ArticleProceedings of the National Academy of Sciences of the United States of America2004
DNA A-tract bending in three dimensions: solving the dA4T4 vs. dT4A4 conundrum.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 82 papers.
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Who cites it
82 citing papers in PubMed.
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- New Insights into the Phototoxicity of Anthracene-Based Chromophores: The Chloride Salt Effect†.Chemical research in toxicology · 2023Article
- Deep statistical modelling of nanopore sequencing translocation times reveals latent non-B DNA structures.Bioinformatics (Oxford, England) · 2023Article
- Bisulfite probing reveals DNA structural intricacies.Nucleic acids research · 2023Article
- DeepBend: An interpretable model of DNA bendability.iScience · 2023Article
- Manipulation of topoisomerase expression inhibits cell division but not growth and reveals a distinctive promoter structure in Synechocystis.Nucleic acids research · 2022Article
- Deciphering the mechanical code of the genome and epigenome.Nature structural & molecular biology · 2022Article
- Predicting accurate ab initio DNA electron densities with equivariant neural networks.Biophysical journal · 2022Article
- An integrated model for termination of RNA polymerase III transcription.Science advances · 2022Article
- Development of Force Field Parameters for the Simulation of Single- and Double-Stranded DNA Molecules and DNA-Protein Complexes.The journal of physical chemistry. B · 2022Article
- Revisiting DNA Sequence-Dependent Deformability in High-Resolution Structures: Effects of Flanking Base Pairs on Dinucleotide Morphology and Global Chain Configuration.Life (Basel, Switzerland) · 2022Article
- Structural dissection of sequence recognition and catalytic mechanism of human LINE-1 endonuclease.Nucleic acids research · 2021Article
22 more citing papers are in PubMed but not listed here.
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5 authors.
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Abstract
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 A(4)T(4) are bent, whereas T(4)A(4) is straight. We have determined the solution structures of the DNA duplexes formed by d(GCAAAATTTTGC) [A4T4] and d(CGTTTTAAAACG) [T4A4] with NH(4)(+) 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 approximately 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 approximately 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.
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