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Structure of the DNA duplex d(ATTAAT)2 with Hoogsteen hydrogen bonds.

ABSTRACT: The traditional Watson-Crick base pairs in DNA may occasionally adopt a Hoogsteen conformation, with a different organization of hydrogen bonds. Previous crystal structures have shown that the Hoogsteen conformation is favored in alternating AT sequences of DNA. Here we present new data for a different sequence, d(ATTAAT)2, which is also found in the Hoogsteen conformation. Thus we demonstrate that other all-AT sequences of DNA with a different sequence may be found in the Hoogsteen conformation. We conclude that any all-AT sequence might acquire this conformation under appropriate conditions. We also compare the detailed features of DNA in either the Hoogsteen or Watson-Crick conformations.

SUBMITTER: Acosta-Reyes FJ

PROVIDER: S-EPMC4363561 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

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Structure of the DNA duplex d(ATTAAT)2 with Hoogsteen hydrogen bonds.

Acosta-Reyes Francisco J FJ Alechaga Elida E Subirana Juan A JA Campos J Lourdes JL

PloS one 20150317 3

The traditional Watson-Crick base pairs in DNA may occasionally adopt a Hoogsteen conformation, with a different organization of hydrogen bonds. Previous crystal structures have shown that the Hoogsteen conformation is favored in alternating AT sequences of DNA. Here we present new data for a different sequence, d(ATTAAT)2, which is also found in the Hoogsteen conformation. Thus we demonstrate that other all-AT sequences of DNA with a different sequence may be found in the Hoogsteen conformation ...[more]

PMID: 25781995

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Project description:The exocyclic 1, N(2)-ethenodeoxyguanosine (1,N(2)-is an element of dG) adduct, arising from the reaction of vinyl halides and other vinyl monomers, including chloroacetaldehyde, and lipid peroxidation products with dG, was examined at pH 5.2 in the oligodeoxynucleotide duplex 5'-d(CGCATXGAATCC)-3'.5'-d(GGATTCCATGCG)-3' (X = 1,N(2)-is an element of dG). Previously, X(anti).C(anti) pairing was established in this duplex, containing the 5'-TXG-3' sequence context, at pH 8.6 [Shanmugam, G., Goodenough, A. K., Kozekov, I. D., Harris, T. M., Guengerich, F. P., Rizzo, C. J., and Stone, M. P. (2007) Chem. Res. Toxicol. 20, 1601- 1611]. At pH 5.2, the 1,N(2)-is an element of dG adduct decreased the thermal stability of the duplex by approximately 13 degrees C. The 1,N(2)-is an element of dG adduct rotated about the glycosyl bond from the anti to the syn conformation. This resulted in the observation of a strong nuclear Overhauser effect (NOE) between the imidazole proton of 1,N(2)-is an element of dG and the anomeric proton of the attached deoxyribose, accompanied by an NOE to the minor groove A(20) H2 proton from the complementary strand. The syn conformation of the glycosyl bond at 1,N(2)-is an element of dG placed the exocyclic etheno moiety into the major groove. This resulted in the observation of NOEs between the etheno protons and the major groove protons of the 5'-neighboring thymine. The 1,N(2)-is an element of dG adduct formed a Hoogsteen pair with the complementary cytosine, characterized by downfield shifts of the amino protons of the cytosine complementary to the exocyclic adduct. The pattern of chemical shift perturbations indicated that the lesion introduced a localized structural perturbation involving the modified base pair and its 3'- and 5'-neighbor base pairs. A second conformational equilibrium was observed, in which both the modified base pair and its 3'-neighboring G.C base pair formed tandem Hoogsteen pairs. The results support the conclusion that at neutral pH, in the 5'-TXG-3' sequence, the 1,N(2)-is an element of dG adduct exists as a blend of conformations in duplex DNA. These involve the interconversion of the glycosyl torsion angle between the anti and the syn conformations, occurring at an intermediate rate on the NMR time scale.

Dataset Information

Structure of the DNA duplex d(ATTAAT)2 with Hoogsteen hydrogen bonds.

Publications

Structure of the DNA duplex d(ATTAAT)2 with Hoogsteen hydrogen bonds.

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