Systems, system components and methods for automated macromolecule synthesis

Abstract

A system and method for automated synthesis of a macromolecule from a nucleic acid template is provided, which includes a flow cell with a sipper, a mount with a thermal block, a pump, a selectable valve, a holder, an XYZ gantry, and a controller. The flow cell can be held in a fixed position while the gantry can move the holder to sippers of the flow cell. In this configuration, the sipper length can be reduced or minimized to reduce loss of precious reagents and the synthesized macromolecule.

Description

[0001]new PCT application September 27, 2024 Roche Sequencing Solutions, Inc.R74735PC ATE / LAU / mvfSYSTEMS, SYSTEM COMPONENTS AND METHODS FOR AUTOMATEDMACROMOLECULE SYNTHESISINCORPORATION BY REFERENCE All publications and patent applications mentioned in this specification are herein incorporated by reference to the same extent as if each individual publication or patentapplication was specifically and individually indicated to be incorporated by reference intheir entireties for all purposes. FIELD OF THE INVENTIONThe present invention relates generally to a system and its components as well as amethod for automated synthesis of a molecule, and more particularly, for automated synthesis of a macromolecule from a nucleic acid template, such as an Xpandomer. BACKGROUND OF THE INVENTION Various DNA sequencing technologies have been developed over the past severaldecades. One of the next generation sequencing technologies involves the use ofnanopores, which can be used to determine the sequence of DNA molecules by passing a single strand of the DNA molecule directly through the pore, as is being done by OxfordNanopore. However, this approach can suffer difficulties from reading long sections ofrepeat nucleotides since the signal from the nanopore can remain relatively constant for long periods of time, making it difficult to determine the exact number of repeat molecules. Another approach which solves this problem involves the use of synthesizing a specialized macromolecule, called an Xpandomer, from a nucleic acid template using amodified polymerase and modified nucleotides, as further described in U.S. Patent No.7,939,259 (Kokoris et al.) and International Patent Publication No. WO2020 / 236526A1(O’Connell et al.). The Xpandomer molecule includes a translocation control element thatallows the user to advance the Xpandomer in a controlled fashion through the nanopore, which therefore allows the number of repeat nucleotides to be accurately determined. The synthesis of the Xpandomer can be relatively complex, time consuming, and difficultto perform manually. Therefore, it would be desirable to provide a system capable ofperforming the synthesis of the Xpandomer molecule in an automated fashion withminimal input from the end user, such as a system using flow cells, often also referred to as chips.For the end user of such a system, charging, fixing and preloading of the flow cell(s) canoften be time-consuming, complicated and often not reproducible. This can result in anunreliable process, which can manifest itself in the fact that the preload is unequal withregard to the 4 corners per flow cell and unequal from cell to cell, which in turn can resultin deviating heat transfer results between mount and flow cell(s). Furthermore, in general,fluidic coupling of the flow cell(s) can be very delicate and error-prone.SUMMARY OF THE INVENTIONThe present invention is directed to a system and its components as well as a method forautomated synthesis of a molecule, and more particularly, for automated synthesis of a macromolecule from a nucleic acid template. According to one aspect of the present invention, a system for synthesizing amacromolecule from a sample is provided. The system includes a flow cell including atleast one flow channel, such as one flow channel, two flow channels or at least four flowchannels. The flow channel, which can be serpentine-formed, has a functionalized solidphase surface configured to bind a plurality of capture probes that are configured to bindthe sample, e.g. configured to hybridize to a target nucleotide sequence. The functionalized solid phase surface can be formed from a modification or treatment of theflow channel substrate and may not be formed from a separate coating of the flow channelsubstrate. Each flow channel has an inlet port and an outlet port, where the inlet port is in fluidiccommunication with a sipper, i.e. a component for sipping or drawing a fluid. The sippercan be preattached to the inlet port, and can exhibit a length that is less than a length ofthe flow cell, wherein the length of the sipper can be less than twice a length of the flowcell. In addition, the sipper and the inlet port can extend from the flow cell in an orientationthat is normal to a plane that encompasses the flow channel, and wherein the sipper hasa 90 degree bend. Alternatively, the sipper and the inlet port can extend from the flow cellin an orientation that is parallel to a plane that encompasses the flow channel.The system further includes a heatable mount, also referred to as heated mount, that isconfigured to receive at least one flow cell, which mount can be configured to receive atleast two or four flow cells. Here, the term “to receive” is to be understood as “to support”or “to adjoin”, wherein the configuration of the mount to do so can be achieved by, e.g., acomponent or entity for thermally and / or physically coupling the flow cell to the mount.The mount also includes a thermal block, and a portion of the sipper can be in thermalcontact with the thermal block.The system further includes a holder configured to hold a plurality of reagents and at leastone sample, which holder can be further configured to hold a sample. In addition, theholder can be configured to hold a 96 well plate. Alternatively or additionally, the holdercan be configured to hold a rack of vials or tubes. The holder can include a reagentcartridge with a plurality of liquid reservoirs and drop in locations configured to receive atube or vial. Also, the heatable mount can be configured to hold a flow cell in a verticalorientation while the holder of the system is in a horizontal orientation. The system further includes a gantry configured to move in 3 different axis, i.e., in 3different dimensions, resulting in 3 degrees of freedom to move, a pump for fluidcommunication with the outlet port of the flow channel, a valve configured to selectivelyconnect the outlet port of the flow channel with a waste reservoir and a buffer reservoir,a UV source configured to illuminate the flow channels, and a controller configured tocontrol a temperature of the thermal block, movement of the gantry, selection of the valve,operation of the UV source, and operation of the pump. Here, the gantry can beconfigured to move the holder. Also, the controller can be further configured to control thepump and gantry to mix reagents. No valves can be positioned in a fluid path betweenthe flow channels and the reagents and sample in the holder. The system can further include a piercer for piercing a covering disposed over the reagents, and the system can further include a flow gauge and a pressure gauge tomeasure fluid exiting the outlet of the flow cell. Also, the system can further include aplurality of pumps, with one dedicated pump in fluid communication with each outlet of the flow cell. Moreover, the system can further include a second thermal block in thermalcontact with the holder. Also, the system can further include a mixing tube configured toperform fluid mixing operations on a sensitive reagent in the holder, wherein the mixingtube is not in fluid communication with the flow cell. Here, the sensitive reagent can bean anhydride, such as succinic anhydride. Furthermore, the system can further include athermal pad disposed between the flow cell and the thermal block. According to another aspect of the present invention, a method for synthesizing amacromolecule from a nucleic acid template is provided. The method includes performingthe steps described herein using the system described herein. Accordingly, a method forsynthesizing a macromolecule from a nucleic acid template is provided, wherein themethod includes providing a system as described above. The method includesintroducing a plurality of single stranded nucleic acid molecules into the flow channel of the flow cell through the sipper, where the single stranded nucleic acid molecules arestored on the holder. The method further includes hybridizing the single stranded nucleicacid molecules to a plurality of capture probes that have been attached to the surface ofthe flow channel, where the temperature of the heatable mount is controlled by thecontroller during the hybridization step. The method also includes, after the hybridization step is complete, introducing a wash buffer into the flow cell to remove nonhybridizedsingle stranded nucleic acid molecules from the flow cell. Moreover, the method includesintroducing an extension reaction mixture into the flow channel of the flow cell through the sipper to synthesize a plurality of macromolecules by using the hybridized single stranded nucleic acid molecules as templates, where the extension reaction includes a polymerase and nucleotide analogues, where the extension reaction mixture is stored on the holder.The method additionally includes controlling the temperature of the heatable mount withthe controller during the synthesis step; The method further includes applying an UV lightfrom the UV source to the macromolecules to release the macromolecules from the capture probes; and eluting the macromolecules from the flow cell and, for example,through the sipper, into a collection tube. The method can further include, after thesynthesis step is complete, introducing an acid into the flow channel of the flow cell to selectively cleave chemical bonds holding the macromolecules in a compactconfiguration. Also, the method can further include, after the cleavage step, introducingan additional reagent into the flow channel of the flow cell to further modify themacromolecules, wherein the additional reagent can be succinic anhydride.According to another aspect of the present invention, a flow cell is provided, which flow cell can be used for the above described system for synthesizing a macromolecule from a sample.The flow cell of the present invention comprises a molded portion, a cover portion, and atleast one sipper.In the flow cell of the present invention, the molded portion comprises a flow cell portionand a sipper receiving portion. The flow cell portion comprises at least one flow channel.The flow channel has a functionalized solid phase surface configured to bind a pluralityof capture probes that are configured to bind a sample. Each flow channel has an inletport and an outlet port, and each inlet port is in fluidic communication with a sipper. Thesipper receiving portion comprises at least one sipper receiving recess having a central axis, wherein the sipper receiving recess is configured to accommodate a section of a sipper. In the present invention, the sipper is a tube with two sections and a central axis, wherein the first section comprises a first end of the sipper, and the second section comprises a second end of the sipper. The first end of the sipper is in fluidic communication with the inlet port of a flow channel, and the second end of the sipper is configured to sip, or flow,a fluid to, or from, a fluid container. The fluid can be a sample, a reagent fluid, a washfluid, an elution fluid, for example. In the present invention, the first section of the sipper is at least in part located between the molded portion and the cover portion of the flow cell, and the central axis of the first section is in the same plane as a centre plane of the flow channel, or in a plane parallelthereto. Thereby, a proper fixation of the sipper as well as a sufficient fluid flow throughthe sipper can be achieved. In the present invention, the first section of the sipper is attached to the sipper receiving recess.In the present invention, the cover portion is attached to the molded portion to seal the atleast one flow channel with exception of the inlet port and the outlet port. This means thatthe only openings of the flow channel, once the cover