Flexibility of single-stranded DNA: Use of gapped duplex helices to determine the persistence lengths of poly(dT) and poly(dA)
Flexibility of single-stranded DNA: Use of gapped duplex helices to determine the persistence lengths of poly(dT) and poly(dA)
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DOI：
10.1006/jmbi.1998.2287
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发表时间：
1999-01-08
影响因子：
5.6
通讯作者：
Hagerman, PJ
中科院分区：
文献类型：
--
作者：
Mills, JB;Vacano, E;Hagerman, PJ
一旦组成单链物种的序列相关性质(如固有刚性、有效上升)得到很好的定义，负责二级和高阶核酸结构形成和稳定的作用力就可以得到更充分的理解。了解单链聚合物的构象对于开发用于各种结构或链解离反应的更好的聚电解质模型也很重要。然而，目前关于单链DNA或RNA聚合物中上升或刚性的序列相关性的定量信息很少。为了解决这个问题，我们描述了一种形式的瞬变电双折射(TEB)测量，其中具有中心单链区域(间隙)的DNA分子的旋转衰减时间(tau(Gap))与具有相同长度(以每条链的核苷酸数计)的双链控制分子的相应时间(tau(Dplx))相比较。当镁离子浓度大于1-2 mM时，间隙双链的tau比值(=tau(Gap)/tau(Dplx))达到平台值，高于平台值时，没有观察到tau比值的进一步变化；间隙序列的持续长度(P)和核苷酸间距(H)值由实验的tau比值得到。对于dT(N)，P和P的允许范围分别为每核苷酸20-36埃和5-7埃，最佳值分别为31埃(P)和5.2埃/nT(H)。对于da(N)，低温(4℃)堆积形式的持续长度为78(+/-8)埃，螺旋上升3.2埃/nT。与以前方法相比，当前方法的一个显著优点是使用短(80-100 nT)分子，从而便于通过合成手段产生各种间隙序列。(C)1999年学术出版社。
The forces responsible for the formation and stabilization of secondary and higher-order nucleic acid structure can be more fully understood once the sequence-dependent properties (e.g. intrinsic rigidity, effective rise) of the component single-stranded species are well-defined. Knowledge of the conformations of the single-stranded polymers is also important for the development of better polyelectrolyte models for various structural or strand-dissociation reactions. However, there is at present little quantitative information regarding the sequence dependence of either rise or rigidity in single-stranded DNA or RNA polymers. To address this issue, we describe a form of transient electric birefringence (TEB) measurement in which the rotational decay times (tau(gap)) of DNA molecules possessing central, single-stranded regions (gaps) are compared with the corresponding times (tau(dplx)) for duplex control molecules of the same length (in nucleotides per strand) as the continuous strand in the "gapped duplex". For magnesium ion concentrations above 1-2 mM, the tau ratios (= tau(gap)/tau(dplx)) for the gapped duplexes reach plateau values, above which no further change in tau ratio is observed; values for the persistence length (P) and internucleotide spacing (h) of the gap sequences are obtained from the experimental tau ratios. For dT(n), the permissible ranges of P and it are 20-36 Angstrom and 5-7 Angstrom per nucleotide (nt), respectively, with optimal values of 31 Angstrom (P) and 5.2 Angstrom/nt (h). For dA(n), the persistence length for the low temperature (4 degrees C), stacked form is 78 (+/-8) Angstrom for a helix rise of 3.2 Angstrom/nt One significant advantage of the current method over previous approaches is the use of short (80-100 nt) molecules, thus facilitating the production of various gap sequences through synthetic means. (C) 1999 Academic Press.