illustrated embodiment of compound (II) (FIG. 10), there are 8 aromatic rings across the width of the ribbon-shaped molecule and 36 aromatic rings along its length. As shown, the longer parallel edges, edges 1 and 3, have tooth-like periodicity while the shorter parallel edges have zigzag periodicity, such that the longer edges are non-zigzag (i.e., they contain tooth-like periodicity) and thus the molecule comprises a "non-zigzag" nanoribbon structure in accordance with the nomenclature conventions herein.

[0057] In various embodiments, synthetic bridging molecules for use in molecular sensors include a fused polycyclic aromatic hydrocarbon, PAH-ring core structure, where, as described above, the ribbon core structure is rectangular and sheet-like with two generally parallel longer edges designated the top and bottom edges of the molecule, and two generally parallel shorter edges designated the left and right edges (or ends) of the molecule, where the two longer edges of the ribbon include a zigzag periodicity and the two shorter edges of the molecule include a tooth-like periodicity ("zigzag" nanoribbons) or vice versa ("non-zigzag" nanoribbons). bon), the synthetic crosslinking molecule further comprises at least one left-hand substituent "L" attached to the left (shorter) end of the molecule and at least one right-hand substituent "R" attached to the right (opposite shorter) end of the molecule, where L and R are capable of binding to a metal electrode or to a metal contact disposed on the electrode, and the binding of the functional groups L and R to the ribbon core structure can comprise a direct covalent bond to a carbon atom of one of the terminal benzene rings, or L and / or R may be linked to the ribbon core structure by any number of intervening atoms (referred to as a "linker"). Generally, both L and R have functional groups that facilitate binding of the nanoribbon to a metal, such as gold. In various aspects, L and R comprise a sulfur atom, and in some examples, L and R each comprise a thiol, thiol ether, disulfide, or disulfide ether. In other embodiments, one or both of L and R comprise a reactive carbene moiety capable of binding to gold and other metals. In certain embodiments, L or R can include a thiol functional group, while other groups L or R can include reactive carbenes, such as to provide orientation of the PAH crosslinking molecule. In various examples, L and / or R include a carbene precursor that can form a reactive carbene for binding to gold or other metals.

[0058] In various embodiments, L and / or R may include reactive carbene atoms or carbene precursors that can provide reactive carbene atoms that can subsequently be bonded to gold or other metals. The term "reactive carbene" is used broadly herein to include any substituent with a carbene atom, defined in chemistry as a divalent neutral carbon atom with one additional unshared pair of electrons. Thus, in various embodiments, L and / or R include at least one carbene atom. The carbene atom may be flanked by any other type of atom. In various aspects, the carbene atom may be flanked on both sides by N atoms. When the N atom and the central carbene atom are consecutive within the ring, the reactive carbene moiety is referred to as an "N-heterocyclic carbene" or "NHC". The stability and / or persistence of the reactive carbene in the NHC is sometimes sterically promoted by having bulky substituents, such as i-propyl, t-butyl, or adamantyl groups, on each N-atom. Additionally, the term "carbene precursor" is used to refer to a moiety that generates a reactive carbene atom, such as upon reaction with a base. In various aspects, the carbene precursor has the structure - + It contains N=CH-N-, which upon reaction with base (deprotonating the central alkenyl carbon atom) produces the reactive carbene -NCN-. Various embodiments of stabilized carbenes and carbenes that bind to gold are disclosed in Crudden, CM, et al., "Ultra Stable Self-Assembled Monolayers of N-Heterocyclic Carbenes on Gold," Nature Chemistry, 6, 409-414 (2014), which is incorporated herein by reference.

[0059] In various embodiments, L and / or R include a carbene precursor further comprising a diazole or benzodiazole group. Each N-atom may further comprise a sterically bulky group, such as an i-propyl group, a t-butyl group, or an adamantyl group. In certain examples, the L and / or R terminal group for attachment to gold comprises the following structure, 6-[1,3-diisopropyl-1H-benzo[d]imidazol-3-ium]-yl, which is capable of reacting with a base, such as KO t Deprotonated by Bu to give NHC: [ka] can be generated.

[0060] In the above structure, the wavy line indicates the point of attachment to the nanoribbon core structure, i.e., to one of the aromatic rings around the outer edge of the nanoribbon, either directly or through an intervening atom. The above NHC precursor substituents are symmetrical, and therefore the linking groups to the 6-yl or 5-yl positions are equivalent. Note that the substituents can also be isomerized, with the position of the double bond and the transfer of the positive charge to another N atom. As mentioned above, the i-propyl group may be replaced by other sterically bulky groups.

[0061] In other embodiments, the L and / or R end groups for attachment to gold or other metals include the following structure, 6-[1,3-diisopropyl-1H-benzo[d]imidazol-3-ium]-thioyl, which is compatible with bases, e.g., KO t Deprotonated by Bu to give NHC: [ka] can be generated.

[0062] In the above structure, the wavy line indicates the point of attachment to the nanoribbon core structure, i.e., to one of the aromatic rings around the outer edge of the nanoribbon, either directly or through an intervening atom. The above NHC precursor substituents are symmetrical, and therefore the linking groups to the 6-yl or 5-yl positions are equivalent. Note that the substituents can also be isomerized, with the position of the double bond and the transfer of the positive charge to another N atom. As mentioned above, the i-propyl group may be replaced by other sterically bulky groups. The two carbene precursor structures depicted above differ only in their point of attachment linking groups to the nanoribbon, i.e., whether an S atom is intervening or not.

[0063] With continued reference to compound (I) in Figure 9 and compound (II) in Figure 10, nanoribbons according to the present disclosure further include at least one substituent P capable of binding to a probe molecule, such as an enzyme or other binding probe. In various examples, P is attached to the top or bottom edge of the ribbon either directly to an available site on a terminal benzene ring along one of the long edges of the ribbon or through any number of intervening atoms. In various non-limiting examples, P can include an azide, an alkyne, a thiol, biotin, a carboxylic acid, a ketone, an aldehyde, an alcohol, or streptavidin. In various embodiments, these functional group choices for P, i.e., P having reactive azide, alkyne, thiol, biotin, carboxylic acid, ketone, aldehyde or alcohol moieties as part of the structure of the P group, or containing streptavidin, may be spaced apart from portions of the polyaromatic core structure that are linked by AHX linkers (6-aminohexanoic acid), any length of PEG, or any other configuration of tethers with various combinations of C and heteroatoms.

[0064] In various embodiments, P is: [ka] -CH(CH3)-SH; -C(CH3)2-SH; -CH2-C(CH3)2-SH; -(CH2) 10 -N3; -PEG-5-biotin; -(CH2)7-C(=O)NH-(CH2CH2O)4-(CH2)3-N3; -(CH2)9-C(=O)NH-(CH2CH2O)6-(CH2)2-O-NH2; Any other azide or alkyne for click chemistry; Alkoxyamines or ketones or aldehydes for alkoxyme click chemistry, or Streptavidin for biochemical linking groups You can choose from.

[0065] A probe molecule, such as a DNA polymerase or other processive enzyme, can be derivatized with a complementary moiety to enable linkage of the probe molecule to a P group on the polycyclic aromatic bridge compound, such as by formation of a triazole, an alkoxime, a biotin-streptavidin complex, or any combination thereof.

[0066] The synthetic cross-linking molecules represented by compounds (I) and (II) may include one or more side chains, S 1 , S 2 , S 3 etc., each attached to any of the four edges of the ribbon, such as the top or bottom of the longer parallel edges. One or more of these side chains can include PEG esters or PEG ethers, dendrons, or other groups such as short or long chain esters or ethers as described herein.

[0067] As used herein, the abbreviated notation "X-APAH" refers to the width of a nanoribbon-bridge molecule based on a polycyclic aromatic hydrocarbon structure and including X atoms along its width. A PAH ribbon can include a condensation of aromatic rings that defines a width and length for the ribbon, such as that exemplified by compound (II) in FIG. 10, which has a width (w) defined by (8) condensed benzene rings and 17 consecutive carbon atoms derived therefrom. For example, a molecule having alternating condensed tetracene (naphthacene) units has nine carbon atoms aligned end-to-end in a tetracene structure, such that such a molecule can be described as having a "9-APAH" structure. Hexacene, a linear condensation of six benzene rings, results in 13 atoms end-to-end, and thus a structure based on hexacene can be referred to herein as having a "13-APAH" structure. The structure of compound (II) in FIG. 10 can be referred to as having a "17-APAH" structure. In various embodiments, X for X-APAH nanoribbons ranges from about 2 (e.g., linearly fused cyclobutadiene threads) to about 201 (e.g., polycyclic aromatic hydrocarbon ribbons having about 100 benzene rings fused together across the width of the ribbon). For non-zigzag fused benzene ring systems, such as the exemplified structures of compounds (I) and (II), X=2×(number of benzene rings)−1. Thus, for compound (II) in FIG. 10, X=(2×8)−1=17. Thus, the ribbons represented as compounds (I) and (II) can be represented as 17-APAH ribbons.

[0068] Functionalized polycyclic aromatic hydrocarbon nanoribbons have been described previously. However, the molecules disclosed do not include the L, R, P, S groups disclosed herein. 1 , S 2 , S 3(See Y. Huang, et al., "Poly(ethylene oxide) Functionalized Graphene Nanoribbons with Excellent Solution Processability," J. Am. Chem. Soc., 2016, 138 (32), pp 10136-10139).

