An NMR structural study of deaminated base pairs in DNA

Claire Carbonnaux, G. Victor Fazakerley, Lawrence Sowers

Research output: Contribution to journalArticle

50 Citations (Scopus)

Abstract

The structurally aberrant base pairs TG, UG and TI may occur in DNA as a consequence of deamination of 5-methylcytosine, cytosine and adenine respectively. Results of NMR spectroscopic studies are reported here for these deaminated base pairs in a model seven base pair long oligonucleotide duplex. We find that in all three cases, the DNA helix is a normal B form and both mispaired bases are intrahelical and hydrogen bonded with one another in a wobble geometry. Similarly, in all three cases, all sugars are found to be normal C2′ endo in conformation. Symmetric structural perturbations are observed in the helix twist on the 3′ side of the mispaired pyrimidine and on the 5′ side of the mispaired purine. In all three cases, the amino group of the G residue on the 3′ side of the mispaired pyrimidine shows hindered rotation. Although less thermodynamically stable than helices containing only Watson-Crick base pairs, these helices melt normally from the ends and not from the mispair outwards.

Original languageEnglish (US)
Pages (from-to)4075-4081
Number of pages7
JournalNucleic Acids Research
Volume18
Issue number14
StatePublished - Jul 25 1990
Externally publishedYes

Fingerprint

Helix
Base Pairing
DNA
Nuclear magnetic resonance
5-Methylcytosine
Oligonucleotides
Cytosine
Adenine
Sugars
Conformations
Hydrogen
Deamination
Geometry
Conformation
Twist
Perturbation
pyrimidine
purine
Model

ASJC Scopus subject areas

  • Genetics
  • Statistics, Probability and Uncertainty
  • Applied Mathematics
  • Health, Toxicology and Mutagenesis
  • Toxicology
  • Genetics(clinical)

Cite this

Carbonnaux, C., Fazakerley, G. V., & Sowers, L. (1990). An NMR structural study of deaminated base pairs in DNA. Nucleic Acids Research, 18(14), 4075-4081.

An NMR structural study of deaminated base pairs in DNA. / Carbonnaux, Claire; Fazakerley, G. Victor; Sowers, Lawrence.

In: Nucleic Acids Research, Vol. 18, No. 14, 25.07.1990, p. 4075-4081.

Research output: Contribution to journalArticle

Carbonnaux, C, Fazakerley, GV & Sowers, L 1990, 'An NMR structural study of deaminated base pairs in DNA', Nucleic Acids Research, vol. 18, no. 14, pp. 4075-4081.
Carbonnaux C, Fazakerley GV, Sowers L. An NMR structural study of deaminated base pairs in DNA. Nucleic Acids Research. 1990 Jul 25;18(14):4075-4081.
Carbonnaux, Claire ; Fazakerley, G. Victor ; Sowers, Lawrence. / An NMR structural study of deaminated base pairs in DNA. In: Nucleic Acids Research. 1990 ; Vol. 18, No. 14. pp. 4075-4081.
@article{66c5ef3bb9d7453b91c6d5b6030be06e,
title = "An NMR structural study of deaminated base pairs in DNA",
abstract = "The structurally aberrant base pairs TG, UG and TI may occur in DNA as a consequence of deamination of 5-methylcytosine, cytosine and adenine respectively. Results of NMR spectroscopic studies are reported here for these deaminated base pairs in a model seven base pair long oligonucleotide duplex. We find that in all three cases, the DNA helix is a normal B form and both mispaired bases are intrahelical and hydrogen bonded with one another in a wobble geometry. Similarly, in all three cases, all sugars are found to be normal C2′ endo in conformation. Symmetric structural perturbations are observed in the helix twist on the 3′ side of the mispaired pyrimidine and on the 5′ side of the mispaired purine. In all three cases, the amino group of the G residue on the 3′ side of the mispaired pyrimidine shows hindered rotation. Although less thermodynamically stable than helices containing only Watson-Crick base pairs, these helices melt normally from the ends and not from the mispair outwards.",
author = "Claire Carbonnaux and Fazakerley, {G. Victor} and Lawrence Sowers",
year = "1990",
month = "7",
day = "25",
language = "English (US)",
volume = "18",
pages = "4075--4081",
journal = "Nucleic Acids Research",
issn = "0305-1048",
publisher = "Oxford University Press",
number = "14",

}

TY - JOUR

T1 - An NMR structural study of deaminated base pairs in DNA

AU - Carbonnaux, Claire

AU - Fazakerley, G. Victor

AU - Sowers, Lawrence

PY - 1990/7/25

Y1 - 1990/7/25

N2 - The structurally aberrant base pairs TG, UG and TI may occur in DNA as a consequence of deamination of 5-methylcytosine, cytosine and adenine respectively. Results of NMR spectroscopic studies are reported here for these deaminated base pairs in a model seven base pair long oligonucleotide duplex. We find that in all three cases, the DNA helix is a normal B form and both mispaired bases are intrahelical and hydrogen bonded with one another in a wobble geometry. Similarly, in all three cases, all sugars are found to be normal C2′ endo in conformation. Symmetric structural perturbations are observed in the helix twist on the 3′ side of the mispaired pyrimidine and on the 5′ side of the mispaired purine. In all three cases, the amino group of the G residue on the 3′ side of the mispaired pyrimidine shows hindered rotation. Although less thermodynamically stable than helices containing only Watson-Crick base pairs, these helices melt normally from the ends and not from the mispair outwards.

AB - The structurally aberrant base pairs TG, UG and TI may occur in DNA as a consequence of deamination of 5-methylcytosine, cytosine and adenine respectively. Results of NMR spectroscopic studies are reported here for these deaminated base pairs in a model seven base pair long oligonucleotide duplex. We find that in all three cases, the DNA helix is a normal B form and both mispaired bases are intrahelical and hydrogen bonded with one another in a wobble geometry. Similarly, in all three cases, all sugars are found to be normal C2′ endo in conformation. Symmetric structural perturbations are observed in the helix twist on the 3′ side of the mispaired pyrimidine and on the 5′ side of the mispaired purine. In all three cases, the amino group of the G residue on the 3′ side of the mispaired pyrimidine shows hindered rotation. Although less thermodynamically stable than helices containing only Watson-Crick base pairs, these helices melt normally from the ends and not from the mispair outwards.

UR - http://www.scopus.com/inward/record.url?scp=0025346185&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0025346185&partnerID=8YFLogxK

M3 - Article

C2 - 2377453

AN - SCOPUS:0025346185

VL - 18

SP - 4075

EP - 4081

JO - Nucleic Acids Research

JF - Nucleic Acids Research

SN - 0305-1048

IS - 14

ER -