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Biomaterials Science Vol - 2 Issue - 3

Biomaterials Science Vol - 2 Issue - 2

Biomaterials Science Vol -1

Biophysical properties of nucleic acids at surfaces relevant to microarray performance

Content Provider	Royal Society of Chemistry (RSC)
Author	Rao, Archana N. Grainger, David W.
Copyright Year	2014
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.
Starting Page	436
Ending Page	471
Page Count	36
File Format	HTM / HTML PDF
ISSN	20474830
Volume Number	2
Issue Number	4
Journal	Biomaterials Science
DOI	10.1039/c3bm60181a
Language	English
Publisher	Royal Society of Chemistry
Access Restriction	Open
Subject Keyword	Acid RNA DNA Genomics Physical chemistry Nucleic acid hybridization Entropy Microarray Electrostatics Curvature
Content Type	Text
Resource Type	Article
Subject	Materials Science Biomedical Engineering

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BIOPHYSICAL PROPERTIES OF NUCLEIC ACIDS AT SURFACES RELEVANT TO MICROARRAY PERFORMANCE

Secondary structure formation of homopolymeric single-stranded nucleic acids including force and loop entropy: implications for DNA hybridization.

Atomistic Free Energy Model for Nucleic Acids: Simulations of Single-Stranded DNA and the Entropy Landscape of RNA Stem–Loop Structures

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Modeling Effects of Surface Properties and Probe Density for Nanoscale Biosensor Design: A Case Study of DNA Hybridization near Surfaces

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Nonspecific Hybridization Scaling of Microarray Expression Estimates: A Physicochemical Approach for Chip-to-Chip Normalization

Improved Performance of DNA Microarray Multiplex Hybridization Using Probes Anchored at Several Points by Thiol–Ene or Thiol–Yne Coupling Chemistry

Conformational Flexibility Influences Degree of Hydration of Nucleic Acid Hybrids

Biophysical properties of nucleic acids at surfaces relevant to microarray performance

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BIOPHYSICAL PROPERTIES OF NUCLEIC ACIDS AT SURFACES RELEVANT TO MICROARRAY PERFORMANCE

Secondary structure formation of homopolymeric single-stranded nucleic acids including force and loop entropy: implications for DNA hybridization.

Atomistic Free Energy Model for Nucleic Acids: Simulations of Single-Stranded DNA and the Entropy Landscape of RNA Stem–Loop Structures

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Biophysical properties of nucleic acids at surfaces relevant to microarray performance