[0069] Another embodiment of a polycyclic aromatic bridge molecule, compound (III), is illustrated in FIG. 11. Compound (III) comprises ribbons formed from aromatic hydrocarbon rings and further comprises a wide variety of groups that provide any combination of self-assembly anchors and / or water-soluble side chains. In various embodiments, compound (III) comprises substituents that facilitate probe molecule complex formation and attachment to electrodes at each end of compound (III). As specified in the structure, various groups can be attached to the ribbon at more than one carbon atom, such as when the substituent comprises a cyclic structure fused to one of the benzene rings at the ends of the ribbon. The length of the ribbon is determined by integers n and m, and the various substituents R 1 , R 2 , R 3 , R 4 , R 5 , R 6 , R 7 The scope of Y, W, Y', W', Y", and W" are discussed herein below. Depending on the specific selection of the various substituents, compound (III) may have various rotational symmetries.

[0070] FIG. 12 illustrates a 3D space-filling model of an embodiment of a polycyclic aromatic bridged molecule, Compound (IV), that includes a polycyclic aromatic hydrocarbon fused ring nanoribbon structure with polyethylene glycol ("PEG") polymer side chains for enhanced aqueous solubility, and a terminal thiol group for coupling to a metal electrode. The nanoribbon portion of Compound (IV) has a width of about 0.95 nm and a length of about 6 nm. In various embodiments, the molecule can be synthesized to have a length of about 5 nm to about 50 nm by adding additional fused aromatic rings to the core ribbon portion of the molecule.

[0071] FIG. 13 illustrates a 3D space-filling model of an embodiment of a polycyclic aromatic bridged complex, Compound (V), specifically applicable for DNA sequencing. The 3D space-filling model shows E. coli Klenow fragment polymerase with dNTPs complexed thereon, linked to a PAH nanoribbon, which also has some PEG side chains. In this case, the polymerase is conjugated to self-assembled side groups, the remaining PEG side chains provide solubility in water, and thiol end groups are provided at each of the two opposing short ends of the ribbon for coupling to gold electrodes via thiol-gold bonds. The Compound (V) complex measures about 16 nm long by about 6 nm wide by about 7 nm deep. The PAH portion of the molecule measures about 5.7 nm in length. In other variations, the PAH component can be about 5 nm to about 50 nm in length and can include longer PEG side chains, and / or a varying number of PEG side chains. The central atom 130 shown in the model of FIG. 13 is the phosphorus atom of the dNTP molecule complexed with the polymerase.

[0072] 14, 15 and 16 illustrate non-limiting embodiments of low molecular weight cyclic aromatic rings that can be used as building blocks or reaction intermediates in the synthesis of the polycyclic aromatic bridged molecules herein, or as examples of various moieties or polymer units found in the final bridged molecule structures disclosed herein.

[0073] In various embodiments of the present disclosure, the polycyclic aromatic bridged molecules are "precisely manufacturable," which means herein that the manufacturing includes bottom-up synthesis using techniques of organic synthetic chemistry and polymer chemistry to achieve atomically precise molecular structures. This synthesis method provides the benefit of reducing the variability of sensor performance and enabling efficient and precise mass production at the scale required for commercial applications using self-assembly chemical synthesis methods. Another benefit is that such molecules can be designed to be highly conductive or semiconductive with energy band gaps, such as by using regular carbon ring polymer structures or other aromatic ring groups, which provide electrical performance properties that are beneficial as transducers in molecular electronic circuits. Such aromatic molecules are known to facilitate electronic conduction, and the nanoscale dimensions of such structures are known to facilitate energy band gaps. Higher currents can provide more efficient measurement of the signal current, improving the signal-to-noise ratio. Furthermore, the introduction of band gaps can provide larger or nonlinear current signal responses to the modulation coefficient. Another benefit is that such molecules include self-assembly groups that allow for precise self-assembly of the sensor construct. The chemistries herein offer particular advantages for commercial deployment in highly scalable, multi-sensor formats, particularly as large-scale sensor arrays on CMOS chips, enabling thousands, millions or even billions of sensors in an economical, mass-producible format.

[0074] An additional benefit of the molecules disclosed herein is that side chains on certain nanoribbons can be used to promote solubility as is important for their use in different solutions of interest. In various embodiments, such as in aqueous solutions, the PEG-like side chains impart water solubility to core aromatic ribbons that are particularly poorly soluble in the absence of such side groups.

[0075] Use of polycyclic aromatic bridge molecules for DNA sequencing applications.

[0076] In various embodiments, the polycyclic aromatic bridge molecule disclosed herein finds use in molecular electronic sensors for DNA sequencing.For DNA or genome sequencing applications, the bridge molecule in the molecular sensor may be conjugated to a polymerase probe molecule, such as those conceptually illustrated in Figures 4 and 5 and 13 for the specific embodiment of the PAH bridge-probe complex, which is compound (V).For this application, the current flowing through the bridge molecule under the pressure of the applied voltage is monitored as the polymerase synthesizes the complementary strand of the test DNA template.The signals of the incorporation event and the base-specific incorporation event provide the sensing capability for DNA sequencing applications.In one embodiment, a natural polymerase enzyme and natural dNTPs (dATP, dCTP, dGTP and dTTP) are used in a standard enzyme buffer to provide such an electrical signal.

[0077] In another embodiment, the element using molecular sensor may be modified to directly or indirectly enhance the regulation of current and to increase the sequence-related signal of incorporation or base discrimination, such as using modified dNTPs and modified buffer compositions.In all of these settings, the use of appropriately designed and optimized polycyclic aromatic bridge molecules can realize the benefits of enhanced signal, increased signal-to-noise ratio, improved self-assembly process, or improved precision manufacturing of such DNA sequence sensors, compared to other options for molecular bridges, such as biopolymer molecular wires (DNA in Figure 4, or proteins), molecular scale wires formed from materials such as carbon nanotubes, silicon nanowires or metal nanowires, or bridges formed from 2D materials such as graphene, molybdenum disulfide (MoS2).These advantages are related to precise control of structure, organization, solubility, conductivity, and efficient mass production and manufacturing, as described above.

[0078] In the context of a sensor for DNA sequencing, two or more polycyclic aromatic bridge molecules according to the present disclosure may be attached as "arms" to two separate sites on a polymerase probe molecule, the other ends of which are coupled to an electrode, so that the polymerase directly forms the central element of the entire conductive path between both electrodes. The coupling of the bridge molecule arms to the polymerase can be based on various conjugation methods. For example, the polymerase may be mutated to include a surface cysteine ​​group, and a cysteine-binding terminus, such as a maleimide, may be provided at the end of the arm intended to bind to the polymerase. In other examples, two or more of such arms may be used for this application. Furthermore, bridge molecules that are structured to promote interaction with dNTPs (natural or modified) during incorporation or with the polymerase (natural or mutant) can further enhance signaling. For example, such interactions may modify the rate of enzymatic processing of dNTP substrates, such as slowing down the rate of enzymatic processing of dNTP substrates, amplifying conformational changes, or directly interacting with incorporated dNTPs (natural or modified).In the case of polycyclic aromatic bridges that contain hydrocarbon rings, stacking of pyrene or other polycyclic aromatic moieties on the bridges may promote bridge-polymerase or bridge-dNTP interactions, or promote bridge-polymerase self-assembly via the addition of pyrene-type groups to polymerases or dNTPs.In such cases of hydrocarbon aromatic ring bridges, various detergents, or specifically pyrene-based detergents, may have beneficial effects that prevent aggregation of bridge molecules during assembly or prevent undesirable interactions during sensor operation.

[0079] Described below are various embodiments of polycyclic aromatic bridge molecules, their production also by synthetic chemical processes, and their methods of use, particularly for DNA sequencing applications.

[0080] Structure of polycyclic aromatic hydrocarbon (PAH) crosslinked molecules

[0081] One type of class of polycyclic aromatic bridged molecules herein are polycyclic aromatic hydrocarbon (PAH) bridged molecules, such as those generally represented by compound (I) shown in Figure 9 and compound (II) shown in Figure 10, where the aromatic nanoribbon backbone of the molecule contains fused hydrocarbon rings, such as benzene rings, or other building blocks and substructures, such as those more generally represented in Figures 14 and 15. Specific embodiments of single and multi-component PAH bridged molecules are described herein.

[0082] Single PAH Electrode Bridge (PAHEB) Molecules for DNA Sequencing

[0083] Disclosed herein is a single conductor PAH electrode bridge molecule (herein "PAHEB") intended for use in DNA sequencing sensor.In these embodiments, the probe molecule that PAHEB will bind to can include polymerase.It is understood that other binding probe molecules can replace polymerase for other detection applications, and others can derive benefits from the bridge molecule structure disclosed herein.