portion is attached to the moldedportion, are the inlet port and the outlet port. The cover portion can be a thin film, forexample a thin film made from a cyclic olefin polymer or cyclic olefin copolymer. Alternatively, the cover portion can be an additional molded portion. Accordingly, themolded portion comprises the at least one flow channel, and the cover portion, e.g. inform of the thin film or the additional molded portion is attached to the molded portion toseal the at least one flow channel, optionally wherein the cover portion can be made froma cyclic olefin polymer or cyclic olefin copolymer.The sipper receiving recess can further comprise at least one throughhole extendingthrough the molded portion in a plane perpendicular to the centre plane of the flowchannel. The through-hole can be used for the application of an adhesive for attachingthe first section of the sipper to the sipper receiving recess. The throughhole can be located adjacent to the inlet port. This configuration provides the possibility to efficiently fix the first section of the sipper to the sipper receiving recess, thereby ensuring that the first end of the sipper remains in fluidic communication with the inlet port of a flow channel.The sipper receiving recess can further comprise a further throughhole extending throughthe molded portion in a plane perpendicular to the centre plane of the flow channel. Thefurther throughhole can provide access to a second attachment point, thereby strengthening the attachment of the first section of the sipper to the sipper receiving recess. The first section of the sipper can be attached to the flow cell by any means known in the art, for example by pressure exerted by screws or clamps.In the present invention, the first section of the sipper can be fixedly attached to the sipperreceiving portion. This means that, after attaching, the first section of the sipper cannot be removed from the sipper receiving portion without damaging it. The attachment canbe achieved by an adhesive applied onto the first section of the sipper accommodated inthe sipper receiving recess, thereby attaching the first section of the sipper to the sipperreceiving recess. The adhesive can be a light curable adhesive, such as an UV curableadhesive.In the present invention, the central axis of the sipper receiving recess can be arrangedoff-centre in regard to a central axis of the molded portion. This configuration has the advantage of providing a larger contiguous surface area on the sipper receiving portion compared to a configuration wherein the sipper receiving recess is located on a central axis of the molded portion, which can be used for example to accommodate an identifier, such as a two-dimensional matrix barcode (i.e. QR code).In the present invention, the first end of the sipper comprises a surface in fluidiccommunication with the inlet port. The sipper’s first end surface can be oriented at anangle of about 90° relative to the central axis of the first section of the sipper. This allowsan efficient seal with the inlet port, thereby minimizing the dead volume in the interface ofthe flow channel and the sipper. Minimizing dead volume is advantageous as it allows the efficient use of fluids without waste. This is of particular interest, if the fluids are expensive reagents, such as is the case in the nucleic acid synthesis methods.In the present invention, the second end of the sipper comprises a surface configured forfluidic communication with a fluid container. The sipper’s second end surface cancomprise a first region orientated at an angle of about 90° relative to the central axis of the second section of the sipper, and a second region that is orientated at an angle ofabout 45° relative to the central axis of the second section of the sipper. This configurationallows an efficient intake of fluid from a fluid container, allowing the use of substantially all of the fluid comprised in a container without waste. This is of particular interest, if the fluids are expensive reagents, such as is the case in the nucleic acid synthesis methods.In the present invention, the length of the second region of the sipper’s second endsurface, measured perpendicularly to the central axis of the second section of the sippercan be greater than the length of the first region of the sipper’s second end surface,measured perpendicularly to the central axis of the second section of the sipper. Thisconfiguration further increases the capability of the sipper to take in fluid from the fluid container. In the present invention, the sipper receiving portion comprises a first surface and a second surface, wherein the sipper receiving recess is located on the first surface. Thesipper receiving portion can further comprise a handle, wherein the handle is located onthe second surface of the sipper receiving portion. A central axis of the handle can extendat an angle of about 45° to 135°, such as about 90°, relative to the centre plane of theflow channel. The handle allows efficient and easy handling of the flow cell, for examplefor placing the flow cell into the system for synthesizing a macromolecule from a sampleof the invention, or for removing the flow cell from the system.In the present invention, the flow cell can further comprises an identifier located on thesecond surface of the molded portion, such as a bar code, e.g. a two-dimensional matrixbarcode (i.e. QR code). In another aspect, the present invention is also concerned with a method of producing theflow cell of the present invention. The method comprises the following steps:(a) providing the molded portion, the cover portion, and the at least one sipper;(b) bonding the molded portion and the cover portion;(c) inserting the first section of the sipper into the sipper receiving recess;(d) establishing fluidic communication of the inlet port of the flow channel with thefirst end of the sipper; and (e) attaching the first section of the sipper to the sipper receiving recess;wherein the attaching step is accomplished by applying an adhesive onto the first section of the sipper.In the method of the present invention, step b) can occur prior to step c), or after step d)and prior to step e).In the method of the present invention, the adhesive can be a light curable adhesive, andlight can then be applied to cure the adhesive. The light curable adhesive can be a UV curable adhesive, and UV light can then be applied to cure the adhesive.In the method of the present invention, the adhesive can be applied onto the first sectionof the sipper through the throughhole located adjacent to the inlet port of the flow channel.In the bonding step (b), the molded portion and the cover portion, such as a thin film, arebonded together. It is particularly important that there is no gap or delamination at the transition from the fluidic channel to the bonding surface. The bond should be as clean as possible up to the edge of the transition to prevent any fluidic dead volume in corners or potentially delaminated areas. The bond can be achieved using various joining techniques, e.g., pure thermal bonding,ultraviolet (UV) / vacuum ultraviolet (VUV) activated thermal bonding, solvent-activatedbonding, laser welding bonding, etc..In the present invention, a thermal bonding process can be used because it does notrequire any additional adhesive additives, which could interfere with functional compatibility. The thermal bonding process typically involves temperature, joining pressure, and vacuum over a defined period. With the thermal bonding process, very clean adhesive surfaces can be achieved up to the edges of the fluidic channel(s). In the thermal bonding process, temperatures above or close to the glass transition temperature (Tg) of the respective materials to be joined are typically used. It is particularly advantageous to use a film material with a lower Tg than the Tg of the chip material with channel structure. This allows the joining temperature to be chosen below or at least only minimally above the Tg of the chip material. In general, the higher the joining temperature above Tg, the greater the potential deformation of the parts to be joined, as the materials become softer. In one embodiment, after the bonding step, the first section of the sipper is inserted intothe sipper receiving portion. The sipper can be pushed into the sipper receiving portionup to the mechanical stop in the molded portion, (i.e. the inlet port of the flow channel),thereby establishing fluidic communication of the inlet port of the flow channel with thefirst end of the sipper. This can be done manually or automated with a gripper handling. The sipper should then be advantageously held in position.The first section of the sipper can then be attached to the sipper receiving recess withadhesive, thereby simultaneously achieving a seal around the sipper towards the inlet port of the flow channel.Attachment can be achieved by dripping or applying adhesive through at least onethroughhole in the sipper receiving recess. If necessary, this could also be done withadditional pressure. Optimally, the adhesive can be drawn into the sipper receiving recessby capillary forces, enveloping the sipper and filling the space between the sipper and the sipper receiving recess. Various common types of adhesives could be considered as the adhesive material. In one embodiment of the present invention, an ultraviolet light-curing adhesive (UVadhesive) is used. This adhesive offers the great advantage that the location and timingof when the adhesive curing should occur can be controlled. For example, the adhesive front could be monitored over time with a camera during the flow. This allows the timing for the UV light exposure to be precisely determined at the local adhesive site. For the application of the flow cell, a minimal dead volume at the transition into the fluid channel is crucial. This is supported by having the local adhesive site as close to the transition as possible, without gluing the sipper outlet and the transition into the inlet port of the flow channel. The sipper can also be inserted into the sipper receiving recess prior to the bonding step(b). However, the attachment step preferably takes place as the last step to achieve atight and precise connection between the first section of the sipper, the molded portion, and the cover portion (e.g. a thin film). The present invention is also concerned with a flow cell obtained by the method ofproducing the flow cell of the present invention as disclosed herein.The present invention is also concerned with a system for synthesizing a macromoleculefrom a sample, the system comprising at least one flow cell, or at least two flow cells, or4 flow cells as disclosed herein.According to a further aspect of the present invention, a coupling assembly for the abovedescribed system for synthesizing a macromolecule from a sample is provided, wherein the system comprises at least the following components, which have already been described above in detail: at least one flow cell with at least one flow channel, wherein each flow channel has an inlet port and an outlet port, and wherein the flow cell can be a flow cell structured as defined above; a heatable mount configured to receive the at least one flow cell; and a pump in fluid communication with the outlet port of the flow channel. The coupling assembly itself comprises a movable coupling member for each flow cell, with the movable coupling member being provided for establishing a fluid connection between the pump and the outlet port of the flow channel of the flow cell, and with themovable coupling member being provided for simultaneously establishing a clampingconnection between the flow cell and the mount, i.e., at the same time as establishing thefluid connection. The movable coupling member is adapted to hold a connection end of an outlet tube, and the coupling member can comprise a slot for accommodating the sipper of the respective flow cell. Furthermore, the coupling assembly comprises a guiding member for guiding the coupling member along a coupling path from a first position into a second position. In regard to the coupling path of the coupling member, the first position of the coupling path is a position of the coupling member in which no fluid connection between the outlet tube and the outlet port and no clamping connection between