DNA and RNA: NMR studies of conformations and dynamics in solution

Patel, Dinshaw J.; Shapiro, Lawrence; Hare, Dennis R.

doi:10.1017/s0033583500004224

Cited by 183 publications

(169 citation statements)

References 194 publications

Supporting

Mentioning

167

Contrasting

Order By: Relevance

“…Resonance Assignments a) Non-exchangeable DNA Protons-The sequential assignment for the 1,N 2 -εdG duplex was accomplished using standard protocols (40,41). An expanded plot of 1 H NOE sequential connectivities between the base protons (7.0-8.6 ppm) and the sugar H1′ and dC H5 protons (5.0-6.4 ppm) is plotted in Figure 1.…”

Section: Characterization Of the Modified Duplexmentioning

confidence: 99%

“…However, the spectrum of PdG opposite dC in duplex DNA sharpens considerably as pH is lowered (44). Likewise, when PdG is mismatched with dA in duplex DNA an ordered structure is stabilized at pH 5.8 (40,41). On the other hand, when PdG is mismatched with dG, an ordered structure is formed which is independent of pH (40).…”

Section: Structural Comparison To the 1n 2 -Propano-2′-deoxyguanosinmentioning

confidence: 99%

See 1 more Smart Citation

Structure of the 1,N²-Etheno-2′-Deoxyguanosine Adduct in Duplex DNA at pH 8.6

Shanmugam

Goodenough

Kozekov

et al. 2007

Chem. Res. Toxicol.

View full text Add to dashboard Cite

The structure of the 1,N 2 -εdG adduct, arising from the reaction of vinyl chloride with dG, was determined in the oligonucleotide duplex 5′-d(CGCATXGAATCC)-3′•5′-d(GGATTCCATGCG)-3′ (X=1,N 2 -εdG) at pH 8.6 using high resolution NMR spectroscopy. The exocyclic lesion prevented Watson-Crick base-pairing capability at the adduct site and resulted in an ~17 °C of the C decrease in T m oligodeoxynucleotide duplex. At neutral pH, conformational exchange resulted in spectral line broadening near the adducted site, and it was not possible to determine the structure. However, at pH 8.6, it was possible to obtain well-resolved 1 H NMR spectra. This enabled a total of 385 NOE based distance restraints to be obtained, consisting of 245 intra-and 140 inter-nucleotide distances. The 31 P NMR spectra exhibited two downfield-shifted resonances, suggesting a localized perturbation of the DNA backbone. The two downfield 31 P resonances were assigned to G 7 and C 19 . The solution structure was refined by molecular dynamics calculations restrained by NMR derived distance and dihedral angle restraints, using a simulated annealing protocol. The generalized Born approximation was used to simulate solvent. The emergent structures indicated that the 1,N 2 -εdG-induced structural perturbation was localized at the X 6 •C 19 base pair, and its 5′-neighbor T 5 •A 20 . Both 1,N 2 -εdG and the complementary dC adopted the anti conformation about the glycosyl bonds. The 1,N 2 -εdG adduct was inserted into the duplex but was shifted towards the minor groove as compared to dG in a normal Watson-Crick C•G base pair. The complementary cytosine was displaced toward the major groove. The 5′-neighbor T 5 •A 20 base pair was destabilized with respect to Watson-Crick base pairing. The refined structure predicted a bend in the helical axis associated with the adduct site.

show abstract

Section: Characterization Of the Modified Duplexmentioning

confidence: 99%

Section: Structural Comparison To the 1n 2 -Propano-2′-deoxyguanosinmentioning

confidence: 99%

Structure of the 1,N²-Etheno-2′-Deoxyguanosine Adduct in Duplex DNA at pH 8.6

Shanmugam

Goodenough

Kozekov

et al. 2007

Chem. Res. Toxicol.

View full text Add to dashboard Cite

show abstract

“…The imino and amino protons have been assigned as described elsewhere. 34,35 The NOE patterns between different imino protons are identified in (a) and are labeled A to H, and (b) identifies NOEs between imino protons (10.5-14.0 ppm) and amino and non-exchangeable protons (3.5 ppm to 8.5 ppm). The NOE cross-peaks between DNA protons are labeled A to F, and NOE cross-peaks between aromatic BP protons and DNA protons are labeled 1-11.…”

Section: Exchangeable Proton Spectramentioning

confidence: 99%

Methylation of Cytosine at C5 in a CpG Sequence Context Causes a Conformational Switch of a Benzo[a]pyrene diol epoxide-N2-guanine Adduct in DNA from a Minor Groove Alignment to Intercalation with Base Displacement

