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首页> 外文期刊>Spectrochimica acta, Part A. Molecular and biomolecular spectroscopy >Parallel DNA double helices incorporating isoG or m(5) isoC bases studied by FTIR, CD and molecular modeling
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Parallel DNA double helices incorporating isoG or m(5) isoC bases studied by FTIR, CD and molecular modeling

机译：通过FTIR，CD和分子建模研究的结合有isoG或m（5）isoC碱基的平行DNA双螺旋

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FTIR spectroscopy has been used to follow the formation of parallel stranded DNA duplexes incorporating isoG or m(5)isoC bases and determine their base pairing scheme. The results are discussed in comparison with data concerning anti-parallel duplexes with comparable base composition and sequence. In duplexes containing A-T and isoG-C or m(5)isoC-G base pairs shifts of the thymine C2=O2 and C4=O4 carbonyl stretching vibrations (to lower and higher wavenumbers, respectively, when compared to their positions in classical cis Watson-Crick (WC) base pairs) reflect the formation of trans Watson-Crick A-T base pairs. All carbonyl groups of cytosines, m(5)isocytosines, guanines and isoguanines are found to be involved in hydrogen bonds, indicative of the formation of isoG-C and m(5)isoC-G base pairs with three hydrogen bonds. Molecular modeling shows that both structures form regular right handed helices with C2'endo sugar puckers. The role of the water content on the helical conformation of the parallel duplexes has been studied by FTIR and CD. It is found that a conformational transition similar to the B --> A transition observed for anti-parallel duplexes induced by a decrease of the water content of the samples can occur for these parallel duplexes. Their helical flexibility has been evidenced by FTIR studies on hydrated films by the emergence of absorption bands characteristic of A type geometry, in particular by an S-type --> N-type repuckering of the deoxyribose. All sugars in the parallel duplex with alternating d(isoG-A)/d(C-T) sequence can adopt an N-type geometry in low water content conditions. The conformational transition of the parallel hairpin duplex with alternating d(isoG-A)/d(C-T) sequence was followed by circular dichroism in water/trifluoroethanol solutions and its free energy at 0 degreesC was estimated to be 6.6 +/- 0.3 kcal mol(-1). (C) 2004 Elsevier B.V. All rights reserved.
机译：FTIR光谱已被用于跟踪并入isoG或m（5）isoC碱基的平行链DNA双链体的形成，并确定其碱基配对方案。与具有可比较的碱基组成和序列的反平行双链体的数据相比较，讨论了结果。在包含AT和isoG-C或m（5）isoC-G碱基对的双链体中，胸腺嘧啶C2 = O2和C4 = O4羰基拉伸振动的位移（与经典顺式Watson中的位置相比，分别降低和降低了波数） -Crick（WC）碱基对）反映了反式Watson-Crick AT碱基对的形成。发现胞嘧啶，m（5）异胞嘧啶，鸟嘌呤和异鸟嘌呤的所有羰基均参与氢键，这表明具有三个氢键的isoG-C和m（5）isoC-G碱基对的形成。分子建模表明，这两个结构均形成带有C2'endo糖褶的规则右旋螺旋。 FTIR和CD已研究了水含量对平行双链体螺旋构象的作用。已经发现，对于这些平行双链体，可能发生类似于B→构象转变的现象，该构象转变是由样品的水含量降低引起的反平行双链体所观察到的。 FTIR在水合膜上的研究表明，它们的螺旋柔韧性是通过A型几何特征吸收带的出现，特别是脱氧核糖的S型-> N型再折叠来证明的。平行双链体中具有交替的d（isoG-A）/ d（C-T）序列的所有糖在低含水量条件下均可采用N型几何形状。在水/三氟乙醇溶液中，平行发夹双链体具有交替的d（isoG-A）/ d（CT）序列的构象转变，随后呈圆二色性，其在0摄氏度的自由能估计为6.6 +/- 0.3 kcal mol （-1）。 （C）2004 Elsevier B.V.保留所有权利。

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