کد مقاله | کد نشریه | سال انتشار | مقاله انگلیسی | نسخه تمام متن |
---|---|---|---|---|
10232004 | 1433 | 2005 | 5 صفحه PDF | دانلود رایگان |
عنوان انگلیسی مقاله ISI
Effects of DNA secondary structure on oligonucleotide probe binding efficiency
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کلمات کلیدی
موضوعات مرتبط
مهندسی و علوم پایه
مهندسی شیمی
بیو مهندسی (مهندسی زیستی)
پیش نمایش صفحه اول مقاله
![عکس صفحه اول مقاله: Effects of DNA secondary structure on oligonucleotide probe binding efficiency Effects of DNA secondary structure on oligonucleotide probe binding efficiency](/preview/png/10232004.png)
چکیده انگلیسی
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.
ناشر
Database: Elsevier - ScienceDirect (ساینس دایرکت)
Journal: Computational Biology and Chemistry - Volume 29, Issue 6, December 2005, Pages 393-397
Journal: Computational Biology and Chemistry - Volume 29, Issue 6, December 2005, Pages 393-397
نویسندگان
Ryan T. Koehler, Nicolas Peyret,