Zhang

Lin

Huang

et al. 2005

Journal of Molecular Biology

Self Cite

View full text Add to dashboard Cite

It is well known that CpG dinucleotide steps in DNA, which are highly methylated at the 5-position of cytosine (meC) in human tissues, exhibit a disproportionate number of mutations within certain codons of the p53 gene. There is ample published evidence indicating that the reactivity of guanine with anti-B[a]PDE (a metabolite of the environmental carcinogen benzo[a]pyrene) at CpG mutation hot spots is enhanced by the methylation of the cytosine residue flanking the target guanine residue on the 5′-side. In this work we demonstrate that such a methylation can also dramatically affect the conformational characteristics of an adduct derived HHS Public Access

show abstract

“…We have constructed a second canonical coordinate, can2, which maximally separates the two clusters. can2 = -0.0605(δ C2′ + δ C3′ ) -0.0556 δ C4′ -0.0524 δ C5′ [4] This coordinate, it should be noted, is considerably different from that which we gave in our preliminary report (21). While the largest average difference in chemical shifts is at the C5′ position, the C5′ chemical shift also has considerable scatter within each group, and the average (C2′ + C3′) shift is actually a better discriminant than that of C5′.…”

Section: Exocyclic Torsion Anglementioning

confidence: 99%

“…Thus, the observed chemical shifts observed in the solid state correspond to specific sugar ring conformations, rather than to average values over the many conformations which exist in rapid equilibrium in solution (2). One approach to determining oligonucleotide and RNA structure in solution has been to measure the steadystate or transient nuclear overhauser enhancement between adjacent protons, either by one-dimensional (3) or two-dimensional methods (4). Such measurements are still the workhorses of most structural determinations.…”

Section: Introductionmentioning

confidence: 99%

Dependence of 13C NMR Chemical Shifts on Conformations of RNA Nucleosides and Nucleotides

Ebrahimi

Rossi

Rogers

et al. 2001

Journal of Magnetic Resonance

View full text Add to dashboard Cite

Cross-polarization magic-angle spinning solid-state NMR spectroscopy has been used to investigate the dependence of 13 C sugar chemical shifts on specific conformational parameters of a variety of ribonucleotides and ribonucleosides. Solid-state NMR is a valuable tool for nucleoside and nucleotide structural studies since it provides the means to acquire spectra that correspond to single conformations, as opposed to 13 C solutionNMRmethods. The distinct effects of sugar puckering on the C1′, C4′, and C5′ resonances of C2′ endo (S type) and C3′ endo (N type) furanoid conformations allow us to separate them into two groups. Further analysis of each group reveals an additional dependence of the C1′ and C5′ resonances on the glycosidic and C4′-C5′ exocyclic torsion angles, respectively. However, it is found that the glycosidic conformation cannot independently be determined from sugar 13 C chemical shift data. The statistical methods of exploratory data analysis and discriminant analysis are used to construct two canonical coordinates-linear combinations of chemical shifts which give the statistically optimal determination of the conformation from the NMR data.

show abstract

DNA and RNA: NMR studies of conformations and dynamics in solution

Cited by 183 publications

References 194 publications

Structure of the 1,N²-Etheno-2′-Deoxyguanosine Adduct in Duplex DNA at pH 8.6

Structure of the 1,N²-Etheno-2′-Deoxyguanosine Adduct in Duplex DNA at pH 8.6

Methylation of Cytosine at C5 in a CpG Sequence Context Causes a Conformational Switch of a Benzo[a]pyrene diol epoxide-N2-guanine Adduct in DNA from a Minor Groove Alignment to Intercalation with Base Displacement

Dependence of 13C NMR Chemical Shifts on Conformations of RNA Nucleosides and Nucleotides

Contact Info

Product

Resources

About

DNA and RNA: NMR studies of conformations and dynamics in solution

Cited by 183 publications

References 194 publications

Structure of the 1,N2-Etheno-2′-Deoxyguanosine Adduct in Duplex DNA at pH 8.6

Structure of the 1,N2-Etheno-2′-Deoxyguanosine Adduct in Duplex DNA at pH 8.6

Methylation of Cytosine at C5 in a CpG Sequence Context Causes a Conformational Switch of a Benzo[a]pyrene diol epoxide-N2-guanine Adduct in DNA from a Minor Groove Alignment to Intercalation with Base Displacement

Dependence of 13C NMR Chemical Shifts on Conformations of RNA Nucleosides and Nucleotides

Contact Info

Product

Resources

About

Structure of the 1,N²-Etheno-2′-Deoxyguanosine Adduct in Duplex DNA at pH 8.6

Structure of the 1,N²-Etheno-2′-Deoxyguanosine Adduct in Duplex DNA at pH 8.6