the flow cell and the mount is established, and the second position of the coupling path is a position of the coupling member in which fluid connection between the outlet tube and the outlet port and clamping connection between the flow cell and the mount is established. Moreover, the coupling assembly is movable, i.e. the coupling assembly is adapted to move, along a positioning path from an initial position to a facing position, wherein the initial position of the positioning path is a position of the coupling assembly in which the coupling assembly is, along a longitudinal axis of the coupling assembly, away from the flow cell, i.e. in which the coupling assembly is neither in contact with nor facing the flow cell, and wherein the facing position of the positioning path is a position of the coupling assembly in which the coupling assembly is, along the longitudinal axis of the coupling assembly, close to the flow cell, i.e. in which the coupling assembly is facing the flow cell, but is still not in contact with the flow cell. Overall, the positioning path lies above and at a predetermined distance from the flow cell or flow cells. Also, the coupling assembly is movable along the positioning path towards a stopper until abutting against the stopper. When the coupling assembly is in the facing position of the positioning path, the coupling member is held in a movable manner in relation to the guiding member along the coupling path from the first position towards the flow cell and the mount into the second position. Here, the first position of the coupling path of the coupling member is, as defined above,a position of the coupling member in which no fluid connection between the outlet tubeand the outlet port and no clamping connection between the flow cell and the mount is established, and, at the same time, is a position in which the coupling member is facing the flow cell at a predetermined distance. Further, the second position of the coupling path of the coupling member is, as defined above, a position of the coupling member in which fluid connection between the outlet tube and the outlet port and clamping connection between the flow cell and the mount is established, and, at the same time, is a position in which the coupling member is aligned with the flow cell and the mount, wherein the connection end of the outlet tube is fluidly connected to the outlet port, and the flow cell is clamped against the mount by the coupling member with a predeterminedpressure. With such a coupling assembly for a system for synthesizing a macromoleculefrom a sample, positioning one or several flow cells in tight thermal contact with theheatable mount and connecting the outlet port of each flow cell with a respective outlettube of the system can easily be managed by a user without fail, in a guided failsafemanner, in order to achieve exact positioning of each flow cell and excellent thermalconnection between the flow cell and the mount. As an example, the guiding member and the movable coupling member can be connected by means of a pin-and-groove connection, with either one of them exhibiting the pin part or the groove counterpart for guiding the pin, which pin-and-groove connection is for establishing the coupling path of the coupling member. As an example, the guiding member can comprise the groove part of the pin-and-groove connection, whereas the coupling member or a coupling member frame or coupling member unit can comprise the pin part which is guided within the groove. Here, the pin part can also comprise a slide bearing or ball bearing, in order to ease the movement within the groove. For example, the guiding member can comprise two parallel guiding plates with the movable coupling member arranged in between the two guiding plates in movable connection. Here, each guiding plate can comprise at least one kidney-shaped groove for guidance of a pin of thecoupling member. Furthermore, the guiding member, or each guiding plate, can exhibitmore than one groove part, e.g. two grooves, and the coupling member or coupling member frame or coupling member unit can comprise a pin part for each groove. With such structure, an exact guidance of the coupling member on its coupling path can be ensured. The coupling assembly can be guided along the positioning path between the initial position to the facing position by means of guide rails framing the coupling assembly. Accordingly, the guide rails, which are fixed in relation to the mount, constitute a connection between the mount and the coupling assembly. As an example, the guide rails can guide the guiding member in a linear manner, e.g. by means of a pin-and-groove connection, with the coupling assembly providing the pin part and the guide rails providing the groove part. Guiding by the guide rails can be achieved by means of a slide bearingor ball bearing structure provided at the pin part, wherein each side of the couplingassembly guided by one guide rail can exhibit two or more guide pins running within a linear guide groove of the guide rails.In particular, in case of more than one flow cell and more than one respective couplingmember, the guiding member can sandwich a support frame holding a coupling member for each flow cell, such as 4 coupling members arranged next to each other, wherein such support frame adapts the function of the above mentioned coupling member frame or coupling member unit. The support frame can be guided by the guiding member along the coupling path, as is described above in relation to the guiding of the coupling member. In this regard, each movable coupling member can be spring-loaded against the supportframe, for providing a clamping force onto the flow cell and against the mount in thesecond position of the guiding member, i.e. in a position in which fluid connection between the outlet tube and the outlet port and clamping connection between the flow cell and the mount is established. Accordingly, each coupling member can be held within the support frame and can be guided by means of the support frame and the thereto connected guide member towards the respective flow cell, until the coupling member abuts against the flow cell and presses the flow cell, by means of the spring-force of the spring-load, against the mount. At the same time, the outlet tube is inserted into or at least connected to the outlet port of the respective flow cell, in order to establish fluid connection. The connection end of the outlet tube of each coupling member can be spring biased against the support frame, in order to establish a fluidtight connection between the connection end of the outlet tube and the outlet port of the respective flow cell in the second position of the guiding member. With such spring-loaded structures, tight fluid connection between flow cell and outlet tube and tight thermal connection between flow cell and mount can be established, in order to achieve excellent performance of the flow cell. In addition, sincethe preload is generated by springs, the preload will always be the same within the springtolerance range, resulting in reproducible excellent heat transfer. Accordingly, since thefluid connection, also referred to as fluidic docking, is implemented by the spring biasedlink, i.e. a connection preloaded by a spring, a standardised process can be achievedwhich leads to complete fluid tightness of the interface, and damage to the often sensitivesippers can be prevented by minimizing manual intervention.Further details and explanations in regard to the configuration and structure of theinstrument above can be gathered further below. The above described method steps arepreferably carried out in the given order in a subsequent / sequential manner.Usually, a laboratory automation system which is commonly employed in state-of-the-artlaboratories for automatically processing biological sample, can comprise the abovedescribed system, for carrying out the above described methods. Here, the term “laboratory instrument” or “instrument” of the laboratory encompasses any apparatus or apparatus component operable to execute one or more processing steps / workflow steps on one or more biological samples, and covers analytical instruments, pre-analytical instruments, and also post-analytical instruments. The expression “processing steps” thereby refers to physically executed processing steps. The above described method steps can be controlled by a controller or control unit of such automated processing system, which can also control any kind of actuation or monitoring of the above described device and its components, wherein the term “controller” or “control unit” as used herein encompasses any physical or virtual processing device, such as a CPU or the like, which can also control the entire instrument or even an entire workstation comprising one or more laboratory instruments in a way that workflow(s) and workflow step(s) are conducted. The control unit may, for example, carry different kinds of application software and instruct the automated processing system or a specific instrument or device thereof to conduct pre-analytical, post-analytical and analytical workflow(s) / workflow step(s). The control unit may receive information from a data management unit regarding which steps need to be performed. Further, the control unit might be integral with a data management unit, may be comprised by a server computer and / or be part of one instrument or even distributed across multiple instruments of the automated processing system. The control unit may, for instance, be embodied as a programmable logic controller running a computer-readable program provided with instructions to perform operations. Here, in order to receive such instructions by a user, a user interface can additionally be provided, wherein the term “user interface” as used herein encompasses any suitable piece of application software and / or hardware for interactions between an operator and a machine, including but not limited to a graphical user interface for receiving as input a command from an operator and also to provide feedback and convey information thereto. Also, a system / device may expose several user interfaces to serve different kinds of users / operators. The terms "plurality", “multiple” or “multitude” refer to two or more, i.e.2 or >2, with integer multiples, wherein the terms “single” or “sole” refer to one, i.e. =1. Furthermore, the term “at least one” is to be understood as one or more, i.e.1 or >1, also with integer multiples. Accordingly, words using the singular or plural number also include the plural and singular number, respectively. Additionally, the words “herein”, “above”, “previously” and “below”and words of similar import, when used in this text, shall refer to this text as a whole andnot to any particular portions of the text. Furthermore, certain terms are used for reasons of convenience and are not intended to limit the invention. The terms “right”, “left”, “up”, “down”, “under“ and “above“ refer to directions in the figures. The terminology comprises the explicitly mentioned terms as well as their derivations and terms with a similar meaning. Also, spatially relative terms, such as “under”, "beneath", "below", "lower", “base”, "above", “over”, "upper", “top”, "proximal", "distal", and the like, may be used to describe one element's or feature's relationship to another element or feature as illustrated in the figures. These spatially relative terms are intended to encompass different positions and orientations of the devices in use or operation in addition to the position and orientation shown in the figures. For example, if a device in the figures is turned over, elements described as "below" or "beneath" other elements or features would then be "above" or "over" the other elements or features. Thus, the exemplary term "below" can encompass both positions and orientations of above and below. The devices may be otherwise oriented (rotated 90 degrees or at other orientations), and the spatially relative descriptors used herein interpreted accordingly. Likewise, descriptions of movement along and around various axes include various special device positions and orientations. Similarly, the terms “upwardly”, “downwardly”, “vertical”, “horizontal” and the like are used herein for the purpose of explanation only unless specifically indicated