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.Základní údaje
Originální název
DNA A-tract bending in three dimensions: Solving the dA4T4 vs. dT4A4 conundrum
Název česky
Prostorový ohyb A-traktu DNA: Řešení hlavolamu rozdílu mezi dA4T4 a dT4A4
Autoři
ŠTEFL, Richard (203 Česká republika), Haihong WU (156 Čína), Sapna RAVINDRANATHAN (356 Indie), Vladimír SKLENÁŘ (203 Česká republika, garant, domácí) a Juli FEIGON (840 Spojené státy)
Vydání
Proceedings of the National Academy of Sciences of the U.S.A. 2004, 0027-8424
Další údaje
Jazyk
angličtina
Typ výsledku
Článek v odborném periodiku
Obor
10610 Biophysics
Stát vydavatele
Spojené státy
Utajení
není předmětem státního či obchodního tajemství
Impakt faktor
Impact factor: 10.452
Kód RIV
RIV/00216224:14310/04:00021192
Organizační jednotka
Přírodovědecká fakulta
UT WoS
000188796800016
Klíčová slova anglicky
helical bending; NMR; structure; residual dipolar couplings
Příznaky
Mezinárodní význam
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.
Česky
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.
Návaznosti
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