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Comparative NMR study of A_n-bulge loops in DNA duplexes: intrahelical stacking of A, A-A, and A-A-A bulge loops

Rosen, Mark A. and Live, David and Patel, Dinshaw J. (1992) Comparative NMR study of A_n-bulge loops in DNA duplexes: intrahelical stacking of A, A-A, and A-A-A bulge loops. Biochemistry, 31 (16). pp. 4004-4014. ISSN 0006-2960. doi:10.1021/bi00131a016.

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We have prepared a series of deoxyoligonucleotide duplexes of the sequence d(G-C-A-T-C-G-X-G-C-T-A-C-G)•d(C-G-T-A-G-C-C-G-T-C), in which X represents either one (A), two (A-A), or three (A-A-A) unpaired adenine bases. Using two-dimensional proton and phosphorus NMR spectroscopy, we have characterized conformational features of these bulge-loop duplexes in solution. We find that Watson-Crick hydrogen bonding is intact for all 12 base pairs, including the GC bases that flank the bulge loop. Observation of NOE connectivities in both H_2O and D_2O allows us to unambiguously localize all of the bulged adenine residues to intrahelical positions within the duplex. This is in contrast to an earlier model for multiple-base bulge loops in DNA [Bhattacharyya, A., & Lilley, D. M. J. (1989) Nucleic Acids Res. 17, 6821-68401, in which all but the most 5’ bulged base are looped out into solution. We find that insertion of two or three bases into the duplex results in the disruption of specific sequential NOEs for the base step across from the bulge loop site on the opposite strand. This disruption is characterized by a partial shearing apart of these bases, such that certain sequential NOEs for this base step are preserved. We observe a downfield-shifted phosphorus resonance, which we assign in the A-A-A bulge duplex to the 3‘ side of the last bulged adenine residue. Proton and phosphorus chemical shift trends within the A,-bulge duplex series indicate that there is an additive effect on the structural perturbations caused by additional unpaired bases within the bulge loop. This finding parallels previous observations [Bhattacharyya, A., & Lilley, D. M. J. (1989) Nucleic Acids Res. 17, 6821-6840; Hsieh, C.-H., & Griffith, J. D. (1989) Proc. Nutl. Acud. Sci. U.S.A. 86,4833-48371 on the magnitude of the induced bending of DNA duplexes by multiple-base bulge loops.

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Additional Information:© 1992 American Chemical Society. Published in print 28 April 1992. This research was supported by NIH Grant GM34504 to D.P. M.R. was supported by NIH MSTP Training Grant 5-T32-GM07376. The NMR spectrometers were purchased from funds donated by the Robert Woods Johnson Trust toward setting up an NMR center in the Basic Medical Sciences at Columbia University.
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NIH Predoctoral Fellowship5-T32-GM07376
Robert Woods Johnson TrustUNSPECIFIED
Issue or Number:16
Record Number:CaltechAUTHORS:20180209-131519218
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Official Citation:Comparative NMR study of An-bulge loops in DNA duplexes: intrahelical stacking of A, A-A, and A-A-A bulge loops Mark A. Rosen, David Live, and Dinshaw J. Patel Biochemistry 1992 31 (16), 4004-4014 DOI: 10.1021/bi00131a016
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:84767
Deposited By: Ruth Sustaita
Deposited On:13 Feb 2018 21:48
Last Modified:15 Nov 2021 20:22

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