otherwise. When a feature or element is herein referred to as being “on” another feature or element, it can be directly on the other feature or element or intervening features and / or elements may also be present. In contrast, when a feature or element is referred to as being “directly on” another feature or element, there are no intervening features or elements present. It will also be understood that, when a feature or element is referred to as being “connected”, “attached” or “coupled” to another feature or element, it can be directly connected, attached or coupled to the other feature or element or intervening features or elements may be present. In contrast, when a feature or element is referred to as being “directly connected”, “directly attached” or “directly coupled” to another feature or element,there are no intervening features or elements present. Although described or shown withrespect to one embodiment, the features and elements so described or shown can apply to other embodiments. It will also be appreciated by those of skill in the art that references to a structure or feature that is disposed “adjacent” another feature may have portions that overlap or underlie the adjacent feature. Terminology used herein is for the purpose of describing particular embodiments only and is not intended to be limiting of the invention. For example, as used herein, the singular forms “a”, “an” and “the” are intended to include the plural forms as well, unless the context clearly indicates otherwise. It will be further understood that the terms “comprises” and / or “comprising,” when used in this specification, specify the presence of stated features, steps, operations, elements, and / or components, but do not preclude the presence or addition of one or more other features, steps, operations, elements, components, and / or groups thereof. Accordingly, the term “comprising” will be understood to imply the inclusion of any stated elements or steps but not the exclusion of any otherelements or steps. As used herein, the term “and / or” includes any and all combinationsof one or more of the associated listed items and may be abbreviated as “ / ”. Although the terms “first” and “second” may be used herein to describe various features / elements (including steps), these features / elements should not be limited by these terms, unless the context indicates otherwise. These terms may be used todistinguish one feature / element from another feature / element. Thus, a firstfeature / element discussed below could be termed a second feature / element, and similarly, a second feature / element discussed below could be termed a first feature / element without departing from the teachings of the present invention. As used herein in the specification and claims, including as used in the examples and unless otherwise expressly specified, all numbers may be read as if prefaced by the word “about” or “approximately,” even if the term does not expressly appear. The phrase “about” or “approximately” may be used when describing magnitude and / or position to indicate that the value and / or position described is within a reasonable expected range ofvalues and / or positions. For example, a numeric value may have a value that is + / - 0.1%of the stated value (or range of values), + / - 1% of the stated value (or range of values),+ / - 2% of the stated value (or range of values), + / - 5% of the stated value (or range ofvalues), + / - 10% of the stated value (or range of values), etc. Any numerical values givenherein should also be understood to include about or approximately that value, unless the context indicates otherwise. For example, if the value “10” is disclosed, then “about 10” is also disclosed. Any numerical range recited herein is intended to include all sub-ranges subsumed therein. It is also understood that when a value is disclosed that “less than or equal to” the value, “greater than or equal to the value” and possible ranges between values are also disclosed, as appropriately understood by the skilled person. Forexample, if the value “X” is disclosed, the “less than or equal to X” as well as “greater thanor equal to X” (e.g., where X is a numerical value) is also disclosed. It is also understoodthat, throughout the present text, data is provided in a number of different formats, andthat this data represents endpoints and starting points, and ranges for any combination of the data points. For example, if a particular data point “10” and a particular data point “15” are disclosed, it is understood that greater than, greater than or equal to, less than, less than or equal to, and equal to 10 and 15 are considered disclosed as well as between 10 and 15. It is also understood that each unit between two particular units are also disclosed. For example, if 10 and 15 are disclosed, then 11, 12, 13, and 14 are also disclosed. Although various illustrative embodiments are described above, any of a number of changes may be made to various embodiments without departing from the scope of the invention as described by the claims. For example, the order in which various described method steps are performed may often be changed in alternative embodiments, and in other alternative embodiments one or more method steps may be skipped altogether. Optional features of various device and system embodiments may be included in some embodiments and not in others. Therefore, the foregoing description is provided primarily for exemplary purposes and should not be interpreted to limit the scope of the invention as it is set forth in the claims. The examples and illustrations included herein show, by way of illustration and not of limitation, specific embodiments in which the subject matter may be practiced. As mentioned, other embodiments may be utilized and derived there from, such that structural and logical substitutions and changes may be made without departing from the scope of this disclosure. Such embodiments of the inventive subject matter may be referred to herein individually or collectively by the term “invention” merely for convenience and without intending to voluntarily limit the scope of this application to any single invention or inventive concept, if more than one is, in fact, disclosed. Thus, although specific embodiments have been illustrated and described herein, any arrangement calculated to achieve the same purpose may be substituted for the specific embodiments shown. This disclosure is intended to cover any and all adaptations or variations of various embodiments. Combinations of the above embodiments, and other embodiments not specifically described herein, will be apparent to those of skill in the art upon reviewingthe above description. To avoid repetition in the figures and the descriptions of the variousaspects and illustrative embodiments, it should be understood that many features are common to many aspects and embodiments. The description of specific embodiments of the disclosure is not intended to be exhaustive or to limit the disclosure to the precise form disclosed. Omission of an aspect from a description or figure does not imply that the aspect is missing from embodiments that incorporate that aspect. Instead, the aspect may have been omitted for clarity and to avoid prolix description. In this context, the following applies to the rest of this description: If, in order to clarify the drawings, a figure contains reference signs which are not explained in the directly associated part of the description, then it is referred to previous or following description sections. Further, for the reason of lucidity, if in a section of a drawing not all features of a part are provided with reference signs, it is referred to other sections of the same drawing. Like numbers in two or more figures represent the same or similar elements. BRIEF DESCRIPTION OF DRAWINGS The novel features of the invention are set forth with particularity in the claims that follow. A better understanding of the features and advantages of the present invention will be obtained by reference to the following detailed description that sets forth illustrative embodiments, in which the principles of the invention are utilized, and the accompanying drawings of which:FIGS. 1A and 1B illustrate an embodiment of a system for automated synthesis of amacromolecule. FIG.1C illustrates a mixing tube that can be used in the system shown in FIGS.1A and 1B.FIGS. 1D and 1E illustrate the synthesis steps that can be performed on the systemillustrated in FIGS.1A and 1B. FIG.2A illustrates an embodiment of a flow cell. FIG.2B illustrates a functionalized flow channel surface and how a capture probe can be used to immobilize the template to the flow channel surface. FIGS.2C and 2D illustrate an embodiment of the flow cell with a thin film bonded to a molded portion of the flow cell. FIG.3 illustrates an embodiment of a mount for receiving the flow cell. FIG.4A illustrates an embodiment of a holder. FIGS.4B and 4C illustrate embodiments of reagent cartridges that can be placed in the holder shown in FIG. 4A.FIGS. 5A to 5F illustrate further embodiments of a flow cell of the invention.FIGS. 6A to 6D illustrate an embodiment of a coupling assembly for the system forautomated synthesis of a macromolecule as exemplarily depicted inFIGS: 1A and 1B.FIGS. 7A to 7C illustrate a functional scheme of the coupling assembly of FIGS. 6Ato 6D.FIGS. 8A to 8C illustrate the functional scheme of Figs. 7A to 7C in a sectional viewalong A-A in FIG.6B; andFIGS. 9A to 9C illustrate the functional scheme of Figs. 7A to 7C in a sectional viewalong B-B in FIG.6B. REFERENCE NUMERALS100 system150 functionalization step152 hybridization step154 wash step156 extension reaction step158 wash step160 cleave step162 wash and neutralization step164 modification step166 wash step168 UV illumination and elution step200 flow cell201 (injection) molded portion202 flow channel203 cover portion, e.g. thin film204 flow channel surface, e.g. functionalized solid phase surface206 capture probes208 sample, e.g. sample polynucleotide, e.g. single stranded nucleic acid molecule210 Macromolecule, e.g. Xpandomer molecule220 inlet port222 outlet port224 sipper225 flow cell portion of the molded portion226 sipper receiving portion of the molded portion227 sipper receiving recess229 first section of the sipper230 second section of the sipper231 first end of the sipper232 second end of the sipper233 first surface of the sipper receiving portion234 second surface of the sipper receiving portion235 handle236 throughhole(s)237 identifier, e.g. bar code or QR code300 mount, e.g. heatable mount301 engagement cam302 thermal block310 coupling assembly311 coupling member, e.g. movable coupling member311a linear support bearing, e.g. spring-loaded linear support bearing311b connection component, e.g. annular connection component311c spring311d gap312 outlet tube connection end313 outlet tube314 guiding member315a guiding plate315b guiding plate316a kidney-shaped groove316b kidney-shaped groove317a pin317b pin318 guide rail320 support frame330 stopper341 channel, e.g. u-shaped channel340 protective shield400 holder / vial rack402 96 well plate404 vial or tube holder 406 piercing tool410 reagent cartridge412 plurality of different types of liquid reservoirs414 cover416 tubes / vials / Eppendorf tubes500 XYZ gantry600 pump, e.g. syringe pump602 flow and pressure gauge604 waste container / waste reservoir606 buffer container / buffer reservoir608 valve, e.g. selectable valve, such as a rotary valve700 mixing tube702 coiled portion800 UV sourceDETAILED DESCRIPTION OF THE INVENTION Xpandomer Synthesis Method The Xpandomer molecules can be synthesized using a synthesis process as further described in U.S. Patent No. 7,939,259 and International Patent Publication No. WO2020 / 236526A1. As shown in FIGS. 1A and 1B, a system 100 can be used to automate the Xpandomer synthesis process.Other macromolecules can be synthesized on the system 100. Polymers with repeatingsubunits are suitable macromolecules for synthesis on the system 100. For example, polynucleotides and polypeptides may be synthesized using the system 100.FIGS. 1D and 1E are flowcharts that illustrate an embodiment of the synthesis processthat can be performed by the system 100 shown in FIGS.1A and 1B. In functionalizationstep 150, a flow channel surface 204 shown in