[0084] Two exemplary structural classes of PAHEB are represented by compound (IX) in FIG. 33 and compound (X) in FIG. 34. In both compound (IX) and compound (X), the structure "cap-polymer1-branch-polymer2-cap" illustrated in FIG. 33 and FIG. 34 includes a continuous fused polycyclic aromatic hydrocarbon nanoribbon that is derivatized at each of its short edges and that measures from about 3 nm to about 1000 nm in length, from about 5 nm to about 100 nm in length, from about 10 nm to about 50 nm in length, or from about 15 nm to about 30 nm in length. In the case of non-zigzag nanoribbons, the structure "cap-polymer1-branch-polymer2-cap" includes from 6 to about 2173 benzene rings, from about 10 to about 217 benzene rings, or from about 21 to about 108 benzene rings along its length. In the case of a zigzag nanoribbon, the structure "cap-polymer 1-branch-polymer 2-cap" contains from about 12 to about 4346 benzene rings, from about 20 to about 434 benzene rings, or from about 42 to about 216 benzene rings along its length.

[0085] In both compound (IX) and compound (X), each "cap" depicted in Figures 33 and 34 represents a single monomeric unit capable of specifically binding and self-assembling to each of two spaced apart electrodes in a pair of electrodes, such as by specific binding to a gold electrode surface through the use of thiols, thioethers, disulfides, disulfide ethers, gold-binding peptides, dithiocarboxylates or reactive carbenes on a PAH ribbon, or any combination thereof. There may be left and right "cap" moieties of different chemical structures to facilitate directional binding to distinct left and right electrode materials or anchor sites.

[0086] Both Compound (IX) and Compound (X), depicted in Figures 33 and 34 as "Polymer 1" and "Polymer 2," respectively, represent polymer moieties derivatized with at least one solubilizing group, such as polyethylene glycol (PEG), that allows for dissolution in organic solvents, such as tetrahydrofuran, and dispersion in water. The length of the PEG moiety may be of any suitable length to overcome solubility problems that the unsubstituted polymer may have in a particular solvent, such as water.

[0087] For both compound (IX) and compound (X), the "branch" depicted in Figures 33 and 34 represents a single monomeric unit or short molecular linker (either one of which is bivalent) that is linked, for example, by one or more S-alkyl or S-aryl linkages to one or more sites on a DNA polymerase via surface cysteine ​​residues on the polymerase. Such surface cysteine ​​sites may include naturally occurring or mutated sites on the enzyme.

[0088] In both compound (IX) and compound (X), "-S-" represents a divalent sulfide linker to the polymerase. Compound (IX) in Figure 33 illustrates the use of one sulfide linker, while compound (X) in Figure 34 illustrates the use of two sulfide linkers to the polymerase.

[0089] In various embodiments, a single conductor PAHEB, such as compounds (IX) and (X), is attached to each of the two electrodes in a pair of spaced apart electrodes by "cap" functional groups provided on opposite ends of the PAH ribbon.

[0090] Polycyclic aromatic bridged molecule embodiments for molecular electronic sensors

[0091] The following are non-limiting exemplary embodiments of bridging molecules for various molecular electronic sensor applications. It is understood that each of these embodiments has numerous further variations that are obvious to those skilled in the art of organic chemistry and molecular sensing. It is also understood that these embodiments are presented for teaching and to enhance understanding, to highlight useful structures, and are in no way intended to limit the scope of the present disclosure.

[0092] Substantially rectangular nanoribbon structures with nearly uniform width

[0093] In various embodiments, the bridged molecules according to the present disclosure include a general structure that is conceptually represented by compound (I) in FIG. 9 and more clearly by the type of structure of compound (II) in FIG. 10. In compounds (I) and (II), the conductive nanoribbons include aromatic rings fused together in a polycyclic system. These rings can be carbocyclic or heterocyclic, and the ribbons can be formed from one ring type or a mixture of ring types arranged in a well-defined structure. In various embodiments, the fused ring systems, such as those exemplified by compound (II) in FIG. 10, can include any number of nitrogen atoms at various positions in the ribbon. For example, any number of rings can include, for example, pyridines or pyrimidines interspersed throughout the structure. The nanoribbons can be conceived in accordance with the following design rationale: the ring structure of the ribbon provides the conductive and structural properties. The left (L) and right (R) end groups provide for self-assembly into electrodes, potentially with orientation of the left and right ends of the molecules depending on the chemical nature of L and R. These end groups provide electrical conductivity from the crosslinker to the electrode through direct bonding interactions (e.g., S-Au bonds), through aromatic π-cloud interactions with the electrode surface, or through both types of contact. The functional substituents (P) provide self-assembled conjugates to the probe molecules. Side chains on any of the edges of the nanoribbon core structure provide solubility, structural and / or conformational properties.

[0094] In various embodiments, a bridging molecule according to the present disclosure comprises the structure represented by compound (III) in FIG. 11, where the conductive oligomeric ribbon = 7-APAH (a 7 atom wide polycyclic aromatic hydrocarbon with anthracene units spanning the entire width of the molecule). Compound (III) is approximately 0.7 nm wide. FIG. 17 shows a variety of compound (III) with the functional regions of the molecule appropriately labeled below the structure. In various embodiments, a probe molecule such as a polymerase is coupled to the R in the branch region. 3 and / or R 4 The cross-compatible pairs may be linked to the central monomer in the synthetic molecular bridge, such as directly via a linker or via a bivalent linker, and may have the following cross-compatible pairs: a. Azide or alkyne (for click chemistry); b. Alkoxyamines or ketones / aldehydes (for alkoxyme click chemistry); or c. Biotin or streptavidin (for biochemical linkage) It may further contain 1 to 3 linkable groups selected from:

[0095] A probe molecule (e.g., a DNA polymerase or other binding probe) can be derivatized with a complementary moiety to enable linkage of the probe molecule to the conductive PAH ribbon, such as by formation of a triazole, alkoxime, biotin-streptavidin complex, or any combination thereof.

[0096] In various embodiments, a synthetic cross-linking molecule according to the present disclosure comprises compound (IV), illustrated as a 3D space-filling model in Figure 12. Compound (IV) is a molecular species within the class of structures represented by compound (III) (Figure 11); R 1 =PEG-20, Y and W are -O-; R 3 and R 4 is azide-(CH2) 10 and biotin-PEG-5, R 5=H, R 6 = methylthiol, R 7 =H.

[0097] In various embodiments, a synthetic cross-linking molecule according to the present disclosure comprises compound (III), as illustrated in FIG. n and m are independently 0 to 30; W and Y are -O-, -CH2-, CR 8 R 9 , CH2CR 8 R 9 , C.R. 8 CR 9 CH2, OCR 8 R 9 and C.R. 8 R 9 independently selected from O and R 8 and R 9 are attached to the same carbon atom and are H, CH3, C2H5, CH2CH2CH3 or (CH2) x (OCH2CH2) y OR 10 wherein x is 2 to 10, y is 10 to 40, and R 10 is H, Me or Et, R 8 and R 9 can optionally be linked to form a ring, O is optionally directly linked to the aromatic ring, W and Y can optionally be interchanged within the ring, W' and Y' are -O-, -CH2-, CR 8 R 9 , CH2CR 8 R 9 , C.R. 8 CR 9 CH2, OCR 8 R 9 and C.R. 8 R 9 independently selected from O and R 8 and R 9 are attached to the same carbon atom and are H, CH3, C2H5, CH2CH2CH3 or (CH2) x (OCH2CH2) yOR 10 wherein x is 2 to 10, y is 10 to 40, and R 10 is H, Me or Et, R 8 and R 9 can optionally be linked to form a ring, O is optionally directly linked to the aromatic ring, W' and Y' can optionally be interchanged within the ring, R 1 is an ester-linked PEG chain (CH2) x CO(OCH2CH2) y OR 13 or (CH2) x OC=OCH2CH2CH2(OCH2CH2) y OR 13 wherein x is 0 to 10, y is 10 to 40, and R 13 is Me or H, R 1 Also, water-soluble PEG chains (CH2CH2O) z R 14 wherein z is 1 to 8, and R 14 is H or Me, and R 1 can optionally include 1) photocleavable, 2) redox cleavable, 3) acid cleavable, or 4) base cleavable linkers between the atom and the PEG chain or dendron, such that the PEG chain or dendron can be removed by using 1) light, 2) oxidizing or reducing agents, 3) plus acid, or 4) base, respectively, after coupling the cap portion of the molecule to the gold electrode; R 2 is an ester-linked PEG chain (CH2) x CO(OCH2CH2) y OR 13 or (CH2) x OC=OCH2CH2CH2(OCH2CH2) y OR 13 wherein x is 0 to 10, y is 10 to 40, and R 13 is Me or H, R 2Also, water-soluble PEG chains (CH2CH2O) z R 14 wherein z is 1 to 4, and R 14 is H or Me, and R 2 can optionally include 1) photocleavable, 2) redox cleavable, 3) acid cleavable, or 4) base cleavable linkers between the atom and the PEG chain or dendron, such that the PEG chain or dendron can be removed by using 1) light, 2) oxidizing or reducing agents, 3) plus acid, or 4) base, respectively, after coupling the cap to the gold electrode; W" and Y" are -S-, -CH2-, CH2CH2, CR 11 R 12 and SCR 11 R 12 are independently selected from R 11 and R 12 are attached to the same carbon atom and are independently selected from H, CH, C2H5, CH2CH2CH3, CH2CH2SCH3, SCH3, or SCH2CH2SCH3; R 8 and R 9 can optionally be linked to form a ring, S is optionally directly linked to the aromatic ring, W″ and Y″ can optionally be interchanged within the ring; R 5 is H, SMe or CH2CH2SMe, R 6 is H, SMe, SCH2CH2SMe, SCH2C(CH2SMe)3, SH, CS2H, CH2SMe, CH2SH, CH2CS2H, 6-[1,3-diisopropyl-1H-benzo[d]imidazol-3-ium]-yl or 6-[1,3-diisopropyl-1H-benzo[d]imidazol-3-ium]-thioyl; R 7 is H, SMe, SCH2CH2SMe, SH, CS2H, CH2SMe, CH2SH or CH2CS2H.

