Stability and mismatch discrimination of locked nucleic acid-DNA duplexes.
Stability and mismatch discrimination of locked nucleic acid-DNA duplexes.
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DOI：
10.1021/bi200904e
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发表时间：
2011-11-01
期刊：
影响因子：
2.9
通讯作者：
Tataurov, Andrey V.
中科院分区：
文献类型：
--
作者：
Owczarzy, Richard;You, Yong;Groth, Christopher L.;Tataurov, Andrey V.
锁核酸（LNA;碱基符号+A、+C、+G和+T）被引入化学合成的寡核苷酸中以增加双链体稳定性和特异性。为了理解这些影响，我们已经确定了连续LNA核苷酸的热力学参数。我们提出了LNA寡核苷酸设计指南，并介绍了可预测任何LNA双链体寡聚体稳定性的免费在线软件。热力学分析表明，单链-双链转变的特征是有利的熵变和不利的熵损失。单个LNA修饰限制了核苷酸的局部构象，当单链被限制为刚性双链体结构时，引起较小的、不太不利的熵损失。额外的LNA邻近的初始修改似乎增强堆叠和H-键合的相互作用，因为它们增加了双链体稳定的双链贡献。新的最近邻参数正确地预测了LNA对失配鉴别的正面和负面影响。特异性在大多数序列中增强，并且取决于错配类型和相邻碱基对;最大的区别性增强发生在+T+C+C序列内的中心+C·C错配和+T+A+G序列内的+A·G错配。LNA不影响某些序列的特异性，甚至对许多+G·T和+C·A错配的特异性造成损害。在+G+G+C序列中，中心+G·T错配和+G+C+G序列中，+C·A错配的错配辨别力下降最大。我们假设这些歧视的变化不是独特的功能LNA，但起源于双链体构象从B型到A型的转变。
Locked nucleic acids (LNA; symbols of bases, +A, +C, +G, and +T) are introduced into chemically synthesized oligonucleotides to increase duplex stability and specificity. To understand these effects, we have determined thermodynamic parameters of consecutive LNA nucleotides. We present guidelines for the design of LNA oligonucleotides and introduce free online software that predicts the stability of any LNA duplex oligomer. Thermodynamic analysis shows that the single strand–duplex transition is characterized by a favorable enthalpic change and by an unfavorable loss of entropy. A single LNA modification confines the local conformation of nucleotides, causing a smaller, less unfavorable entropic loss when the single strand is restricted to the rigid duplex structure. Additional LNAs adjacent to the initial modification appear to enhance stacking and H-bonding interactions because they increase the enthalpic contributions to duplex stabilization. New nearest-neighbor parameters correctly forecast the positive and negative effects of LNAs on mismatch discrimination. Specificity is enhanced in a majority of sequences and is dependent on mismatch type and adjacent base pairs; the largest discriminatory boost occurs for the central +C·C mismatch within the +T+C+C sequence and the +A·G mismatch within the +T+A+G sequence. LNAs do not affect specificity in some sequences and even impair it for many +G·T and +C·A mismatches. The level of mismatch discrimination decreases the most for the central +G·T mismatch within the +G+G+C sequence and the +C·A mismatch within the +G+C+G sequence. We hypothesize that these discrimination changes are not unique features of LNAs but originate from the shift of the duplex conformation from B-form to A-form.
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影响因子：
2.9
作者：
MARKY, LA;BRESLAUER, KJ
通讯作者：
BRESLAUER, KJ
影响因子：
5.6
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影响因子：
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作者：
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影响因子：
2.9
作者：
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通讯作者：
Toulme, Jean-Jacques
DOI：
10.1073/pnas.83.24.9373
发表时间：
1986-12-01
影响因子：
11.1
作者：
FREIER, SM;KIERZEK, R;TURNER, DH
通讯作者：
TURNER, DH