FIG. 2B and further described below canbe functionalized with the characteristics Alkyne and EO, 2mM, 12pmole, 60µl, 45’, 600mm2. This functionalization process may be performed by the system 100 on flow cell 200 by drawing the appropriate reagents into the flow cell 200 using sipper(s) 224 and reagents on a holder 400. Alternatively, the flow channel surface 204 can be functionalized prior to shipment to the consumer so that the consumer does not need toperform the functionalization step 150. The functionalization process includes attachinga plurality of probes to the flow channel surface 204 that are capable of binding to the sample. In hybridization step 152, the sample, which can be template nucleic acid molecules from a single stranded DNA or RNA library, can be introduced into the flow cell 200 and flow channel(s) 202 by using the sipper(s) 224 to draw 60µL of the template, e.g. 8µl ssLib, from the holder 400. The template can be allowed to hybridize to the capture probe, which itself can be a polynucleotide. The temperature during the hybridization step 152 can be controlled by the controller by heating and / or cooling the thermal block 302 attached tothe mount 300. For example, the temperature can be varied between about 37° Celsiusand 90° Celsius during the hybridization step 152 for 3 minutes. Other temperatures canalso be used in this step, depending on the probe and template combination used.Next, in wash step 154, a wash can be performed at least one time. The wash procedurecan involve multiple washes, e.g., 1000 µL and 100 µL washes for one minute. This can also be performed at a controlled temperature, such as 37° Celsius, for example. A washsolution can include at least one solvent H and at least one detergent W. Here, at leastone surfactant and / or at least one buffer can optionally also be included.Next, in extension step 156, an extension reaction can be performed by introducing 75µl of a frozen Mix A solution to the flow channel. Mix A can include solvent(s), buffer(s), salt(s), a polymerase, and nucleotide analogs (XNTP). The controller can control the temperature of this reaction by varying the temperature and holding period duration at each temperature as desired. For example, the extension reaction can include a firstincubation period at 37° Celsius for a first duration, e.g. 110 minutes, and secondincubation period at 42° Celsius for a second duration, e.g. 10 minutes, and a thirdincubation period at 50° Celsius for a third duration, e.g. 5 minutes.Next, in wash step 158, a wash can be performed at a controlled temperature of e.g. 23°to 50° Celsius, using a desired amount of wash buffer, e.g., 1000 uL of Mix B, for a desired duration (i.e., 5 minutes). Mix B can include at least one solvent and at least onedetergent. Here, at least one surfactant and / or at least one buffer can optionally also beincluded.Next, in step 160, a cleave step is performed using 200 µL of Mix C at 23° Celsius for 40minutes. Mix C can include an acid in solvent. Next, in step 162, a wash and neutralization step is performed using 2000 µL of Mix B at23° Celsius for one minute.Next, in step 164, a modification step is performed using 300 µL of Mix B and Mix Mod at23° Celsius for five minutes. Mix Mod can be succinic anhydride in solution.Next, in step 166, a wash step is performed using 3000 uL of Mix D at 23° Celsius for oneminute. Mix D can include a solvent and optionally a stabilizer molecule.Finally, in step 168, a UV and elution step is performed using 60 µL of Mix D at 37° Celsiusfor 2 minutes under UV illumination. The synthesized molecule can be eluted into a tube in the holder using the pump in push operation. FIGS. 1A and 1B illustrate an embodiment of a system 100 used for macromolecule synthesis. The system 100 includes a removable and disposable flow cell (i.e. card or chip) 200, a mount 300 (including a thermal block described below) for receiving the flow cell 200, a holder / vial rack 400, an XYZ gantry 500, a pump (e.g. syringe pump) 600, a flow and pressure gauge 602, a waste container 604, a buffer container 606, a selectable valve (e.g. rotary valve) 608, a UV source 800, and a controller (not shown). The holder 400 can also be used to hold sample and the end product or anything else that can becontained in a tube, container, vial, or reservoir that can be placed in the holder 400.As shown in FIG. 1A and 1B, a pump 600 can be used in a pull mode to draw fluid intothe inlet port 220 of the flow cell 200 via the sipper(s) 224, and the fluid can be drawn out of the flow cell 200 through the outlet ports 222 of the flow cell 200 and into a waste reservoir 604. The pump 600 can also be used in a push mode to pump fluid, such as a wash solution or elution buffer, from a buffer reservoir 606 and into the flow cell 200through the outlet port 222, and then the fluid can be pushed out of the flow cell 200through the inlet port 220 and through the sipper(s) 224 into a product collection tube. Arotary valve 608 or other type of valve can be used with the pump 600 to switch betweenthe waste reservoir 604 and the buffer reservoir 606 in order to allow the pump 600 to operate in both a push and pull configuration. The pump 600 can be a syringe pump or other type of pump that is capable of precisely metering out very small amounts of fluid (i.e., in the microliter to milliliter range).The controller can control the XYZ gantry 500 and pump 600 to perform liquid mixingoperations within the flow cell 200 or directly on / in the holder 400. Consumable device / cartridge FIG.2A illustrates a perspective view of one embodiment of a flow cell 200 that the usercan load into the system 100. The flow cell 200 can be a consumable device or cartridgethat is disposed of after use. The flow cell 200 encloses at least one flow channel 202 that provides a functionalized solid phase surface to which a plurality of capture probes206 can be attached. The flow cell 200 can have at least 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 flowchannels 202, wherein the flow cell 200 can have exactly 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10flow channels 202. The flow channel 202 can be made of a substrate that is directlyfunctionalized, instead of being coated with a material that is then functionalized. The flow channels 202 can be fabricated using microfluidic techniques and can be used to perform reactions involving fluid volumes in the microliter range. The flow channel 202 can have a cross-section that is about 0.6 mm x 0.3 mm, or about 0.8 mm x 0.4 mm, or less than about 1 mm x less than 0.5 mm, or less than 2 mm x less than 1 mm. The volume of the flow channel 202 can be about 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400, 500, 600, 700, 800, 900, or 1000 uL. The surface area to volume ratio can be about 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 40, or 50 mm-1. The flow channel 202 canbe serpentine, i.e. serpentine-shaped, to increase the flow length and surface areaavailable to carry out the reactions and / or to aid in mixing. The flow cell 200 can be fabricated from a single injection molded portion 201 that is bonded to a thin film 203, as shown in FIGS. 2C and 2D. For example, the injectionmolded portion 201 can include the base substrate, the inlet ports 220, the outlet ports222, and a portion of the flow channels 202. The thin film 203 can be disposed over the base substrate and flow channels 202 to enclose and complete the formation of the flow channels 202. The thin film 203 that forms the base of the flow cell 200 can be placedagainst a thermal block 302, as further described below. The thin film 203 can have a lowthermal resistance which allows efficient heat transfer from a thermal block 302 to the flow cell 200, which allows the rapid heating and cooling of the flow cell 200 to facilitatethe different temperature reactions of the Xpandomer synthesis process. In order toachieve the desired thermal resistance, the thin film 203 can have a thickness between about 100 µm to about 500 µm. The thickness can be less than about 500, 400, 300, 200, or 100 µm, wherein the thickness can be about 100, 200, 300, 400, or 500 µm. The thin film can be made of a cyclic olefin polymer (COP) or a cyclic olefin copolymer (COC). Other types of polymers may also be used to form the thin film, such UV transparent polymers that can be functionalized (i.e., proton abstractable polymers) and bonded tothe injection molded portion 201 of the flow cell 200. Other polymers that can be usedinclude but are not limited to polypropylene and polyethylene. The thin film 203 can be bonded to the injection molded portion 201 using a variety of techniques, such as thermal bonding, laser welding, or chemical bonding. Each flow channel 202 of the flow cell 200 has an inlet port 220 and an outlet port 222 that provide access to the flow channel 202. Affixed to the inlet port 220 is a sipper 224 that can be used to draw reagents, buffers, wash solution, sample, etc. into the flow cell 200 when the pump 600 is operated in a pull mode. As noted above, the sipper 224 can also be used to deposit the finished product from the flow cell 200 into a collect tube whenthe pump 600 is operated in a push mode. The sipper 224 can be preattached to the inletport 220 so that the end user does not need to attach the sipper 224 to the flow cell 200 before use. Instead, the end user can simply insert the preassembled flow cell 200 intothe mount 300 as shown in FIGS. 1A and 3. The sipper 224 can have a length that is lessthan the length of the flow cell 200. The sipper 224 can be less than about 5x, 4x, 3x, 2x,1x, 0.9x, 0.8x, 0.7x, 0.6x, 0.5x, 0.4x, 0.3x, 0.2x, or 0.1x the length of the flow cell 200. Reducing or minimizing the length and volume of the sipper 224 is advantageous in reducing the loss and / or carryover of precious reagents, sample, and the synthesized molecule (i.e., the Xpandomer) during the synthesis process. The sipper 224 configuration also provides a direct path to the flow cell 200 that does not need to pass through a valve, which can reduce contamination and leak issues, especially when using corrosive reagents. As can be seen in FIG.1A, the inlet port 220 and outlet port 222 extend from the flow cell 200 in an orientation that is normal to a plane that encompasses the flow channel 202. The sipper 224 can also extend from the inlet port 220 in an orientation that is normal toa plane that encompasses the flow channel 202. The sipper 224 can have a 90 degreebend, or whatever angle is needed, to orient the end of the sipper 224 towards the holder400, as shown in FIG. 1A. The inlet port 220 can extend from the flow cell 200 in anorientation that is parallel to a plane that encompasses the flow channel 202, and thesipper 224 can extend from the inlet port 220 is the same orientation towards the holder400, and the sipper 224 can be straight and without a bend.FIG. 2B illustrates an embodiment of the flow channel surface 204 that has been functionalized to bind capture probes 206 that can bind to a portion of the sample. For example, the capture probe 206 can include a polynucleotide sequence that is complementary to and can hybridize to a sequence in a binding region of the sample polynucleotide 208. An Xpandomer molecule 210 can be synthesized from the sample polynucleotide 208 using a specialized Xpandomer extension reaction that involves a modified polymerase and modified nucleotides to synthesize the Xpandomer molecule 210 from the sample polynucleotide 208, which is further described in U.S. Patent No. 7,939,259 and International Patent Publication No. WO2020 / 236526A1. After the extension reaction is complete, UV light (from UV source 800) can be used to cleave the capture probe 206 Xpandomer molecule from the flow channel surface 204. FIG. 3 illustrates an embodiment of the mount 300 for receiving the flow cell 200. As shown, the mount 300 can receive two flow cells 200. Alternatively, the mount can receive 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, or 20 flow cells. A thermal block 302 is thermally coupledto the mount 300 and is used to control the temperature of the flow cell 200. The thermalblock 302 can be quickly cooled or heated as desired so that the reactions in the flow cell 200 can be performed at temperatures between about 20 Celsius and 60 Celsius. Alternatively, the