[0098] In various embodiments, R 6 and R 7 The presence of -SH, -SSH, 6-[1,3-diisopropyl-1H-benzo[d]imidazol-3-ium]-yl or 6-[1,3-diisopropyl-1H-benzo[d]imidazol-3-ium]-thioyl moieties in the selection of at least one of R allows the self-assembly of the ribbon-shaped ends of compound (III) to the gold electrode or gold contact points disposed on the metal electrode. The bridging molecules functionalized with -SH and -SSH groups are linked to gold by Au-S bonds, while the bridging molecules functionalized with 6-[1,3-diisopropyl-1H-benzo[d]imidazol-3-ium]-yl or 6-[1,3-diisopropyl-1H-benzo[d]imidazol-3-ium]-thioyl groups are linked to the gold electrode or gold contact points by Au-C bonds. In various examples, the two R 6 Group and four R 7 The selection of groups determines the overall rotational symmetry of the molecule. In various embodiments, R 7 All four examples of 6 The two examples are the same functional group capable of binding to a metal.

[0099] In various embodiments, compound (III) is covalently linked to a probe molecule, such as a polymerase. In one particular example for DNA sequencing, the probe molecule comprises a DNA polymerase, such as the Klenow fragment of E. coli, with a linking group to compound (III) provided by a "click chemistry" linker (a triazole formed from an alkyne and an azide, and / or an O-alkyl-oxime formed from a ketone or an aldehyde and an alkoxyamine RO-NH2), and / or a biological linker (e.g., a biotin linker that can be linked to streptavidin in a streptavidin-detector conjugate). In various embodiments of compound (III), R 4 are optionally: (i) covalently linked to individual cysteine ​​residues in the DNA polymerase molecule (or 3 and R4 (ii) two linking groups from the PAH to the polymerase, depending on the selection of R 3 to form a ring; or is hydrogen (i.e., R 3 (By selecting a non-H for R, a single linking group from the PAH to the polymerase remains.) In various embodiments, R 3 and R 4 can optionally contain one to four aromatic side chains (e.g., phenyl, naphthyl, anthracenyl, phenanthrenyl, pyrenyl, thiophenyl, benzothiophenyl, ferrocenyl, etc.) on a flexible chain such as PEG or polyglycine that is linked to one or more cysteine ​​residues in the polymerase that are proximal to the gamma-phosphate in the dNTP, or proximal to the delta phosphate in a modified dNTP such as dN4P-R (where R is a rigid water-soluble group such as glucose, mannose, or alpha-cyclodextrin). These chains can bind to the PAH through hydrophobic or electrostatic interactions that are disrupted when dN4P-R binds to the active site of the polymerase and undergoes incorporation into the oligonucleotide chain.

[0100] In various embodiments, a synthetic cross-linking molecule according to the present disclosure comprises compound (III), as illustrated in FIG. m+n=10 to 24, Y=W=-CH2- or -O-; Y'=W'=-CH2- or -O-; Y”=W”=-S-, R 1 =-CO-O-(CH2CH2O) n -OCH3, n is between 2 and 7 or between 20 and 48; R 2 =-CO-O-(CH2CH2O) n -OCH3, n is between 2 and 7 or between 20 and 48; R 3 =(L-Phe-Gly)-NHOCH2CH2O-N=CH(p-C6H4)CH2-, R4 =H, R 5 =CH2CH2SMe, R 6 =SCH2CH2SMe, R 7 =H.

[0101] In various embodiments, a synthetic cross-linking molecule according to the present disclosure comprises compound (III), as illustrated in FIG. m+n=10 to 24, Y=W=-CH2- or -O-; Y'=W'=-CH2- or -O-; Y”=W”=-S-, R 1 =H, R 2 =-CO-O-(CH2CH2O) n -OCH3, n is between 2 and 7 or between 20 and 48; R 3 =-(CH2) n C(O)NH-CH[(CH2) r (CH2)R 18 ][CH2CH2-O-CH2CH2O-(CH2) s -R 19 ), n, r and s are independently between 2 and 7; R 18 and R 19 is selected from the combinations in Table 1, thus R 18 and R 19 cannot react to each other, [Table 1-1] R 4 =R 5 = p- or m-C6H4-(CH2) t COO(CH2CH2O) u CH3, t is 0 to 10, and u is 5 to 50; R 6 =SCH2CH2SMe, R 7 =H.

[0102] In various embodiments, a synthetic cross-linking molecule according to the present disclosure comprises compound (XIII), illustrated both as a chemical structure in Figure 35a and as a 3D space-filling model (illustrating two rotations of this model) in Figure 35b. The molecule contains long zigzag edges, PEG side chains, a cap with a thiol linking group, and a tethered biotin-containing site for attachment of a probe molecule, such as by self-assembly.

[0103] In various embodiments, a synthetic cross-linking molecule according to the present disclosure comprises compound (VI), illustrated in Figure 18. Compound (VI) comprises a single continuous 13-APAH (a polycyclic aromatic hydrocarbon conductor 13 atoms wide), where the aromatic portion is approximately 1.4 nm wide.

[0104] In various embodiments, a synthetic cross-linking molecule according to the present disclosure comprises compound (VI) (FIG. 18): R 4 =R 5 =H, R 3 =NR 9 R 10 and R 9 is linked to a DNA polymerase cysteine ​​residue, and R 10 is H or polymerase-free R 9 or R 9 In another embodiment, R is linked to a DNA polymerase cysteine ​​residue that is different from the residue linked to R. 3 =H, R 4 is linked to a DNA polymerase cysteine ​​residue, and R 5 is H or polymerase-free R 4 or R 9 The cysteine ​​residue of the DNA polymerase is different from the residue that is linked to the cysteine ​​residue of the DNA polymerase.

[0105] Embodiments of organic reaction schemes useful for the synthesis of compound (VI) are shown in Figures 36-42. Compound (VI) contains a single continuous 13-APAH conductor, and the aromatic ribbon portion of the molecule is approximately 1.4 nm wide.

[0106] In various embodiments, a synthetic cross-linking molecule according to the present disclosure comprises compound (VI) (FIG. 18): R 1 =R 2 = (CH2)4C(O)O-PEG-48, R 3 is (CH2)4C(O)NH-CH2CH2CH(CH2CH2CH2N3)(CH2CH2OCH2CH2OCH2CH2NH-biotin); R 4 =R 5 =H, R 6 =CH2SCH2CH2SCH3 or H, R 7 =CH2SCH2CH2SCH3 or H, R8=CH2SCH2CH2SCH3 or -SH.

[0107] In various embodiments, a synthetic cross-linking molecule according to the present disclosure is represented by compound (VII), illustrated in Figure 19. Compound (VII) comprises a conductive oligomer further comprising a single continuous 9-APAH (polycyclic aromatic hydrocarbon, 9 atoms wide) conductor, where the aromatic portion is approximately 0.95 nm wide.

[0108] In various embodiments, a synthetic cross-linking molecule according to the present disclosure comprises compound (VII), as illustrated in FIG. Four Substituents R 1 , R 2 , R 3 and R 4 Three of the substituents are hydrogen, and the remaining fourth substituent is: (1) Structure (CH2) x CO(OCH2CH2) y OR 13 or (CH2) xOC=OCH2CH2CH2(OCH2CH2) y OR 13 ester-linked PEG chains having the formula (x=3-10, y=10-40, R 13 is Me or H), (2) Structure (CH2) x O-CH2CH2CH2(OCH2CH2) y OR 13 Ether-linked PEG chains having x>2 and y=10-40, R 13 is Me or H, or (3) Water-soluble PEG chain (CH2CH2O) z R 14 Water-soluble ester-linked dendrons linked from a core moiety having 8-64 branches derivatized with 14 is H or Me, and R 1 can optionally include 1) photocleavable, 2) redox cleavable, 3) acid cleavable, or 4) base cleavable linkers between the atom and the PEG chain or dendron, such that the PEG chain or dendron can be removed by using 1) light, 2) oxidizing or reducing agents, 3) plus acid, or 4) base, respectively, after coupling the cap portion of the molecule to the gold electrode. is selected from Four R's bonded at one end of the molecule 8 Three of the substituents are hydrogen and the fourth R 8 The substituents are short chain alkyl groups (1-5 carbons) optionally substituted with methoxy or carboxyl groups; R 7 is CH2SCH2CH2SCH3 or -SH.

[0109] In various embodiments, a synthetic crosslinking molecule according to the present disclosure includes compound (VIII), illustrated in Figure 20. This compound is referred to herein as a "2-mono PEG-PAH single component polymer" and is a crosslinking molecule with no branching monomers. The central monomer shown allows for PAH crosslinks of various lengths, if desired. This type of compound has as many monomer units as desired and optional PEG chains, which affect solubility.

