标题： 同源多聚单链核酸的二级结构形成包括力和环熵：对DNA杂交的启示 显示英文标题

标题： Secondary structure formation of homopolymeric single-stranded nucleic acids including force and loop entropy: implications for DNA hybridization

摘要： 环是折叠DNA和RNA分子中的重要二级结构元件，在熔化转变附近大量出现。 使用一种考虑长度为m的环的对数熵c ln m的核酸二级结构理论，我们研究了在外力作用下和温度变化时的均聚单链核酸。 在长链的热力学极限下，链在低温/低力的紧凑（折叠）结构和高温/高力的熔融（展开）结构之间表现出相变。 c对相图、临界指数、熔化和力-伸展曲线的影响被解析地推导出来。 当拉力消失时，只有在有限的环指数范围2 < c < 2.479内才可能发生熔化转变；对于c <= 2，链始终处于折叠相，而对于2.479 < c始终处于展开相。 对于所有环指数c < 2.479，可以发生具有奇异行为的力诱导熔化转变，并可以通过单分子力光谱实验观察到。 这些发现对双链核酸的杂交或变性有影响。 用于核酸双链熔化的波兰-谢拉加模型不允许双链变性区域中同一链上的核苷酸之间形成碱基配对。 如果序列允许这些链内碱基对，我们显示对于现实的环指数c ~ 2.1，单链内部会出现显著的二级结构。 这导致双链的熔化温度低于波兰-谢拉加模型的预测。 此外，这些二级结构会重整有效环指数c^，该指数表征双链变性区域的权重，从而影响双链熔化转变的普遍特性。 显示英文摘要

摘要： Loops are essential secondary structure elements in folded DNA and RNA molecules and proliferate close to the melting transition. Using a theory for nucleic acid secondary structures that accounts for the logarithmic entropy c ln m for a loop of length m, we study homopolymeric single-stranded nucleic acid chains under external force and varying temperature. In the thermodynamic limit of a long strand, the chain displays a phase transition between a low temperature / low force compact (folded) structure and a high temperature / high force molten (unfolded) structure. The influence of c on phase diagrams, critical exponents, melting, and force extension curves is derived analytically. For vanishing pulling force, only for the limited range of loop exponents 2 < c < 2.479 a melting transition is possible; for c <= 2 the chain is always in the folded phase and for 2.479 < c always in the unfolded phase. A force induced melting transition with singular behavior is possible for all loop exponents c < 2.479 and can be observed experimentally by single molecule force spectroscopy. These findings have implications for the hybridization or denaturation of double stranded nucleic acids. The Poland-Scheraga model for nucleic acid duplex melting does not allow base pairing between nucleotides on the same strand in denatured regions of the double strand. If the sequence allows these intra-strand base pairs, we show that for a realistic loop exponent c ~ 2.1 pronounced secondary structures appear inside the single strands. This leads to a lower melting temperature of the duplex than predicted by the Poland-Scheraga model. Further, these secondary structures renormalize the effective loop exponent c^, which characterizes the weight of a denatured region of the double strand, and thus affect universal aspects of the duplex melting transition.