Two-dimensional 1H and 31P NMR spectra and restrained molecular dynamics structure of a mismatched GA decamer oligodeoxyribonucleotide duplex.
Two-dimensional 1H and 31P NMR spectra and restrained molecular dynamics structure of a mismatched GA decamer oligodeoxyribonucleotide duplex.
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错配 GA 十聚体寡脱氧核糖核苷酸双链体的二维 1H 和 31P NMR 谱和受限分子动力学结构。
DOI：
10.1021/bi00489a048
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发表时间：
1990
期刊：
影响因子：
2.9
通讯作者：
Gorenstein,DG
中科院分区：
文献类型：
--
作者：
Nikonowicz,EP;Gorenstein,DG
Department of Chemistry, Purdue University, West Lafayette, Indiana 47907 Received March 29, 1990; Revised Manuscript Received June 12, 1990 abstract: Assignment of the and 31P NMR spectra of a tandem GA mismatched base pair decamer oligodeoxyribonucleotide duplex, d (CCAAGvlTTGG) 2, has been madeby two-dimensional- and heteronuclear 31P-'H correlated spectroscopy. Unusual downfield 31P resonances have been assigned by a pure absorption phase constant-time heteronuclear 31P-'H correlated spectrum to be associated with the phosphates on the 5'-and 3'-sides of the mismatched guanosine residue./H3-_P coupling constants for each of the phosphates of the decamer were obtained from the* H-31P/-resolved selective proton-flip 2D spectrum. The two most downfield-shifted 31P resonances each appear to consist of two overlapping signals that can be resolved into two distinct doublets with different coupling constants in the/-resolved spectrum. This as well as the temperature dependence of the 31P spectra demonstrates that two distinct conformationsexist at lower temperatures. By use of a modified Karplus relationship, the C4,-C3'-03'-P torsional angles (e) were obtained. A linear correlation between 31P chemical shifts and the measured coupling constants is quite good (only when the larger set of coupling constants of the two mostdownfield 31P signals is included). The 3, P chemical shifts as well as the measured coupling constants tend to follow the positionalvariation seen in other duplexes of interior phosphates resonating more upfield than terminal residues and of interior phosphates exhibiting smaller coupling constants; however, this pattern is disrupted at the site of the mismatch. Modeling and initial NOESY distance restrained molecular mechanics energy minimization and restrained molecular dynamics support previous observations that the mismatched guanine and adenine bases are both in anti conformations. Most significantly, the e backbone torsional angle variaions calculatedfrom the NOESY distance restrained structures are in agreement with both the crystal structurevalues and the measured/H3/_P coupling constants. e formation of base pair mismatches in DNA and the associated problems during replication, transcription, and gene activation if left unrepaired are current topics of concern (Modrich, 1987; Radman & Wagner, 1986). Their recog-nition and efficiencies of repair have been studied in bacteria (Fazakerley et al., 1986; Lu et al., 1984; Radman & Wagner, 1984), the latter having been found to besequence dependent. Both X-ray crystallography and NMR spectroscopy have been used to probe the structural anomalies of mismatched base pairs (Brown et al., 1986; Dodgson & Wells, 1977a, b; Hare et al., 1986a; Kan et al., 1983; Kouchakdjian et al., 1988; Patel et al., 1984a, b; Prive et al., 1987). One of the first nonstandard types of base pairs to be structurally investigated in solution was the naturally occurring purine-pyrimidine base pair GU
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DOI：
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