[0110] In various embodiments, the synthetic cross-linking molecule comprises compound (VIII) in FIG. n=3, m=3-1000, or in various embodiments, 3-10; The Four R's 15 Three of the substituents are hydrogen and the fourth R 15 The substituent has the structure (CH2CH2)O(CH2CH2O) 24 A PEG chain having CH3, The 8 R's 16 Six of the substituents are hydrogen, and the remaining R 16 Two of the substituents are 2-methoxyethyl. R 17 are -S-CH3, respectively.

[0111] In various embodiments, a synthetic crosslinking molecule according to the present disclosure comprises compound (XV), illustrated in Figure 21. Compound (XV) comprises a methylthiol end group and an optional number of central monomer units n and m, where n=2 and m=3-1000 or 3-10. The presence of PEG side chains improves the solubility of the otherwise hydrophobic aromatic core structure.

[0112] 22-30 illustrate embodiments of synthetic protocols for preparing compound (XV). In various embodiments, compound (XV) contains 3 or more carbons located between the aromatic ring and the PEG oxygen atom, or an ester linkage to any PEG substituent.

[0113] FIG. 22 illustrates the synthesis of tosyl-PEG-24 (22b) involving the reaction of PEG-24 (22a) with tosyl-Cl and KOH in aqueous THF. FIG. 23 illustrates the synthesis of tetraphenyldiiodobenzene methoxy ether (23c) starting from perbromobenzene, 1-bromo-4-(2-methoxyethyl)benzene, and bromobenzene. FIG. 24 illustrates the synthesis of monomeric alcohol (24e) by demethylation of the previous methoxy monomer with trimethyliodosilane in dichloromethane. FIG. 25 illustrates the synthesis of PEG monomer (25f) by SN2 reaction of the previous tosyl-PEG-24 with the anion of the alcohol monomer formed by NaH in THF. FIGs. 26 and 27 illustrate thermal and microwave Suzuki-Miyaura coupling reactions of 1,4-benzenediboronic acid bis(pinacol) ester (26a) and PEG monomer (25f) to generate various fused ring systems. Figure 28 illustrates a further Suzuki-Miyaura coupling to produce nanoribbon intermediate CX-13-336. Figure 29 shows a further Suzuki-Miyaura coupling to produce nanoribbon intermediate CX-13-337. Finally, Figure 30 illustrates the synthesis of compound (XV) by treatment with FeCl3.

[0114] In various embodiments, the conductive synthetic organic bridge molecule is solubilized by at least one dendron. For example, compound (XVI) illustrated in Figure 31a shows a simplified version of the bridge molecule that includes a polyanthracene nanoribbon and only one dendron attached thereto. Usable embodiments of compound (XVI) further include (i) more than one dendron along both long edges of the nanoribbon, for example, as many as one dendron for every 1-3 nm of the length of the nanoribbon, and (ii) -SH or -S-alkyl groups at each of the left and right ends of the molecule for attachment to metal electrodes.

[0115] FIG. 31b shows a 3D structural model of compound (XVI), which contains only one dendron and no other substituents on the nanoribbon.

[0116] In various embodiments, the conductive synthetic organic bridge molecule comprises compound (XVII), illustrated in Figure 32. This schematic illustrates the use of two separate polycyclic aromatic molecules as arms to directly wire a sensor probe molecule into a sensor circuit. As illustrated, the electrical conductivity runs from the Au binding site, through one of the arms, through the sensor probe molecule, then through the second arm, to the second Au binding site. "cap1-polymer1-branch-polymer2-cap2" and "cap1'-polymer1'-branch'-polymer2'-cap2'" represent two separate fused polycyclic aromatic hydrocarbon molecular arms that are derivatized at the edges and are about 5 to about 100 nm in length, about 8 to about 60 nm in length, or about 10 to about 30 nm in length, respectively; Cap1 and Cap1' are single monomeric units that can be attached to an electrode surface, e.g., a gold surface, by thioethers, reactive carbenes, gold-binding peptides or other material-binding sequences, i.e., thiols and / or dithiocarboxylates; Cap2 and Cap2' are single underivatized monomeric units, Polymer 1, Polymer 1', Polymer 2 and Polymer 2' are polyaromatic fused ring segments that are optionally derivatized with any number of solubilizing groups, such as PEG groups to allow for dissolution in organic solvents such as tetrahydrofuran and dispersion in water. In various embodiments, the Polymer 1 and Polymer 1' segments can be of any length and can be the same or different from the Polymer 2 and Polymer 2' segments; the fork and the fork' are each linked to a different finger or helix on the DNA polymerase and are selected such that the distance between the fork and the fork' changes when the polymerase incorporates a dNTP via one or more of the S-alkyl or S-aryl linkages; L is an optional linking moiety such as a divalent anchoring linking group that (i) connects individual polyaromatic arms together, (ii) connects one or both arms to an electrode in a pair of spaced apart electrodes, (iii) connects one or both arms to an underlying substrate supporting the electrodes as shown, and / or provides an additional attachment point from any position along one or both arms to a sensor probe molecule. In various embodiments, there can be at least one divalent linking group shown to anchor one or more arms of the crosslinkable complex. In various embodiments, each L, when present, is selected from the group consisting of (poly)methylene, -(CH2) of any length. x -(CH2) containing any number of intervening heteroatoms instead of C x -, PEG of any length, a polypeptide, a variety of ring structures, such as 1,4-phenylene, or any combination of the above.

[0117] In various embodiments, compound (XVII) in Figure 32 contains two functional groups, one at each of the opposing ends, in this case labeled "Au-binder" at each end. The "Au-binders" at the opposing ends of each arm can contain metal binding moieties such as -SH, -SMe, or -CSH.

[0118] In various embodiments, the synthetic cross-linking molecules according to the present disclosure are based on compound (II) of Figure 10, where the conductive nanoribbon core structure comprises phenyl-substituted 12-APAH conductive ribbons with zigzag edges. Various examples are described below.

[0119] In various embodiments, the synthetic crosslinking molecule comprises compound (XIII), illustrated in Figure 35a. This molecule comprises a zigzag edge PAH crosslinker based on a 12-APAH ribbon conductor structure. Compound (XIII) is fully functionalized with PEG ester side chains, capped with a thiol linking group for attachment to a metal electrode, and side chains containing tethered biotin for binding to probe molecules and for sensor self-assembly. In various embodiments of compound (XIII), the PEG ester side chains have the structure -p-(CH)-(CH) t COO(CH2CH2O) u It includes CH3, t is 0 to 10, and us is 5 to 50.

[0120] FIG. 35b shows a 3D model of compound (XIII).

[0121] In general, the synthetic bridge molecules comprising fused polycyclic aromatic hydrocarbon nanoribbons disclosed herein can be obtained by a convergent synthetic scheme based on palladium-catalyzed Suzuki-Miyaura cross-coupling between boron compounds and organic halides. A convergent synthesis rather than a linear synthetic scheme is practical here due to the size of these molecules. The key steps in assembling these molecules include (i) palladium- or microwave-catalyzed Suzuki-Miyaura cross-coupling of aryl 4,4,5,5-tetramethyl-1,3,2-dioxaborolanes with aryl halides to form biaryls, and (ii) FeCl3-catalyzed intramolecular dehydrogenative coupling to form fused ring nanoribbons (see, for example, Y. Huang, et al., supra). In various embodiments of the synthetic schemes herein, the order of steps in the synthesis can be altered such that key side chain moieties are attached before or after the palladium- or FeCl3-catalyzed coupling reaction, for example, based on the suitability of a particular side chain for these reaction conditions.

[0122] An embodiment of a synthetic route to compound (VI) (Figure 18) is illustrated in Figures 36-42. Figures 36 and 37 illustrate the synthesis of the left polymer portion of compound (VI) by Suzuki coupling. Figures 38 and 39 illustrate the synthesis of the right polymer portion of compound (VI) by Suzuki coupling. Figures 40 and 41 illustrate the generation of the 13AGNR compound precursor by Suzuki coupling to the central branch point substructure of the left and right polymer portions (Figure 41). Finally, FeCl3 treatment completes the aromatization of the 13AGNR precursor to compound (VI).

[0123] In various embodiments, the synthetic cross-linking molecule comprises compound (XII), illustrated in Figure 43. Compound (XII) comprises a phenyl-substituted 12-APAH ribbon with zigzag edges.

