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Base sequence dependence of the structure and dynamics, and thermodynamic properties of oligonucleotides

寡核苷酸的结构和动力学以及热力学性质的碱基序列依赖性

基本信息

批准号：
59470134
负责人：
SHINDO Heisaburo
金额：
$ 4.16万
依托单位：
Tokyo College of Pharmacy
依托单位国家：
日本
项目类别：
Grant-in-Aid for General Scientific Research (B)
财政年份：
1984
资助国家：
日本
起止时间：
1984 至 1986
项目状态：
已结题

来源：
https://kaken.nii.ac.jp/en/grant/KAKENHI-PROJECT-59470134/
关键词：
^<31>P NMR ^1H NMR ^2H NMR Structure and Dynamics of DNA oligonucleotide conformational change オリゴ核酸分子運動 NMR 熱測定重水素NMR

项目摘要

From the analyses of ^<31>P NMR spectral line shapes of oriented DNA fibers we have previously shown that the backbone conformation of B-DNA is nonuniform which seemed base sequence dependent. Along this finding we proceeded this project to prove the base sequence effects in many other systems and extend it to other properties of DNA.1. ^<31>P NMR studies of oriented DNA fibers led the following conclusions: i) homo poly(dA).poly(dT) had unusual structure which could be interpreted as if the helix axis bended to form supercoiled form, ii) RNA-DNA hybrid, poly(rA).poly(dT) exhibited (rA)_n chain as being A form and (dT)_n as being B form, iii) B-DNA in the fibers at high relative humidities underwent three modes of molecular motions i.e., rotaion about the helix axis, rapid fluctuation of atomic groups and reorientation about the tilted axis, and iv) the base planes of A-DNA tiled by 20゜ from the plane perpendicular to the helix axis, while that of B-DNA is nearly perpendicular to the h … More elix axis.2. Thermodynamic properties of conformational transition of DNA. The study of ethanol-induced A-B transition of DNA demonstrated that apparent free energy change for this transition in aqueous solution was 21.2 kcal/mol, and that DNA-solvent interaction was unfavorable in ethanol solution so that A form was stabilized. Using a mismatched oligonucleotide, d(CGCGAATTACGCG), it was shown that activation energy and entropyfor the hairpin loop formation from the double stranded oligomer was 56 kcal/mol and 137 cal/mol/K, respectivley, and therefore concluded that this hairpin formation directly occurred with separation of the complementarychains but not through an intermediate such as cruciform.3. Structure and dynamics of synthetic oligonucleotides in solution. Total assignments of ^1H proton spectra of 12 kinds of decanuleotides were made and the chemical shift values of aromativ protons were discussed in terms of base seqeunce effects. Thus, a given proton chemical shift was found to be determined within 0.04 ppm by nearest neighbor residues, especially by the one at 5'-side. Theoretically calculated chemical shifts were in good agreement with the observed values for adenosine H2 protons but not for cytidine H5 and H6 protons. The relaxationtimes T_1 and T_2 of aromatic trotons were measured at various frequencies and interpreted in terms of molecular motions including internal motion. Thus, it was found that correlation time for the overall motion was 3.5 ns and that for internal motion was 0.1 ns with and order parameter s=0.9. Less

从定向DNA纤维的^<31>P NMR谱线形状的分析中，我们先前已经表明B-DNA的主结构是不均匀的，这似乎依赖于碱基序列。沿着这一发现，我们继续这个项目，以证明碱基序列效应在许多其他系统中，并将其扩展到dna的其他特性。^<31>P核磁共振定向DNA纤维的研究得出以下结论：i) homo poly（dA）。poly（dT）具有不寻常的结构，可以解释为如果螺旋轴弯曲形成超卷曲形式；ii) RNA-DNA杂交，poly（rA）。poly（dT）显示（rA）_n链为A形式，（dT）_n为B形式，iii)高相对湿度下纤维中的B- dna经历了三种分子运动模式，即围绕螺旋轴旋转，原子群的快速波动和围绕倾斜轴的重新定向，iv) A- dna的基面从垂直于螺旋轴的平面平铺了20，而B- dna的基面几乎垂直于h…More螺旋轴。DNA构象转变的热力学性质。乙醇诱导DNA A- b转变的研究表明，该转变在水溶液中的表观自由能变化为21.2 kcal/mol，并且在乙醇溶液中DNA与溶剂的相互作用不利，从而使A形式稳定下来。利用错配寡核苷酸d(CGCGAATTACGCG)，表明双链寡聚物形成发夹环的活化能和熵分别为56 kcal/mol和137 cal/mol/K，因此得出结论，这种发夹环的形成直接发生在互补链的分离过程中，而不是通过十字链等中间体。溶液中合成寡核苷酸的结构和动力学。对12种十核肽的^1H质子谱进行了总赋值，并根据碱基序列效应讨论了芳香质子的化学位移值。因此，一个给定的质子化学位移被发现在0.04 ppm内由最近邻残基确定，特别是由5'侧的残基确定。理论计算的化学位移与腺苷H2质子的观测值一致，而与胞苷H5和H6质子的观测值不一致。测量了不同频率下芳香族质子的弛豫时间T_1和T_2，并用分子运动（包括内运动）进行了解释。因此，整体运动的相关时间为3.5 ns，内部运动的相关时间为0.1 ns，阶参量s=0.9。少