Structural studies of symmetric DNA undecamers containing non-symmetrical sheared (PuGAPu):(PyGAPy) motifs

被引:14
作者
Chou, SH [1 ]
Tseng, YY
Chen, YR
Cheng, JW
机构
[1] Natl Chung Hsing Univ, Inst Biochem, Taichung 402, Taiwan
[2] Natl Chung Hsing Univ, Dept Chem, Taichung 402, Taiwan
[3] Natl Tsing Hua Univ, Dept Life Sci, Div Struct Biol & Biomed Sci, Hsinchu 300, Taiwan
关键词
NMR structures; (PuGAPu)/(PyGAPy); (PyGAPu)2; sheared G center dot A pair; unusual DNA;
D O I
10.1023/A:1008351213029
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Interstrand purine-purine stacks originate from tandem sheared purine.purine pairing and represent one of the most important motifs in both DNA and RNA structures. Several RNA and DNA structures, solved recently in both solution and the solid state, contain these special motifs, which greatly increase the structural diversity of nucleic acid molecules. The direct evidence for the sheared purine-purine pairing at neutral pH in solution remains, however, elusive. In this manuscript, we have used high resolution NMR methods to study a series of symmetrical DNA duplexes containing two non-symmetrical 5'-(PuGAPu)/(PyGAPy)-3' motifs. Many strong- and medium-strength NOEs across the G . A base pair were detected in the H2O-NOESY spectra collected at a relatively low temperature (-5 degrees C ). These NOEs, especially those from A-(NH2)-N-6 to G-H1', G-H4', and G-(NH2)-N-2, clearly define the proposed side-by-side sheared G.A pairing nature. Another interesting feature is the strong NOEs exhibited by the unpaired G-imino proton in the G.A pair to its own G-(NH2)-N-2, which implies that G-(NH2)-N-2 is involved in H-bonding with a base in the minor groove edge. The finding that non-symmetrical (PuGAPu):(PyGAPy) motif also form similarly stable structures loosens the requirement for a more restricted (PyGAPu)(2) motif in forming the interstrand purine-purine stacks.
引用
收藏
页码:157 / 167
页数:11
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