[0124] In various embodiments, the synthetic cross-linking molecule comprises compound (XII) of FIG. n=2, m=3 to 500; R 1 is as follows: (1) Structure (CH2) x CO(OCH2CH2) y OR 13 or (CH2) x OC=OCH2CH2CH2(OCH2CH2) y OR 13 ester-linked PEG chains having the formula (x=3-10, y=10-40, R 13 is Me or H), (2) structure (CH2) x O-CH2CH2CH2(OCH2CH2) y OR 13 Ether-linked PEG chains having x>2 and y=10-40, R 13 is Me or H), or (3) a water-soluble PEG chain (CH2CH2O) z R 14 Water-soluble ester-linked dendrons linked from a core moiety having 8-64 branches derivatized with 14is H or Me; R 1 can optionally include 1) photocleavable, 2) redox cleavable, 3) acid cleavable, or 4) base cleavable linkers between the atom and the PEG chain or dendron, such that the PEG chain or dendron can be removed by using 1) light, 2) oxidizing or reducing agents, 3) plus acid, or 4) base, respectively, after coupling the cap portion of the molecule to the gold electrode; R 2 is as follows: (1) Structure (CH2) x CO(OCH2CH2) y OR 13 or (CH2) x OC=OCH2CH2CH2(OCH2CH2) y OR 13 ester-linked PEG chains having the formula (x=3-10, y=10-40, R 13 is Me or H), (2) structure (CH2) x O-CH2CH2CH2(OCH2CH2) y OR 13 Ether-linked PEG chains having x>2 and y=10-40, R 13 is Me or H), or (3)-H is selected from R 3 =-(CH2) n C(O)NH-CH[(CH2) r (CH2)R 18 ][CH2CH2-O-CH2CH2O-(CH2) s -R 19 ), n, r and s are independently between 2 and 7; R 18 and R 19 is selected from the combinations in Table 1, thus R 18 and R 19 cannot react to each other, [Table 1-2] R 4 is H or SCH2CH2SCH3, R 5is -SH or SCH2CH2SCH3.

[0125] In various embodiments, the synthetic crosslinker molecule comprises compound (XIX), illustrated in Figure 44a. This crosslinker molecule comprises PEG side chains, -S-CH3 end groups, and a PAH nanoribbon conductive core structure. Representative lengths of this form, ranging from about 5 nm to 30 nm, were synthesized by the method outlined below. A 3D model of compound (XIX) is shown in Figure 44b. This synthetic product, compound (XIX), is shown in bulk in Figure 42c, suspended in THF, and shown by TEM images in THF solvent. The mass spectrum of compound (XIX) is shown in Figure 42d, and an NMR spectrum partially characterizing the size and composition of these products is also shown in Figure 42e. The spectra illustrate the range of masses present, and the ratio of PEG groups to aromatic rings.

[0126] Synthesis protocol

[0127] The following illustrates an embodiment of the synthesis of a series of intermediate building blocks and the final ribbon for an embodiment of PAHEB.

[0128] Synthesis of Tosyl-PEG-24 (22b) (Figure 22)

[0129] To a suspension of PEG-24 (22a) (0.750 g, 0.689 mmol) and tosyl chloride (0.197 g, 1.03 mmol) in 1.5 ml of anhydrous tetrahydrofuran at 0° C. was added 16 M potassium hydroxide (aqueous) (0.140 ml) in four portions over 1 h at that temperature. Once the addition was complete, the reaction was stirred at room temperature under an inert atmosphere for 16 h. The reaction was diluted with dichloromethane / water and stirred until the layers became clear. The layers were separated and the aqueous phase was extracted with additional dichloromethane. The combined organics were washed three times with water, dried over sodium sulfate and concentrated in vacuo. The crude material was purified by flash chromatography (silica gel, 0-10% methanol / dichloromethane) to give tosyl PEG-24 (22b) (0.678 g, 79% yield) as a white amorphous solid. 1 H NMR (499 MHz, Chloroform-d) δ 7.80 (d, J = 8.3 Hz, 2H), 7.34 (d, J = 8.0 Hz, 2H), 4.18 - 4.13 (m, 2H), 3.81 - 3.45 (m, 89H), 3.38 (s, 3H), 2.45 (s, 3H), 1.71 (s, 5H).MS:C 56 H 106 O 27 Calculated mass of S: 1242.66; Found: Positive (m / z): 1243.5 (M+H) + , 1265.5(M+Na) + , 1281.9(M+K) + .

[0130] Synthesis of tetraphenyldiiodobenzene methoxy ether (23c) (Figure 23)

[0131] To a suspension of magnesium turnings (1.22 g, 50.3 mmol) in 47 ml of anhydrous tetrahydrofuran, a mixture of 1-bromo-4-(2-methoxyethyl)benzene (1.68 g, 7.80 mmol) and bromobenzene (4.04 g, 25.7 mmol) was added slowly over 1 hour, careful not to boil the solvent. Once the addition was complete, the reaction was stirred at room temperature for an additional hour until the exotherm had subsided. The reaction was then cooled to 0° C., after which perbromobenzene (1.85 g, 3.35 mmol) was added and the reaction was stirred at room temperature under an inert atmosphere for 16 hours. The reaction was cooled to 0° C. and iodine (8.51 g, 33.5 mmol) dissolved in 10 ml of tetrahydrofuran was added until a deep purple color (characteristic of iodine) remained and stirred for an additional 2 hours. The reaction was diluted with water and chloroform and the iodine was quenched with saturated sodium thiosulfate solution. The phases were separated and the aqueous phase was extracted twice with 100 ml of chloroform. The combined organics were washed twice with saturated sodium bicarbonate, once with brine, dried over sodium sulfate and concentrated in vacuo. The crude material was purified by flash chromatography (silica gel, 0-40% ethyl acetate / hexanes) to give 3',6'-diiodo-4-(2-methoxyethyl)-4',5'-diphenyl-1,1':2',1"-terphenyl (23c) (0.328 g) (14-179p11), and a less pure sample (djs-14-179p12) which was repurified by flash chromatography (silica gel, 0-30% ethyl acetate / hexanes) to give additional product (23c) (0.175 g) in total (0.503 g, 22% yield) as a pale yellow solid. 1 H NMR (499 MHz, Chloroform-d) δ 7.20 - 6.92 (m, 19H), 3.50 (t, J = 7.3 Hz, 2H), 3.28 (s, 3H), 2.78 (t, J = 7.2 Hz, 2H);MS:C 33 H 26 Calculated mass of IO: 692.01; Found: Positive (m / z): 715.1 (M+Na) + , 731.1(M+K) + .

[0132] Synthesis of monomeric alcohol (24e) (Figure 24)

[0133] To a solution of methoxy monomer (23c) (0.190 g, 0.274 mmol) in 5.0 ml of anhydrous dichloromethane was added iodotrimethylsilane (0.284 g, 1.42 mmol) and the deeply colored reaction was stirred at room temperature under an inert atmosphere for 16 hours. The reaction was quenched with 2.0 ml of concentrated ammonia (aqueous) and stirred for 20 minutes. The reaction was diluted with water and the phases were separated. The aqueous phase was extracted twice with dichloromethane and the combined organics were washed with water, brine, dried over sodium sulfate and concentrated in vacuo. The crude material was used in the next step (silyl ether cleavage) without further purification.

[0134] To a solution of crude silyl ether monomer (24d) in 15.0 mL of anhydrous tetrahydrofuran was added tetrabutylammonium fluoride TBAF (0.612 mmol, 1.0 M in THF) and the reaction was stirred at room temperature under inert atmosphere for 16 h. The reaction was concentrated in vacuo, dissolved in dichloromethane / water, and the phases separated. The aqueous phase was extracted two more times with dichloromethane, and the combined organics were washed with brine, dried over sodium sulfate, and concentrated in vacuo. The crude material was purified by flash chromatography (silica gel, 0-50% ethyl acetate / hexanes) to give the alcohol monomer (24e) (60% yield over two steps) as a white solid. 1 H NMR (499 MHz, Chloroform-d) δ 7.19 - 6.97 (m, 19H), 3.76 (t, J = 6.5 Hz, 2H), 2.77 (t, J = 6.4 Hz, 2H),MS:C 32 H 24 Calculated mass of IO: 677.99; Found: Positive (m / z): 701.0 (M+Na) + , 716.8(M+K) + .

[0135] Synthesis of PEG-24-monomer (25f) (Figure 25)

[0136] To a 0° C. solution of the alcohol monomer (24e) (0.040 g, 0.059 mmol) in 1.0 mL of anhydrous tetrahydrofuran was carefully added 60% sodium hydride (8.0 mg, 0.206 mmol) and the reaction was stirred at reflux under an inert atmosphere for 1 hour. The reaction was cooled and tosyl PEG-24 (22b) (0.077 g, 0.062 mmol) in 1.1 mL of anhydrous tetrahydrofuran was added dropwise and the reaction was stirred at reflux under an inert atmosphere for 16 hours. The reaction was cooled and charged with additional sodium hydride (10 mg) and stirred at reflux for an additional 24 hours. The reaction was quenched with a few drops of water and concentrated in vacuo. The resulting residue was dissolved in dichloromethane / water and the phases were separated. The aqueous phase was saturated with sodium chloride and extracted six more times with dichloromethane, and the combined organics were washed with brine, dried over sodium sulfate, and concentrated in vacuo. The crude material was purified by flash chromatography (silica gel, 0-10% methanol / dichloromethane) to give PEG-24-monomer (25f) (0.058 g, 57% yield) as a clear solid. 1 H NMR (499 MHz, Chloroform-d) δ 7.22 - 6.90 (m, 19H), 3.81 - 3.45 (m, 211H), 3.38 (s, 7H), 2.79 (t, J = 7.2 Hz, 2H), NMR indicates approximately 50% excess PEG; MS: C 81 H 122 I2O 25 Calculated mass: 1748.64; Found: Positive (m / z): 1771.7 (M+Na) + .