temperature range can between about 5 Celsius and 90 Celsius. As shown in FIG.3, the thermal block 302 can include fins to radiate heat and a fan toaid in heat transfer from the thermal block 302. The thermal block 302 can be thermallyattached to the mount 300 or can be integrally formed with the mount 300. For example, one face of the thermal block 302 can be formed to receive the flow cells 200. Thecontroller can provide real-time thermal control of the thermal block 302.A thermal pad can be placed between the mount 300 and flow cell 200 to improve heattransfer from the thermal block 302 to the flow cell 200. The thermal pad can be placedon or pre-attached to the mount 300. The thermal pad can be place on or pre-attached tothe base of the flow cell 200. Also, a thermal paste or gel can be used instead of a thermal pad.A portion of the sipper 224 can be disposed against the thermal block 302 or mount 300in order to preheat the fluids as they are drawn into the flow cell 200. The portion of the sipper 224 that is disposed against the thermal block 302 or mount 300 can be serpentine, i.e. serpentine-shaped. The flow cell 200 can be mounted on the mount 300, e.g. by means of a coupling means, such that the flow cell 200 is oriented in a vertical direction, such that the sipper 224 is pointed towards the reagents in the holder 400, as shown in FIG.1A. Depending on the orientation and configuration of the inlet port 220 on the flow cell 200, the sipper 224 can include a bend, such as a 90 degree bend or other angle if needed, to orient the inlet of the sipper 224 towards the reagents. It is advantageous to use the vertical orientation of the flow cell 200 so that the holder 400 can be oriented horizontally such that open reagent containers maintain the fluids within the container with gravity.However, as an alternative, both the flow cell 200 and the holder 400 can be orientedhorizontally, and the sipper 224 can include a 90 degree bend or a 180 degree bend, forexample, depending on the orientation of the inlet port 220 on the flow cell 200. If the inletport 220 is also oriented horizontally in line with the plane encompassing the flow channels 202, then the sipper 224 can include a 90 degree bend to direct the inlet of the sipper 224 towards the reagents. Similarly, if the inlet port 220 is oriented normally instead, the sipper 224 can have a 180 degree bend.In cases where the flow cell 200 has more than one flow channel 202 and more than onesipper 224, the spacing between the sippers 224 after being secured to the mount 300 iscompatible for use with 96 well plates, which allows the reagents and / or sample to be stored in a 96 well plate, which can be loaded onto the holder 400. FIG. 4A illustrates an embodiment of a holder 400. The holder 400 can hold reagents, samples, buffers, and other liquids used in the synthesis method. As shown, a 96 well plate 402 (or plate with another well count) and vial or tube holder 404 can be included in the holder 400. Reagent trays, bottles, and other containers for holding liquids can also be secured to the holder 400. The openings of the containers, such as the openings of the tubes in the tube holder 404 and the wells of the 96 well plate 402 can all be located on the same plane or height. This makes it easier for a covering to be applied over the openings and pierced when needed with a piercing tool 406. Height adapters can be used if needed to adjust the heights of openings so that they are level. Alternatively, custom vial or tube racks and well plates with preadjusted heights can be used with the holder 400 to simplify user operation and reduce user error. The liquid holders can be removably attached to the holder 400 to allow for user customization. The holder 400 can be moved in all three axes with the XYZ gantry 500, as shown in FIG. 1A. This configuration allows the flow cell 200 and sipper 224 and the piercing tool 406 to remain in a fixed position while the holder 400 is moved by the gantry 500 to the piercing tool 406 when the covering over the openings needs to be pierced and then to the sippers 224 once the coverings have been pierced. To access different reagents and samples, the gantry 500 can move the holder away from the sippers 224 and then align the sippers 224 with the new reagents and / or samples. One benefit from holding the flow cell 200 in a fixed position is that it reduces the movement of wiring and tubing attached to the flowcell 200, thermal block 302, UV source 800, and other associated components. Repeatedmovement of these components may cause disconnects or damage to these sensitive components, and therefore, it may be beneficial to adopt a configuration where these components remain stationary.Alternatively, the gantry 500 can be used to move the holder 400 with the flow cell 200and piercing tool 406 while the reagent holder 400 and reagents are stationary. This can be accomplished by attaching the mount 300 and flow cell 200 to the gantry 500, whilethe holder 400 can remain fixed in place on the deck of the instrument. The UV sourcecan still optionally remain fixed in one location since the flow cell 200 can be moved in position in front of the UV source 800 when needed. FIGS. 4B and 4C illustrate a reagent cartridge 410 that can be loaded onto the holder 400. The reagent cartridge 410 can include a plurality of different types of liquid reservoirs 412 of different sizes and / or shape as well as a cover 414 that can be used to seal thereagent cartridge 410. The gantry 500 can move the reagent cartridge 410 and press thereagent cartridge 410 against the cover 414, which can be held in a fixed horizontalposition in order to seal the reagent cartridge 410. The reagent cartridge 410 can alsoinclude drop in locations to receive tubes 416 or vials (e.g., Eppendorf tubes). Although described as tubes 416, other containers or reservoirs can be used instead to hold the liquids and reagents. These tubes can be provided by the manufacturer to contain premade Library or master mix solutions. In addition, a tube can be used to collect the synthesized molecule. The gantry 500 can also be optionally used with the sippers 224 or a separate mixing tube 700 to perform liquid mixing and / or bubble mixing operations on the reagent cartridge if desired, as shown in FIG. 1C. The mixing tube 700 can be attached to a dedicated pump 600 and can optionally have an internal volume that is sufficient toaspirate all the fluid in the tube 416 that needs to be mixed. In order to achieve the internalvolume needed, the mixing tube 700 can optionally have a coiled portion 702 to accommodate a relatively long length of tubing in a small space within the chassis of the device. The inlet of the mixing tube 700 can be fixed to a specific location within the chassis of the device so that the gantry 500 can move tubes 416 to the inlet of the mixing tube 700 when needed. Certain reagents that are unstable in water (e.g. succinic anhydride, acetic anhydride, other anhydrides) and need to be used relatively quickly after being formed into a solution can be provided in dry form within a tube or vial. Just before use of these sensitive reagents, a liquid such as water or a buffer can be added to the vial and a mixing procedure, such as bubble mixing, can be performed to dissolve the reagent. Bubble mixing can be performed by inserting a sipper or pipette tip into the liquid and introducing a gas, such as air, into the liquid to agitate the liquid. Air gaps can optionally be introduced between the different fluids being introduced into flow cell as part of the Xpandomer synthesis process. Alternatively, an immiscible fluidcan be introduced between the different fluids being introduced into the flow cell 200.Separation of the different fluids and reagents going into the flow cell 200 prevents orreduces reactions from occurring outside the target area in the flow cell 200 where the Xpandomer synthesis reactions are occurring. The channels 202 in the flow cell 200 canbe relatively narrow in diameter so that the bubbles or immiscible fluid completely fill thediameter of the flow channels 202 so that fragments of the bubbles or the immiscible fluiddo not become trapped within the flow cell 200. The air gaps or immiscible fluid can beintroduced through the sippers 224 that are used to draw reagents into the flow cell 200.For example, the sipper 224 can draw in the reagent, then be lifted out of the reagent into the air, and then draw in a bolus of air.Alternatively, a train or plurality of bubbles can be introduced into the flow cell 200, sippers224, and other components in order to help clean the components. For example, bubbles can be introduced between small plugs of reagents, wash buffer, or other fluids to help with surface clean up and / or to help control elution of the Xpandomer from the flow cell 200.Figs.5A to 5F illustrate another embodiment of a flow cell 200. Fig 5A shows the moldedportion 201 of a flow cell 200 of the invention. The flow cell portion 225 of the moldedportion comprises the flow channel 202, the flow channel surface 204, the inlet port 220and the outlet port 222. The sipper receiving portion 226 of the molded portion comprisesthe sipper receiving recess 227on the first surface 233 of the sipper receiving portion. Onthe flow cell shown on the right, the sipper 224, comprising the first section 229, thesecond section 230, the first end 231 and the second end 232, is shown inserted into thesipper receiving recess, with fluidic communication of the first end with the inlet portestablished. The handle 235 extending from the second surface 234 of the sipperreceiving portion can be seen. Fig. 5B, in the upper panel, shows the molded portion 201of a flow cell 200 of the invention. This sipper 224 is inserted and the handle 235 can beseen. In the middle panel, a flow cell of the invention can be seen, including the coverportion 203, and an inserted sipper. In the lower panel, the sipper is missing. The sippercan be inserted into the sipper receiving recess 227. Fig. 5C shows a flow cell of thepresent invention, including a view of the second surface 234 of the sipper receivingportion. A throughhole 236 in the sipper receiving portion can be seen, as can the handle235. The lower panel shows the sipper 224 inserted into the sipper receiving recess 227.Fig.5D shows a flow cell of the present invention, including a view of the second surface234 of the sipper receiving portion. A throughhole 236 in the sipper receiving portion canbe seen, as can the handle 235. The flow cell on the left comprises two through-holes236. The sipper 224 is inserted into the sipper receiving recess 227, and the flow cellcomprises an identifier 237 on the second surface 234 of the sipper receiving portion. Fig.5E shows the two sections 229, 230 of the sipper with their respective ends 231, 232,showing the geometry of said ends. The sipper’s first end surface is oriented at an angleof about 90° relative to the central axis of the first section 229 of the sipper. The sipper’ssecond end surface comprises a first region orientated at an angle of about 90° relativeto the central axis of the second section 230 of the sipper 224, and a second region thatis orientated at an angle of about 45° relative to the central axis of the second section 230of the sipper 224. In Fig. 5E, the length of the second region, measured perpendicularlyto the central axis of the second section 230 of the sipper 224 is greater than the lengthof the first region, measured perpendicularly to the central axis of the second section 230of the sipper. In Fig. 5F, a side-sectional view of a part of a flow cell of the presentinvention can be seen. The sipper 224 is inserted into the sipper receiving recess. Thehandle 235 and the throughhole 236 can be seen.Figs.6A to 9C illustrate an example of a coupling means for mounting the flow cell 200 on the mount 300, i.e. a means for allowing the mount 300 to receive at least one flow cell 200, in the form of a coupling assembly 310 for a system 100 for automated synthesisof a macromolecule as described above. In further detail, Figs. 6A to 6D illustrate anembodiment of a coupling assembly 310 for such system 100 in different views. FIGS.7Ato 7C illustrate a functional scheme of the coupling assembly 310 as depicted in FIGS.6A to 6D, i.e. a moving path of parts of the coupling