Journal
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
Volume 125, Issue 20, Pages 6090-6097Publisher
AMER CHEMICAL SOC
DOI: 10.1021/ja021285d
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Funding
- NIDCR NIH HHS [DE07202-10] Funding Source: Medline
- NIGMS NIH HHS [GM 22939, GM 53826] Funding Source: Medline
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The 1-propynylation at C5 of consecutive pyrimidines in DNA can enhance DNA:RNA hybrid stability at 37 degreesC by over 1 kcal/mol of substitution [Barnes, T. W., 111; 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 degreesC 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 NIVIR 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 duplexes is caused by preorganization of the propynylated single strand and different interactions in the double strand. The propynyl group provides volume exclusion, enhanced stacking, and possibly different solvation.
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