Rinkel L J, Altona C
Gorlaeus Laboratories of the State University of Leiden, the Netherlands.
J Biomol Struct Dyn. 1987 Feb;4(4):621-49. doi: 10.1080/07391102.1987.10507665.
A graphical method is presented for the conformational analysis of the sugar ring in DNA fragments by means of proton-proton couplings. The coupling data required for this analysis consist of sums of couplings, which are referred to as sigma 1' (= J1'2' + J1'2''), sigma 2' (= J1'2' + J2'3' + J2'2''), sigma 2'' (= J1'2'' + J2''3' + J2'2'') and sigma 3' (= J2'3' + J2''3' + J3'4'). These sums of couplings correspond to the distance between the outer peaks of the H1', H2', H2'' and H3' [31P] resonances, respectively, (except for sigma 2' and sigma 2'' in the case of a small chemical shift difference between the H2' and H2'' resonances) and can often be obtained from 1H-NMR spectra via first-order measurement, obviating the necessity of a computer-assisted simulation of the fine structure of these resonances. Two different types of graphs for the interpretation of the coupling data are discussed: the first type of graph serves to probe as to whether or not the sugar ring occurs as a single conformer, and if so to analyze the coupling data in terms of the geometry of this sugar ring. In cases where the sugar ring does not occur as a single conformer, but as a blend of N- and S-type sugar puckers, the second type of graph is used to analyze the coupling data in terms of the geometry and population of the most abundant form. It is shown that the latter type of analysis can be carried out on the basis of experimental values for merely sigma 1',sigma 2' and sigma 2'', without any assumptions or restrictions concerning a relation between the geometry of the N- and S-type conformer. In addition, the question is discussed as to how insight can be gained into the conformational purity of the sugar ring from the observed fine structure of the H1' resonance. Finally, a comparison is made between experimental coupling data reported for single-stranded and duplex DNA fragments and covalent RNA-DNA hybrids on the one hand and the predicted couplings and sums of couplings presented in this paper on the other hand.
本文提出了一种通过质子-质子耦合对DNA片段中糖环进行构象分析的图形方法。该分析所需的耦合数据由耦合总和组成，分别称为σ1'（=J1'2'+J1'2''）、σ2'（=J1'2'+J2'3'+J2'2''）、σ2''（=J1'2''+J2''3'+J2'2''）和σ3'（=J2'3'+J2''3'+J3'4'）。这些耦合总和分别对应于H1'、H2'、H2''和H3'[31P]共振外峰之间的距离（H2'和H2''共振化学位移差异较小时，σ2'和σ2''情况除外），并且通常可通过一级测量从1H-NMR谱中获得，无需对这些共振的精细结构进行计算机辅助模拟。讨论了两种用于解释耦合数据的不同类型的图形：第一种类型的图形用于探究糖环是否以单一构象形式存在，如果是，则根据该糖环的几何结构分析耦合数据。在糖环不是以单一构象形式存在，而是以N型和S型糖环皱折混合形式存在的情况下，第二种类型的图形用于根据最丰富形式的几何结构和丰度分析耦合数据。结果表明，后一种类型的分析可以仅基于σ1'、σ2'和σ2''的实验值进行，而无需对N型和S型构象的几何结构之间的关系做任何假设或限制。此外，还讨论了如何从观察到的H1'共振精细结构中了解糖环的构象纯度问题。最后，一方面比较了单链和双链DNA片段以及共价RNA-DNA杂交体报道的实验耦合数据，另一方面比较了本文给出的预测耦合和耦合总和。
