Detailed Information on Publication Record
2004
DNA A-tract bending in three dimensions: Solving the dA4T4 vs. dT4A4 conundrum
ŠTEFL, Richard, Haihong WU, Sapna RAVINDRANATHAN, Vladimír SKLENÁŘ, Juli FEIGON et. al.Basic information
Original name
DNA A-tract bending in three dimensions: Solving the dA4T4 vs. dT4A4 conundrum
Name in Czech
Prostorový ohyb A-traktu DNA: Řešení hlavolamu rozdílu mezi dA4T4 a dT4A4
Authors
ŠTEFL, Richard (203 Czech Republic), Haihong WU (156 China), Sapna RAVINDRANATHAN (356 India), Vladimír SKLENÁŘ (203 Czech Republic, guarantor, belonging to the institution) and Juli FEIGON (840 United States of America)
Edition
Proceedings of the National Academy of Sciences of the U.S.A. 2004, 0027-8424
Other information
Language
English
Type of outcome
Článek v odborném periodiku
Field of Study
10610 Biophysics
Country of publisher
United States of America
Confidentiality degree
není předmětem státního či obchodního tajemství
Impact factor
Impact factor: 10.452
RIV identification code
RIV/00216224:14310/04:00021192
Organization unit
Faculty of Science
UT WoS
000188796800016
Keywords in English
helical bending; NMR; structure; residual dipolar couplings
Tags
International impact
Změněno: 21/4/2011 10:16, prof. RNDr. Vladimír Sklenář, DrSc.
V originále
DNA A-tracts have been defined as four or more consecutive A-T base pairs without a TpA step. When inserted in phase with the DNA helical repeat, bending is manifested macroscopically as anomalous migration on polyacrylamide gels, first observed >20 years ago. An unsolved conundrum is why DNA containing in-phase A-tract repeats of A4T4 are bent, whereas T4A4 is straight. We have determined the solution structures of the DNA duplexes formed by d(GCAAAATTTTGC) [A4T4] and d(CGTTTTAAAACG) [T4A4] with counterions by using NMR spectroscopy, including refinement with residual dipolar couplings. Analysis of the structures shows that the ApT step has a large negative roll, resulting in a local bend toward the minor groove, whereas the TpA step has a positive roll and locally bends toward the major groove. For A4T4, this bend is nearly in phase with bends at the two A-tract junctions, resulting in an overall bend toward the minor groove of the A-tract, whereas for T4A4, the bends oppose each other, resulting in a relatively straight helix. NMR-based structural modeling of d(CAAAATTTTG)15 and d(GTTTTAAAAC)15 reveals that the former forms a left-handed superhelix with a diameter of 110 A and pitch of 80 A, similar to DNA in the nucleosome, whereas the latter has a gentle writhe with a pitch of >250 A and diameter of 50 A. Results of gel electrophoretic mobility studies are consistent with the higher-order structure of the DNA and furthermore depend on the nature of the monovalent cation present in the running buffer.
In Czech
DNA A-tracts have been defined as four or more consecutive A-T base pairs without a TpA step. When inserted in phase with the DNA helical repeat, bending is manifested macroscopically as anomalous migration on polyacrylamide gels, first observed >20 years ago. An unsolved conundrum is why DNA containing in-phase A-tract repeats of A4T4 are bent, whereas T4A4 is straight. We have determined the solution structures of the DNA duplexes formed by d(GCAAAATTTTGC) [A4T4] and d(CGTTTTAAAACG) [T4A4] with counterions by using NMR spectroscopy, including refinement with residual dipolar couplings. Analysis of the structures shows that the ApT step has a large negative roll, resulting in a local bend toward the minor groove, whereas the TpA step has a positive roll and locally bends toward the major groove. For A4T4, this bend is nearly in phase with bends at the two A-tract junctions, resulting in an overall bend toward the minor groove of the A-tract, whereas for T4A4, the bends oppose each other, resulting in a relatively straight helix. NMR-based structural modeling of d(CAAAATTTTG)15 and d(GTTTTAAAAC)15 reveals that the former forms a left-handed superhelix with a diameter of 110 A and pitch of 80 A, similar to DNA in the nucleosome, whereas the latter has a gentle writhe with a pitch of >250 A and diameter of 50 A. Results of gel electrophoretic mobility studies are consistent with the higher-order structure of the DNA and furthermore depend on the nature of the monovalent cation present in the running buffer.
Links
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