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Issue 4, 2014
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Biophysical properties of nucleic acids at surfaces relevant to microarray performance

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Abstract

Both clinical and analytical metrics produced by microarray-based assay technology have recognized problems in reproducibility, reliability and analytical sensitivity. These issues are often attributed to poor understanding and control of nucleic acid behaviors and properties at solid–liquid interfaces. Nucleic acid hybridization, central to DNA and RNA microarray formats, depends on the properties and behaviors of single strand (ss) nucleic acids (e.g., probe oligomeric DNA) bound to surfaces. ssDNA's persistence length, radius of gyration, electrostatics, conformations on different surfaces and under various assay conditions, its chain flexibility and curvature, charging effects in ionic solutions, and fluorescent labeling all influence its physical chemistry and hybridization under assay conditions. Nucleic acid (e.g., both RNA and DNA) target interactions with immobilized ssDNA strands are highly impacted by these biophysical states. Furthermore, the kinetics, thermodynamics, and enthalpic and entropic contributions to DNA hybridization reflect global probe/target structures and interaction dynamics. Here we review several biophysical issues relevant to oligomeric nucleic acid molecular behaviors at surfaces and their influences on duplex formation that influence microarray assay performance. Correlation of biophysical aspects of single and double-stranded nucleic acids with their complexes in bulk solution is common. Such analysis at surfaces is not commonly reported, despite its importance to microarray assays. We seek to provide further insight into nucleic acid-surface challenges facing microarray diagnostic formats that have hindered their clinical adoption and compromise their research quality and value as genomics tools.

Graphical abstract: Biophysical properties of nucleic acids at surfaces relevant to microarray performance

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Article information


Submitted
22 Jul 2013
Accepted
27 Jan 2014
First published
14 Feb 2014

Biomater. Sci., 2014,2, 436-471
Article type
Review Article
Author version available

Biophysical properties of nucleic acids at surfaces relevant to microarray performance

A. N. Rao and D. W. Grainger, Biomater. Sci., 2014, 2, 436
DOI: 10.1039/C3BM60181A

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