Effect of loop sequence on unzipping of short DNA hairpins,Physical Review E

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Effect of loop sequence on unzipping of short DNA hairpins
Physical Review E ( IF 2.2 ) Pub Date : 2021-06-21 , DOI: 10.1103/physreve.103.062411
Anurag Upadhyaya ₁ , Sanjay Kumar ₁

Affiliation

The dependence of stability on the sequence of a DNA hairpin has been investigated through atomistic simulations. For this, a sequence of 16 bases of a hairpin, which consists of a loop of four bases and a stem of six base pairs, has been considered. We have taken eight different sequences, where the first five base pairs were kept fixed in all sequences, whereas the loop sequence and the identity of the duplex base pair closing the loop have been varied. For these hairpin structures, force-induced melting (unzipping) studies were carried out to investigate the effect of the variables on the stability of hairpin. The temperature at which half of the base pairs are open is termed the melting temperature. We defined the unzipping force

F_{h}

(half of the base pairs are open) and showed that it may not provide the effect of closing the base pair or loop sequence on the stability of the DNA hairpin. In order to have a better understanding of the stability of a DNA hairpin, the closing base pair or hairpin loop must be open. This requires complete opening of the stem. We defined a force

F_{c}

at which all base pairs of the stem are open, and we showed that the

F_{c}

gives better understanding of DNA hairpin stability.

中文翻译：

环序列对短DNA发夹解链的影响

已经通过原子模拟研究了稳定性对 DNA 发夹序列的依赖性。为此，已经考虑了发夹的 16 个碱基序列，该序列由四个碱基的环和六个碱基对的茎组成。我们采用了八种不同的序列，其中前五个碱基对在所有序列中保持固定，而环序列和闭合环的双链碱基对的身份已经改变。对于这些发夹结构，进行了力诱导熔化（解链）研究以研究变量对发夹稳定性的影响。一半碱基对打开时的温度称为解链温度。我们定义了解压缩力