NMR studies of DNA single strands and DNA:RNA hybrids with and without 1-propynylation at C5 of oligopyrimidines

Journal of the American Chemical Society
Brent M ZnoskoDouglas H Turner

Abstract

The 1-propynylation at C5 of consecutive pyrimidines in DNA can enhance DNA:RNA hybrid stability at 37 degrees C by over 1 kcal/mol of substitution [Barnes, T. W., III; Turner, D. H. J. Am. Chem. Soc.2001, 123, 4107-4118]. To provide information on the structural consequences of propynylation, two-dimensional NMR spectroscopy was used to study the structures of several oligonucleotides. Intraresidue nuclear Overhauser effect spectroscopy cross peaks were observed at 30 degrees C and a 200 ms mixing time in the H6-H1' region for 5'(dC(P)C(P)U(P)C(P)C(P)U(P)U(P)) (ssPrODN) but not for 5'(dCCUCCUU) (ssODN), suggesting preorganization of the propynylated single strand. NMR structures of the duplexes 5'(dC(P)C(P)U(P)C(P)C(P)U(P)U(P))3':3'(rGAGGAGGAAAU)5' (PrODN:RNA), 5'(dCC(P)U(P)C(P)C(P)U(P)U(P))3':3'(rGAGGAGGAAAU)5' (sPrODN1:RNA), and 5'(dCCUCCUU)3':3'(rGAGGAGGAAAU)5' (ODN:RNA) indicate that their global structures are almost identical. The NMR data, however, suggest that the 5'-end of sPrODN1:RNA is more dynamic than that of PrODN:RNA. In the propynylated duplexes, the propyne group stacks on the aromatic ring of the 5'-base and extends into the major groove. The results suggest that the increased stability of the propynylated du...Continue Reading

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Citations

Jan 17, 2008·The Journal of Physical Chemistry. B·U Deva Priyakumar, Alexander D Mackerell
Aug 25, 2011·Chemical Communications : Chem Comm·Cora Prestinari, Clemens Richert
Dec 30, 2014·PloS One·Daniela AschenbrennerHermann E Gaub
Jun 15, 2007·Bioorganic & Medicinal Chemistry·Chrissy E PraterPaul S Miller
Mar 6, 2007·Bioorganic & Medicinal Chemistry·Srinivasarao MeneniRoman Dembinski
Feb 17, 2018·Chemistry : a European Journal·Nilesh R Kamble, Snorri Th Sigurdsson
Sep 18, 2007·Chemistry : a European Journal·Johannes GierlichThomas Carell
Oct 8, 2009·Chembiochem : a European Journal of Chemical Biology·Michael E ØstergaardPatrick J Hrdlicka
Dec 2, 2017·Microscopy Research and Technique·Alexandre LoukanovSeiichiro Nakabayashi
Nov 17, 2007·Journal of the American Chemical Society·Leslie-Anne FendtEugen Stulz
Oct 27, 2005·Journal of the American Chemical Society·Stefan JägerMichael Famulok

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