BIOPHYSICAL PROPERTIES OF NUCLEIC ACIDS AT SURFACES RELEVANT TO MICROARRAY PERFORMANCE.
BIOPHYSICAL PROPERTIES OF NUCLEIC ACIDS AT SURFACES RELEVANT TO MICROARRAY PERFORMANCE.
复制标题
DOI：
10.1039/c3bm60181a
复制
发表时间：
2014-04-01
影响因子：
6.6
通讯作者：
Grainger DW
中科院分区：
文献类型：
--
作者：
Rao AN;Grainger DW
由基于微阵列的检测技术产生的临床和分析指标都认识到在重复性、可靠性和分析灵敏度方面存在问题。这些问题通常被归因于对固-液界面的核酸行为和性质缺乏了解和控制。核酸杂交是DNA和RNA微阵列形式的核心，取决于结合在表面的单链(Ss)核酸(例如，探针寡聚DNA)的性质和行为。单链DNA的滞留长度、旋转半径、静电、在不同表面和不同分析条件下的构象、链的柔韧性和曲率、离子溶液中的电荷效应以及荧光标记都会影响其在分析条件下的物理化学和杂交。核酸(例如，RNA和DNA)与固定的单链DNA链的靶相互作用受到这些生物物理状态的高度影响。此外，动力学、热力学、焓和熵对DNA杂交的贡献反映了全球探针/靶结构和相互作用动力学。在这里，我们回顾了几个与寡聚核酸相关的生物物理问题，分子在表面的行为及其对双链形成的影响，这些影响了微阵列的分析性能。在大溶液中，单链和双链核酸与其络合物的生物物理方面的关联是很常见的。这样的表面分析并不常见，尽管它对微阵列分析很重要。我们试图对微阵列诊断格式面临的核酸表面挑战提供进一步的见解，这些挑战阻碍了它们的临床采用，并损害了它们作为基因组学工具的研究质量和价值。
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.