[0137] Synthesis of nanoribbon polymers by thermal reaction (Figures 26-27)

[0138] A solution of PEG-monomer (25f) (29 mg, 0.0166 mmol), 1,4-benzenediboronic acid bis(pinacol) ester (26a) (5.5 mg, 0.0166 mmol) and K3PO4 (7.0 mg, 0.0332 mmol) in 1 ml of DMF was degassed by bubbling argon five times. Pd(PPh3)4 (2.0 mg) was then added and the reaction mixture was degassed by bubbling argon three times. The reaction mixture was heated to 100° C. and stirred under argon overnight. The “hot” crude product was used in the following reaction without purification.

[0139] Synthesis of nanoribbon polymer by microwave reaction (Figure 28)

[0140] A solution of PEG-monomer (25f) (47.3 mg, 0.027 mmol) and K3PO4 (11.4 mg, 0.054 mmol) in 1.4 ml DMF was degassed by bubbling argon five times. Pd(PPh3)4 (7.8 mg) was then added and the reaction mixture was degassed by bubbling argon three times. This intermediate solution, containing 19 millimolar concentration of PEG-monomer (25f), is referred to herein as "Solution A."

[0141] A solution of 1,4-benzenediboronic acid bis(pinacol) ester (26a) (12.7 mg, 0.038 mmol) and KPO (16.1 mg, 0.076 mmol) in 2 mL of DMF was degassed five times by bubbling argon through the solution. This intermediate solution, containing 19 mmolar of 1,4-benzenediboronic acid bis(pinacol) ester (26a), is referred to herein as "Solution B."

[0142] Six microwave reactions were prepared using 200 μL of solution B for each reaction and 200 μL (1:1 B:A molar ratio), 160 μL (1:0.8 B:A molar ratio), 140 μL (1:0.7 B:A molar ratio), 124 μL (1:0.62 B:A molar ratio), 100 μL (1:0.5 B:A molar ratio) and 80 μL (1:0.4 B:A molar ratio) of solution A for each reaction individually. Each microwave reaction was irradiated at 150° C. for 10 minutes in the microwave.

[0143] After the microwave reaction, the three reactants in molar ratios of 1:0.62, 1:0.5 and 1:0.4 were combined and then mixed with half of the "thermal reaction" product, followed by reaction with more diiodo-PEG-monomer (25f) (16.7 mg), additional K3PO4 (5.0 mg) and Pd(PPh3)4 (3.0 mg) following the same procedure as above, resulting in the 13-335-I2 polymer (Figure 27), which was used directly in the next step without purification after removing the DMF.

[0144] The other three reactions at molar ratios of 1:1, 1:0.8 and 1:0.7 were combined and then mixed with the other half of the "thermal" product, and then reacted with additional 1,4-benzenediboronic acid bis(pinacol) ester (26a) (6.4 mg), K3PO4 (5.0 mg) and Pd(PPh3)4 (3.0 mg) following the same procedure as above, resulting in 13-335-B2. After removal of DMF, the crude product was used directly in the next step (Figure 28).

[0145] Synthesis of nanoribbon intermediate CX-13-336 (Figure 28)

[0146] A solution of 13-335-I2 polymer, 13-335-B2 polymer and K3PO4 (27.2 mg, 0.128 mmol) in 1 ml of DMF was degassed by bubbling argon five times. Then, Pd(PPh3)4 (4.2 mg) was added and the reaction mixture was degassed by bubbling argon three times. Then, the reaction mixture was heated to 100° C. and stirred under argon overnight. The solvent was removed and the residue was dissolved in 0.5 ml of THF and purified by SEC column to give 7.0 mg of polymer CX-13-336 (FIG. 28).

[0147] Synthesis of nanoribbon intermediate CX-13-337 (Figure 29)

[0148] Polymer CX-13-336 (purified by SEC column) (7.0 mg), 1,4-benzenediboronic acid bis(pinacol) ester (26a) (16.5 mg, 0.049 mmol) and K3PO4 (0.128 mmol, 27.2 mg) in 1 ml of DMF were degassed by bubbling argon five times. Then, Pd(PPh3)4 (4.2 mg) was added and the reaction mixture was degassed by bubbling argon three times. Then, the reaction mixture was heated to 100° C. and stirred under argon overnight. After removing DMF, the crude product was dissolved in 0.5 ml of THF and purified by SEC column.

[0149] The resulting polymer (5.0 mg) was dissolved in 0.5 ml of DMF, and capping compound 29a (9 mg, 0.013 mmol) was added, followed by K3PO4 (5.0 mg, 0.023 mmol), and degassed by argon bubbling five times. Pd(PPh3)4 (3.0 mg) was then added. The reaction mixture was microwaved at 150° C. for 1 h. After cooling, the solvent was removed and the residue was purified by SEC column to give 3.5 g of polymer CX-13-337 (FIG. 29). MALDI / TOF mass spectroscopy suggests that the fraction increased from 20 K Daltons to 40 K Daltons polymer with each Suzuki coupling step and gel permeation chromatography.

[0150] Synthesis of nanoribbon compound (XV) (Figure 30)

[0151] Polymer CX-13-337 (3.5 mg, purified from SEC column) was dissolved in 20 ml of dichloromethane and argon was bubbled through for 10 min. Iron(III) chloride (120 mg) dissolved in 3 ml of nitromethane was slowly added and the resulting mixture was stirred at room temperature for 1 h, after which time about 1-2 mg of an insoluble black precipitate had formed. The reaction mixture was quenched with 20 ml of methanol, the solvent was removed and the residue was purified by SEC column to give 1.5 mg of product. The soluble product was 1 Judging from the integrals of the 1 H NMR spectra, at least 30% of the PEG chains were lost during the dehydrogenation process.

Claims

1. A synthetic cross-linking molecule, the molecule comprising: Conductive sp ２ a hybrid polycyclic aromatic hydrocarbon nanoribbon, the nanoribbon having a rectangular sheet-like configuration and an outer edge defined by two parallel long top and bottom edges and two parallel short left and right edges, the single fixed orientation of each fused ring being zigzag periodic along either the long or short edges of the nanoribbon, the nanoribbon measuring a length between 3 nm and 100 nm and a width between 0.23 nm and 23 nm; a substituent L covalently attached to the left short edge of the nanoribbon; a substituent R covalently bonded to the right short edge of the nanoribbon, where L and R each include at least one sulfur atom or carbene precursor moiety capable of bonding to a metal electrode or a metal contact disposed on an electrode; At least one binding group P covalently attached to any edge of the nanoribbon and capable of binding to a probe molecule; at least one substituent S covalently attached to any edge of the nanoribbon, the substituent S being capable of influencing at least one of the solubility or conformation of the synthetic crosslinking molecule or promoting self-assembly of the synthetic crosslinking molecule onto at least one of the metal electrode, the metal contact of an electrode, or the probe molecule in the fabrication of a molecular electronic sensor; 1. A synthetic cross-linking molecule comprising:

2. L and R are -SH, -SCH ３ , -SSH, -SS-CH ３ 2. The synthetic crosslinking molecule of claim 1, further comprising at least one of the following moieties: 6-[1,3-diisopropyl-1H-benzo[d]imidazol-3-ium]-yl or 6-[1,3-diisopropyl-1H-benzo[d]imidazol-3-ium]-thioyl.

3. 2. The synthetic crosslinking molecule of claim 1, wherein P further comprises at least one of an azide, an alkyne, an alkoxyamine, a ketone, an aldehyde, biotin, or streptavidin.

