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Effects of DNA secondary structure on oligonucleotide probe binding efficiency.

Abstract：

:Secondary structure motifs in nucleic acid probes generally impair intended hybridization reactions and so efforts to predict and avoid such structures are commonly employed in probe design schemes. Another key facet of probe design that has received much less attention, however, is that secondary structure at targeted probe binding site regions may also impair hybridization. Thus, evaluation of both probe and target site secondary structures together should improve hybridization prediction and design effectiveness. Several challenges confound this goal, including imperfect empirical rules and parameters underlying predictions and the fact that folding algorithms scale poorly with respect to sequence length. Here, we attempt to quantify the consequences of target site structure on predicted hybridization using sequences sampled from the human genome. We also provide a methodology for choosing a reasonable "window size" around target sites that is as small as possible without compromising folding algorithm prediction accuracy.

journal_name

Comput Biol Chem

journal_title

Computational biology and chemistry

authors

Koehler RT,Peyret N

doi

10.1016/j.compbiolchem.2005.09.002

keywords:

subject

Has Abstract

pub_date

2005-12-01 00:00:00

pages

393-7

issue

6

eissn

1476-9271

issn

1476-928X

pii

S1476-9271(05)00095-2

journal_volume

29

pub_type

杂志文章

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