Sorting and immobilization system for nucleic acids using synthetic binding systems

Abstract

Methods are provided for producing an array of immobilized nucleic acids on an array device. The array device has a plurality of microlocations each having an electrode. At least one of the microlocations has a synthetic addressing unit coupled to the microlocation. The microlocation is the activated, usually by electronically biasing the electrode of the microlocation. The at least one microlocation is then contacted by a conjugate which has a nucleic acid and a synthetic binding unit. The conjugate is then coupled to the microlocation through an interaction between the synthetic binding unit and the synthetic addressing unit. In one embodiment, the synthetic binding unit and synthetic addressing unit may be pRNA, pDNA, or CNA.

Description

[0001] This is a continuation of U.S. application Ser. No. 09 / 910,469, filed Jul. 19, 2001, which is incorporated herein by reference in its entirety.FIELD OF INVENTION [0002] The present invention relates to conjugates of synthetic binding units and nucleic acids. The present invention also relates to methods for sorting and immobilizing nucleic acids on support materials using such conjugates by specific molecular addressing of the nucleic acids mediated by the synthetic binding systems. Particularly, the present invention also relates to novel methods of utilizing conjugates of synthetic binding units and nucleic acids to in active electronic array systems to produce novel array constructs from the conjugates, and the use of such constructs in various nucleic acid assay formats. In addition, the present invention relates to various novel forms of such conjugates, improved methods of making solid phase synthesized conjugates, and improved methods of conjugating pre-synthesized syn...

AI Technical Summary

Problems solved by technology

The disadvantage of the methods described above is that the sequence used for the immobilization can potentially hybridize with the sequence to be immobilized, forming intramolecular secondary structures, may hybridize with another sequence to be immobilized, forming intermolecular secondary structures, or may hybridize with nucleic acids from the sample.

The risk of such an unwanted or interfering interaction increases with the length of the nucleic acid(s) to be immobilized, as well as with the complexity of a sample (e.g., the possibility of contaminating nucleic acids from unknown organisms.)

Another disadvantage of the use of natural nucleic acids for immobilization is that the stability of duplexes of natural nucleic acids does not increase linearly in proportion to length (number of nucleotides in the sequence) over a large range, but rather approaches a limit which depends only on the relative percentage of CG to AT base pairs (“CG content”).

Binding systems having a duplex stability exceeding the natural limit cannot be prepared using natural nucleic acids.

This limitation is also problematic when applying various stringency conditions to the nucleic acid at its immobilized location: the immobilizing nucleic acid tags will also be subjected to the same stringency conditions (i.e., chaotropic agents, thermal conditions, or electrostatic forces), and may dissociate.

Achieving a fine differentiation in stringency differentiation between immobilization tag interactions (which must remain hybridized) and the target-specific interactions (which are often discriminated at the single base pair mismatch level) is often difficult, especially under clinical-type conditions when the method must be particularly robust and consistent.

Another significant economic and time disadvantage of using natural nucleic acids as immobilization agents is that a certain minimum sequence length is required to reach a practical level of stability and selectivity of the immobilization.

This results in the entire nucleic acid strand (composed of the sequence for recognizing the sample and the sequence for immobilization) becoming relatively long.

The use very long sequences can be disadvantageous for several reasons.

First, the use of long nucleic acid sequences increases the likelihood of secondary structure formation intramolecularly, and also increases the likelihood of transient or stable hybridization between multiple strands in solution.

Another disadvantage of using natural systems for the immobilization of nucleic acids is that such systems can be easily degraded or destroyed during their use.

In particular, degradation by enzymatic components of the sample, or even contaminating DNAses and RNAses from laboratory workers' fingertips, is a concern.

Although a commonly used complex, this provides only one immobilization interaction tool: multiplex reactions with specific localization of the products cannot be done with a biotin-streptavidin affinity system alone.

However, these systems only allow separation under diverse conditions (nickel chromatography, vs antibody binding,) and thus do not overcome the limitations of the biotin-avidin interaction for multiplex reactions.

Since synthetic binding systems, such as pyranosyl-RNA (pRNA) or pyranosyl-DNA (pDNA) binding systems, are, by design, not sterically capable of pairing with nucleic acids, these previously described methods are not applicable to conjugating nucleic acids with synthetic binding units.

However, the solid-phase tandem synthesis of synthetic binding unit / nucleic acid conjugates by phosphoramidite chemistry is not desirable for circumstances in which a nucleic acid is readily available for conjugation (e.g., a bacterial plasmid preparation.)

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