Proton NMR studies of 5 '-d-(TC)(3) (CT)(3) (AG)(3)-3 ' - A paperclip triplex: The structural relevance of turns

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Title:	Proton NMR studies of 5 '-d-(TC)(3) (CT)(3) (AG)(3)-3 ' - A paperclip triplex: The structural relevance of turns
Authors:	Pasternack L.B.;Lin S.B.;Chin T.M.;Lin W.C.;Huang D.H.;Kan L.S.
Contributors:	化學系
Date:	2002
Issue Date:	2009-12-07 11:26:42 (UTC+8)
Abstract:	In this study, we present the results of structural analysis of an 18-mer DNA 5'-T(1)C(2)T(3)C(4)T(5)C(6)C(7)T(8)C(9)T(10)C(11)T(12)A(13)G(14)A(1)5G(16)A(17)G(18)-3' by proton nuclear magnetic resonance (NMR) spectroscopy and molecular modeling. The NMR data are consistent with characteristics for triple helical structures of DNA: downfield shifting of resonance signals, typical for the H3(+) resonances of Hoogsteen-paired cytosines; pH dependence of these H3(+) resonance; and observed nuclear Overhauser effects consistent with Hoogsteen and Watson-Crick basepairing. A three-dimensional model for the triplex is developed based on data obtained from two-dimensional NMR studies and molecular modeling. We find that this DNA forms an intramolecular "paperclip" pyrimidine-purine-pyrimidine triple helix. The central triads resemble typical Hoogsteen and Watson-Crick basepairing. The triads at each end region can be viewed as hairpin turns stabilized by a third base. One of these turns is comprised of a hairpin turn in the Watson-Crick basepairing portion of the 18-mer with the third base coming from the Hoogsteen pairing strand. The other turn is comprised of two bases from the continuous pyrimidine portion of the 18-mer, stabilized by a hydrogen-bond from a purine. This "triad" has well defined structure as indicated by the number of nuclear Overhauser effects and is shown to play a critical role in stabilizing triplex formation of the internal triads.
Relation:	BIOPHYSICAL JOURNAL Volume: 82 Issue: 6 Pages: 3170-3180
Appears in Collections:	[Department of Chemistry & Graduate Institute of Applied Chemistry ] journal articles

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