4. A synthetic cross-linking molecule, said molecule having the structure: 【Chemistry 4】 (In the formula, n and m are independently 0 to 30; W and Y are each independently -O-, -CH ２ -, C.R. ８ R ９ , C.H. ２ CR ８ R ９ , CR8R ９ CH ２ , O.C.R. ８ R ９ and C.R. ８ R ９ R is independently selected from O; ８ and R ９ are bonded to the same carbon atom, and H, CH ３ , C ２ H ５ , C.H. ２ CH ２ CH ３ Or (CH ２ ) ｘ (O.C.H. ２ CH ２ ) ｙ OR １０ where x is 2 to 10, y is 10 to 40, and R １０ is H, Me or Et, and R ８ and R ９ can optionally be linked to form a ring, O is optionally directly linked to the aromatic ring, and W and Y can optionally be interchanged within the ring; W' and Y' are -O-, -CH ２ -, C.R. ８ R ９ , C.H. ２ CR ８ R ９ , CR8R ９ CH ２ , O.C.R. ８ R ９ and C.R. ８ R ９ R is independently selected from O; ８ and R ９ are bonded to the same carbon atom, and H, CH ３ , C ２ H ５ , C.H. ２ CH ２ CH ３ Or (CH ２ ) ｘ (O.C.H. ２ CH ２ ) ｙ OR １０ where x is 2 to 10, y is 10 to 40, and R １０ is H, Me or Et, and R ８ and R ９ can optionally be linked to form a ring, O is optionally directly linked to the aromatic ring, and W' and Y' can optionally be interchanged within the ring; R １ (i) ester-linked PEG chains (CH ２ ) ｘ CO(OCH ２ CH ２ ) ｙ OR １３ Or (CH ２ ) ｘ OC=OCH ２ CH ２ CH ２ (O.C.H. ２ CH ２ ) ｙ OR １３ (x is 0 to 10, y is 10 to 40, and R １３ is Me or H), or (ii) the structure (CH ２ CH ２ O) ｚ R １４ Water-soluble ester-linked dendrons containing 8-64 branches, each derivatized with a water-soluble PEG chain of １４ is H or Me; １ the ester linking group optionally comprises a 1) photocleavable, 2) redox cleavable, 3) acid cleavable, or 4) base cleavable linker, such that the dendron can be removed by using 1) light, 2) an oxidizing or reducing agent, 3) acid, or 4) base, respectively; R ２ (i) ester-linked PEG chains (CH ２ ) ｘ CO(OCH ２ CH ２ ) ｙ OR １３ Or (CH ２ ) ｘ OC=OCH ２ CH ２ CH ２ (O.C.H. ２ CH ２ ) ｙ OR １３ (x is 0 to 10, y is 10 to 40, and R １３ is Me or H); (ii) a water-soluble PEG chain (CH ２ CH ２ O) ｚ R １４ Water-soluble ester-linked dendrons having 4-16 branches, each derivatized with １４ is H or Me; ２ the ester linking group optionally comprises a 1) photocleavable, 2) redox cleavable, 3) acid cleavable, or 4) base cleavable linker, such that the dendron can be removed by using 1) light, 2) an oxidizing or reducing agent, 3) acid, or 4) base, respectively; W" and Y" are -S-, -CH ２ -, CH ２ CH ２ , C.R. １１ R １２ and SCR １１ R １２ and R １１ and R １２ are bonded to the same carbon atom, and H, CH ３ , C ２ H ５ , C.H. ２ CH ２ CH ３ , C.H. ２ CH ２ SCH ３ , S.C.H. ３ or SCH ２ CH ２ SCH ３ and R ８ and R ９ can optionally be linked to form a ring, S is optionally directly linked to the aromatic ring, and W″ and Y″ can optionally be interchanged within the ring; R ５ is H, SMe or CH ２ CH ２ is SMe, R ６ H, SMe, SCH ２ CH ２ SMe, SCH ２ C (CH ２ SMe) ３ , S.H., C.S. ２ H, C.H. ２ SMe, CH ２ S.H., C.H. ２ C.S. ２ H, 6-[1,3-diisopropyl-1H-benzo[d]imidazol-3-ium]-yl or 6-[1,3-diisopropyl-1H-benzo[d]imidazol-3-ium]-thioyl, and R ７ H, SMe, SCH ２ CH ２ SMe, SH, CS ２ H, C.H. ２ SMe, CH ２ S.H., C.H. ２ C.S. ２ H, 6-[1,3-diisopropyl-1H-benzo[d]imidazol-3-ium]-yl or 6-[1,3-diisopropyl-1H-benzo[d]imidazol-3-ium]-thioyl.

1. A synthetic cross-linking molecule comprising:

5. m+n=10 to 24, Y=W=-CH ２ - or -O-, Y'=W'=-CH ２ - or -O-, Y″=W″=-S-, R １ =-CO-O-(CH ２ CH ２ O) ｎ -OCH ３ and n is between 2 and 7 or between 20 and 48; R ２ =-CO-O-(CH ２ CH ２ O) ｎ -OCH ３ and n is between 2 and 7 or between 20 and 48; R ３ =(L-Phe-Gly) ４ -NHOCH ２ CH ２ O-N=CH(p-C ６ H ４ ) CH ２ - and R ４ = H, R ５ =CH ２ CH ２ is SMe, R ６ = SCH ２ CH ２ is SMe, and R ７ 5. The synthetic cross-linking molecule of claim 4, wherein:

6. R １ =PEG-20, Y and W are -O-; R ３ =Azide-(CH ２ ) １０ and R ４ = Biotin-PEG-5, R ５ = H, R ６ = methylthiol, and R ７ 6. The synthetic cross-linking molecule of claim 5, wherein:

7. m+n=10 to 24, Y=W=-CH ２ - or -O-, Y'=W'=-CH ２ - or -O-, Y″=W″=-S-, R １ = H, R ２ =-CO-O-(CH ２ CH ２ O) ｎ -OCH ３ and n is between 2 and 7 or between 20 and 48; R ３ =-(CH ２ ) ｎ C(O)NH-CH[(CH ２ ) ｒ (CH ２ ) R １８ ][CH ２ CH ２ -O-CH ２ CH ２ O-(CH ２ ) ｓ -R １９ ), n, r and s are independently between 2 and 7; and R １８ and R １９ is -N ３ , -CC-H, -NHCO-biotin, -CHO, -COCH ３ and -O-NH ２ Independently selected from １８ and R １９ provided that they cannot react with each other, R ４ = R ５ = p- or m-C ６ H ４ - (CH ２ ) ｔ COO (CH ２ CH ２ O) ｕ CH ３ where t is 0 to 10 and u is 5 to 50; R ６ = SCH ２ CH ２ is SMe, and R ７ 5. The synthetic cross-linking molecule of claim 4, wherein:

8. A synthetic cross-linking molecule, said molecule having the structure: 【Chemistry 5】 (In the formula, n=2, m=3 to 500; R １ (1) Structure (CH ２ ) ｘ CO(OCH ２ CH ２ ) ｙ OR １３ Or (CH ２ ) ｘ OC=OCH ２ CH ２ CH ２ (O.C.H. ２ CH ２ ) ｙ OR １３ where x is 3-10, y is 10-40, and R １３ is Me or H), (2) the structure (CH ２ ) ｘ O-CH ２ CH ２ CH ２ (O.C.H. ２ CH ２ ) ｙ OR １３ ether-linked PEG chains having x>2, y=10-40, and R １３ is Me or H), or (3) each of which is a water-soluble PEG chain (CH ２ CH ２ O) ｚ R １４ Water-soluble ester-linked dendrons having 8-64 branches (z is 1-8, R １４ is H or Me; and R １ the ester-linking group of can optionally include 1) photocleavable, 2) redox-cleavable, 3) acid-cleavable, or 4) base-cleavable linkers, such that the dendron can be removed by using 1) light, 2) oxidizing or reducing agents, 3) acid, or 4) base, respectively, after linking the portion of the molecule to a gold electrode; R ２ (1) Structure (CH ２ ) ｘ CO(OCH ２ CH ２ ) ｙ OR １３ Or (CH ２ ) ｘ OC=OCH ２ CH ２ CH ２ (O.C.H. ２ CH ２ ) ｙ OR １３ where x is 3-10, y is 10-40, and R １３ is Me or H), (2) the structure (CH ２ ) ｘ O-CH ２ CH ２ CH ２ (O.C.H. ２ CH ２ ) ｙ OR １３ ether-linked PEG chains having x>2, y=10-40, and R １３ is Me or H), or (3) —H; R ３ =-(CH ２ ) ｎ C(O)NH-CH[(CH ２ ) ｒ (CH ２ ) R １８ ][CH ２ CH ２ -O-CH ２ CH ２ O-(CH ２ ) ｓ -R １９ ), n, r and s are independently between 2 and 7; and R １８ and R １９ is -N ３ , -CC-H, -NHCO-biotin, -CHO, -COCH ３ and -O-NH ２ Independently selected from １８ and R １９ provided that they cannot react with each other, R ４ is H or SCH ２ CH ２ SCH ３ and R ５ is -SH or SCH ２ CH ２ SCH ３ (It is) 1. A synthetic cross-linking molecule comprising:

9. A synthetic cross-linking molecule, said molecule having the following structure: 【Chemistry 6】 (In the formula, n and m are independently 0 to 30; R １ = R ２ =-(CH ２ ) ４ C(O)O-PEG-48, R ３ =H or -NR ９ R １０ and R ９ is linked to a DNA polymerase cysteine ​​residue, and R １０ is H or R １０ is R ９ is linked to a DNA polymerase cysteine ​​residue that is different from the residue linked to R ４ = R ５ = H, R ６ =CH ２ SCH ２ CH ２ SCH ３ or H, R ７ =CH ２ SCH ２ CH ２ SCH ３ or H, R8=CH ２ SCH ２ CH ２ SCH ３ or -SH) 1. A synthetic cross-linking molecule comprising:

10. R １ = R ２ = (CH ２ ) ４ C(O)O-PEG-48, R ３ (CH ２ ) ４ C(O)NH-CH ２ CH ２ CH (CH ２ CH ２ CH ２ N3) (CH ２ CH ２ OCH ２ CH ２ OCH ２ CH ２ NH-biotin), R ４ = R ５ = H, R ６ =CH ２ SCH ２ CH ２ SCH ３ or H, R ７ =CH ２ SCH ２ CH ２ SCH ３ or H, and R8=CH ２ SCH ２ CH ２ SCH ３ or -SH.

11. R ３ = H, R ４ is linked to a DNA polymerase cysteine ​​residue, R ５ is H or R ５ is R ９ 10. The synthetic crosslinking molecule of claim 9, wherein said crosslinking molecule is linked to a DNA polymerase cysteine ​​residue that is different from said residue linked to said cysteine ​​residue.

12. A synthetic cross-linking molecule, said molecule having the structure: 【Chemistry 7】 where n is an integer selected such that the length of the synthetic cross-linking molecule is between 5 nm and 30 nm.

1. A synthetic cross-linking molecule comprising:

13. A synthetic cross-linking molecule, said molecule having the structure: 【Chemistry 8】 1. A synthetic cross-linking molecule comprising:

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