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Title: Base pair mismatches and carcinogen-modified bases in DNA: An NMR study of G·T and G·O4meT pairing in dodecanucleotide duplexes
Authors: Kalnik, M.W.
Kouchakdjian, M.
Li, B.F.L. 
Swann, P.F.
Patel, D.J.
Issue Date: 1988
Citation: Kalnik, M.W.,Kouchakdjian, M.,Li, B.F.L.,Swann, P.F.,Patel, D.J. (1988). Base pair mismatches and carcinogen-modified bases in DNA: An NMR study of G·T and G·O4meT pairing in dodecanucleotide duplexes. Biochemistry 27 (1) : 108-115. ScholarBank@NUS Repository.
Abstract: High-resolution two-dimensional NMR studies have been completed on the self-complementary d(C-G-C-G-A-G-C-T-T-G-C-G) duplex (designated G·T 12-mer) and the self-complementary d(C-G-C-G-A-G-C-T-O4meT-G-C-G) duplex (designated G·O4meT 12-mer) containing G·T and G·O4meT pairs at identical positions four base pairs in from either end of the duplex. The exchangeable and nonexchangeable proton resonances have been assigned from an analysis of two-dimensional nuclear Overhauser enhancement (NOESY) spectra for the G·T 12-mer and G·O4meT 12-mer duplexes in H2O and D2O solution. The guanosine and thymidine imino protons in the G·T mismatch resonate at 10.57 and 11.98 ppm, respectively, and exhibit a strong NOE between themselves and to imino protons of flanking base pairs in the G·T 12-mer duplex. These results are consistent with wobble pairing at the G·T mismatch site involving two imino proton-carbonyl hydrogen bonds as reported previously [Hare, D. R., Shapiro, L., & Patel, D. J. (1986) Biochemistry 25, 7445-7456]. In contrast, the guanosine imino proton in the G·O4meT pair resonates at 8.67 ppm. The large upfield chemical shift of this proton relative to that of the imino proton resonance of G in the G·T mismatch or in G·C base pairs indicates that hydrogen bonding to O4meT is either very weak or absent. This guanosine imino proton has an NOE to the OCH3 group of O4meT across the pair and NOEs to the imino protons of flanking base pairs. Taken together with data from the NMR of nonexchangeable protons, this shows that both G and O4meT have anti-glycosidic torsion angles and are stacked into the duplex. Comparison of the intensity of the NOEs between the guanosine imino proton and the OCH3 of O4meT as well as other protons in its vicinity demonstrates that the OCH3 group of O4meT adopts the syn orientation with respect to N3 of the methylated thymidine. This rules out both the wobble pairing and the postulated structure in which the imino proton of G is hydrogen bonded to N3 of O4meT for the G·O4meT pair. We propose an alternate base pairing mode stabilized by one short hydrogen bond between the 2-amino group of guanosine and the 2-carbonyl group of O4meT. © 1988 American Chemical Society.
Source Title: Biochemistry
ISSN: 00062960
Appears in Collections:Staff Publications

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