assembly 310, in a perspectivemanner, wherein FIGS. 8A to 8C illustrate the identical functional scheme of Figs. 7A to7C in a sectional view along section line A-A as depicted in FIG.6B, and FIGS.9A to 9C illustrate the functional scheme of Figs.7A to 7C in a sectional view along section line B- B in FIG.6B.The coupling assembly 310 is for use with the above described system 100, whichcomprises at least one flow cell 200, or 4 flow cells 200 in the presently depicted case,each flow cell 200 having at least one flow channel 202 with inlet port 220 and outlet port222, the heatable mount 300 configured to receive the at least one flow cell 200, and the pump 600 in fluid communication with the outlet port 222 of the flow channel 202. As depicted in e.g. FIGS 6A and 6B, each flow cell 200, before being clamped, is arranged on the mount 300 by means of engagement pins or engagement cams 301. These engagement cams 301 can be mushroom-shaped, i.e. formed in a mushroom orumbrella-shaped manner. As shown in an exemplary manner in FIGS. 6A and 6B, 4engagement cams 301 can encompass one flow cell 200, for example at the corner edges of the respective flow cell 200, in order to engage or hold the respective flow cell 200 on the mount 300. Thereby, the flow cell 200 can be oriented coaxially along a longitudinal axis of the mount 300, and preferably without play. Accordingly, each flow cell 200, before being clamped, can be “pre-mounted” by means of the respective engagement cams 301in coinciding manner with the x- an y-axis of the mount 300, wherein each flow cell 200can be pushed vertically at a slight angle in between the engagement cams 301 and pressed towards the mount 300, in order to be engaged by the engagement cams 301.As can be gathered from, e.g. FIGS 6A to 6D, the illustrated example for the couplingassembly 310 comprises 4 movable coupling members 311, with each coupling member311 provided for a respective flow cell 200, wherein each movable coupling member 311is movable in a direction perpendicular to its longitudinal axis and is supported by meansof a plurality of spring-loaded linear support bearings 311a, and wherein each movablecoupling member 311 can establish a fluid connection between the pump 600 and theoutlet port 222 of the flow channel 202 of the flow cell 200. In addition, the movablecoupling member 311 can simultaneously establishing a clamping connection betweenthe flow cell 200 and the mount 300, which mount 300 in this embodiment is configuredto receive / support the 4 flow cells 200. Here, the term “to receive” is to be understood as“to support” or “to adjoin”, wherein the configuration of the mount 300 to do so isimplemented by the provision of the coupling assembly 310 used for thermally and / or physically coupling the flow cells 200 to the mount 300. As can be gathered from e.g. FIG.7C, the 4 flow cells 200 are mounted on the mount 300 by means of the couplingassembly 310 pressing the flow cells 200 against the mount 300, such that the flow cells200 are oriented in a vertical direction. Accordingly, with this orientation of the flow cells200, the respective sipper 224 of each flow cell 200 is pointed downwards, e.g. in a direction towards the reagents in the holder 400, as shown in FIG.1A, so that the holder 400 can be oriented horizontally, i.e. such that open reagent containers maintain the fluids within the container by means of gravity. As can be gathered from e.g. FIGS.7A to 7C, the movable coupling member 311 is O- shaped in a square manner with flattened edges, in order to be able to provide surface pressure on the edges of the respective flow cell 200. Also, the coupling member 311 isadapted to hold a connection end 312 of a respective outlet tube 313, as can be gatheredfrom e.g. the enlarged details in each one of FIGS.8A to 8C. As can be further gathered therefrom, the connection ends 312 of the outlet tubes 313 are bended for about 45°, in order to be directed to the outlet port 222, and to finally be at least attached to the outlet port 222. The other ends of the four outlet tubes 313 run through U-shaped channels 341 of a protective shield 340, which protects the outlet tubes 313 from being bent or kinked, and which achieves that the outlet tubes 313 do not cross, i.e. cannot be confused with each other.As depicted in the sectional view in FIG.8A, in particular in the enlarged detail illustration,the coupling member 311 is held within the support frame 320 in a spring-biased manner by means of the spring-loaded linear support bearings 311a, so that an end face of the coupling member part holding the connection end 312 of the depicted outlet tube 313 is urged away from the coupling member 311. FIG.8A illustrates the coupling assembly 310 in the initial position on the positioning path as well as the coupling member 311 in its first position on the coupling path, wherein the coupling assembly 310 in the initial position is,along a longitudinal axis of the coupling assembly 310, arranged away from the flow cells200, i.e. in which the coupling assembly 310 is neither in contact with nor facing the flow cells 200, and wherein the coupling member 311 in the first position of the coupling path has not established fluid connection between the outlet tube 313 and the outlet port 222and has not yet established clamping connection between the flow cells 200 and themount 300. FIG. 8B illustrates the coupling assembly 310 in its facing position on the positioning path as well as the coupling member 311 in the first position on the couplingpath, wherein the coupling assembly 310 in the facing position of the positioning path isclose to the flow cells 200, along the longitudinal axis of the coupling assembly 310, i.e.in which the coupling assembly 310 is facing the flow cells 200 but is still not in contactwith the flow cells 200, see in particular the enlarged detail illustration of FIG.8B. FIG.8Cillustrates the coupling assembly 310 in the facing position on its positioning path as well as the coupling member 311 in the second position on its coupling path, wherein thecoupling assembly 310, in its facing position of the positioning path, is close to the flowcells 200, along the longitudinal axis of the coupling assembly 310, i.e. in which positionthe coupling assembly 310 is facing the flow cells 200. In addition, as can be gathered from the enlarged detail illustration of FIG.8C, the coupling member 311 is in the secondposition of the coupling path, in which position the coupling member 311 has establishedfluid connection between the outlet tube 313 and the outlet port 222 and has establishedclamping connection between the flow cells 200 and the mount 300. Here, it is particularlypointed out that an annular connection component 311b of the coupling member 311 holding the connection end 312 of the outlet tube 313 is held in a movable manner inrespect to the coupling member 311, by means of a spring 311c. In addition, an innercircumference of an end face of the connection component 311b is chamfered, in order to ease a connection with the outlet port 222. As can be gathered from the enlarged detail in FIG.8C, this structure enables a fluidtight connection between the connection end 312 of the outlet tube 313 and the outlet port 222, wherein a gap 311d is maintained between the connection component 311b and the flow cell 200, in order to avoid static overdetermination and ensure excellent fluid tightness. It is clear from FIGS. 8A to 8C that the coupling assembly 310 can be moved in a linear manner along its longitudinal axis from the initial position to the facing position on the positioning path by means of a pin-and-groove connection with guide rails 318, and back, and each coupling member 311 can be moved from the first position to the second position of the coupling path by means of a pin-and-groove connection with guide plates 315a, 315b, and back, in order to establish not only a clamping connection between the coupling members 311 and the flow cells 200, but also fluidtight connections between the connection ends 312 of the outlet tubes 313 and the respective outlet ports 222. In order to establish the connections in a correct manner, the coupling assembly 310 must first be moved from the initial position to the facing position on the positioning path, and then the coupling member 311 must be moved from the first position to the second position of the coupling path, thereby achieving the fluid connection between the outlet tube 313 and the outlet port 222 andthe clamping connection between the flow cells 200 and the mount 300.Similarly to the above, FIG.9A illustrates the coupling assembly 310 in the initial position on the positioning path as well as the coupling member 311 in its first position on the coupling path. FIG.9B illustrates the coupling assembly 310 in its facing position on the positioning path as well as the coupling member 311 in the first position on the coupling path, and FIG. 9C illustrates the coupling assembly 310 in the facing position on its positioning path as well as the coupling member 311 in the second position on its coupling path. The sectional views of FIGS.9A to 9c illustrate the positioning of the pin-and-grooveconnection between the guiding member 314, i.e. the guiding plates 315a and 315b in anexemplary manner with regard to the guiding plate 315a. Guiding plate 315a comprises two parallelly arranged kidney-shaped grooves 316a, in which two pins 317a of thesupport frame 320, one pin 317a in each of the grooves 316a, can move back and forth.Here, the pins 317a comprise a respective bearing, such as a slide bearing or ball bearingor the like, in order to ease the movement of each pin 317a within the respective groove316a. As can be seen in FIGS. 9A and 9B, the support frame 320 with the couplingmembers 311 in their first position have the respective pins 317a in a position within the respective groove 316a which is the farthest away from a level on which the flow cells200 are arranged (as can be seen by the sipper 224 in FIGS. 9A to 9C). Similarly thereto(but not shown), guiding plate 315b comprises two parallelly arranged kidney-shaped grooves 316b, in which two pins 317b of the support frame 320, one pin 317b in each ofthe grooves 316b, can move back and forth. Here, the pins 317b comprise a respectivebearing, such as a slide bearing or ball bearing or the like, in order to ease the movementof each pin 317b within the respective groove 316b. Again, the support frame 320 withthe coupling members 311 in their first position have the respective pins 317b in a position within the respective groove 316b which is the farthest away from a level on which theflow cells 200 are arranged. In FIG. 9B, the respective guide plate 315a, 315b on eachside of the support frame 320 is moved together with the support frame 320 until the leading end of the support frame 320 abuts against a stopper 330, thereby bringing the linear movement of the support frame 320 to a halt. By further pushing the guide plates 315a, 315b in the same direction, see FIG. 9C, with the support frame 320 hindered to follow, the pins 317a, 317b are urged within the groove towards a position which is the closest to the level on which the flow cells 200 are arranged. In doing so, the support frame 320 together with the coupling members 311 is moved towards the flow cells 200, thereby achieving the fluid connection between the outlet tube 313 and the outlet port 222and the clamping connection between the flow cells 200 and the mount 300 as explainedabove with regard to FIGS.8A to 8C.In general, the coupling assembly 310 is guided along the positioning path between theinitial position to the facing position by means of the guide rails 318 framing the couplingassembly 310 on both lateral sides, wherein the guide rails 318 are fixed in relation to themount 300 and, thus, constitute a moveable connection between the mount 300 and thecoupling assembly 310, with the guide rails 318 guiding the guiding member 314 with itsguide plates 315a, 315b in a linear manner along a longitudinal axis of the couplingassembly 310. While the current invention has been described in relation to its specific embodiments, it is to be understood that this description is for illustrative purposes only. Accordingly, it is intended that the invention be limited only by the scope of the claims appended hereto.

Claims

CLAIMS1. A system (100) for synthesizing a macromolecule (210) from a sample (208), thesystem (100) comprising: at least one flow cell (200) comprising at least one flow channel (202), the flow channel (202) having a functionalized solid phase surface (204) configured to bind a plurality of capture probes (206) that are configured to bind the sample (208), wherein each flow channel (202) has an inlet port (220) and an outlet port (222), and wherein the inlet port (220) is in fluidic communication with a sipper (224); a heatable mount (300) configured to receive the at least one flow cell (200), optionally wherein a first thermal block (302) is attached to the heatable mount (300); a holder (400) configured to hold a plurality of reagents; a gantry (500) configured to move in 3 different axis; a pump (600) in fluid communication with the outlet port (222) of the flow channel (202); a valve (608) configured to selectively connect the outlet port (222) of the flow channel (202) with a waste reservoir (604) and / or a buffer reservoir (606); a UV source (800) configured to illuminate the at least one flow channel (202); and a controller configured to control a temperature of the heatable mount (300), movement of the gantry (500), selection of the valve (608), operation of the UV source (800), and operation of the pump (600).

2. The system (100) of claim 1, wherein the capture probes (206) are configured tohybridize to a target nucleotide sequence.

3. The system (100) of claim 1 or 2, wherein the functionalized solid phase surface(204) is formed from a modification or treatment of a substrate of the flow channel (202) and is not formed from a separate coating of the substrate of the flow channel (202).

4. The system (100) of any one of the preceding claims, wherein the sipper (224) andthe inlet port (220) extend from the flow cell (200) in an orientation that is normal to aplane that encompasses the flow channel (202), optionally wherein the sipper (224) has a 90 degree bend.

5. The system (100) of any one of claims 1 to 3, wherein the sipper (224) and theinlet port (220) extend from the flow cell (200) in an orientation that is parallel to a plane that encompasses the flow channel (202).

6. The system (100) of any one of the preceding claims, wherein the gantry (500) isconfigured to move the holder (400).

7. The system (100) of any one of the preceding claims, wherein the heatable mount(300) is configured to hold the flow cell (200) in a vertical orientation while the holder (400) is in a horizontal orientation.

8. The system (100) of any one of the preceding claims, wherein no valves arepositioned in a fluid path between the at least one flow channel (202) and the holder (400).

9. The system (100) of any one of the preceding claims, further comprising9a) a plurality of pumps (600), with one dedicated pump in fluid communicationwith each outlet of the flow cell (200); 9b) a second thermal block in thermal contact with the holder (400);9c) a mixing tube (700) configured to perform fluid mixing operations on asensitive reagent in the holder (400), wherein the mixing tube (700) is not in fluid communication with the flow cell (200); and / or 9d) a thermal pad disposed between the flow cell (200) and the first thermalblock (302).

10. The system (100) of any one of the preceding claims, wherein a portion of thesipper (224) is in thermal contact with the first thermal block (302).

11. The system (100) of any one of the preceding claims, wherein the flow cell (200)comprises a molded portion (201) and a thin film (203), wherein the molded portion (201) comprises the at least one flow channel (202), and the thin film (203) is attached to the molded portion (201) to seal the at least one flow channel (202), optionally wherein thethin film (203) is made from a cyclic olefin polymer or cyclic olefin copolymer.

12. A method for synthesizing a macromolecule from a nucleic acid template, themethod comprising the steps of: providing a system (100) as described in any one of the preceding claims; introducing (150) a plurality of single stranded nucleic acid molecules (208) into the flow channel (202) of the flow cell (200) through the sipper (224), wherein the single stranded nucleic acid molecules (208) are stored on the holder (400); hybridizing (152) the single stranded nucleic acid molecules (208) to a plurality of capture probes (206) that have been attached to the surface (204) of the flow channel (202), wherein the temperature of the heatable mount (300) is controlled by the controller during the hybridization step (152); after the hybridization step (152) is complete, introducing (154) a wash buffer into the flow cell (200) to remove nonhybridized single stranded nucleic acid molecules from the flow cell (200); by introducing an extension reaction mixture into the flow channel (202) of the flow cell (200) through the sipper (224), synthesizing (156) a plurality of macromolecules (210) by using the hybridized single stranded nucleic acid molecules (208) as templates, wherein the extension reaction comprises a polymerase and nucleotide analogues, with the extension reaction mixture being stored on the holder (400); controlling the temperature of the heatable mount (300) with the controller during the synthesizing step (156); applying (168) an UV light from the UV source (800) to the macromolecules (210) to release the macromolecules (210) from the capture probes (206); and eluting (168) the macromolecules (210) from the flow cell (200) and through the sipper (224) into a collection tube.

13. The method of claim 12, further comprising the step of:after the synthesizing step (156) is complete, introducing an acid into the flow channel (202) of the flow cell (200) to selectively cleave (160) chemical bonds holding the macromolecules (210) in a compact configuration.

14. The method of claim 12 or 13, further comprising the step of:after the cleavage step (160), introducing (164) an additional reagent into the flow channel (202) of the flow cell (200) to further modify the macromolecules (210).

15. The method of claim 14, wherein the additional reagent is succinic anhydride.

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