ArticlePloS one2010
Understanding the sequence-dependence of DNA groove dimensions: implications for DNA interactions.
Article in PloS one, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed, 81 citations in OpenAlex.
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- Energy Landscapes for Base-Flipping in a Model DNA Duplex.The journal of physical chemistry. B · 2022Article
- Dinuclear platinum(II) complexes as the pattern for phosphate backbone binding: a new perspective for recognition of binding modes to DNA.Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry · 2022Article
- DNA-MBF1 study using molecular dynamics simulations : On the road to understanding the heat stress response in DNA-protein interactions in plants.European biophysics journal : EBJ · 2021Article
- Hydrophobic Amino Acids as Universal Elements of Protein-Induced DNA Structure Deformation.International journal of molecular sciences · 2020Article
- Canonical DNA minor groove insertion of bisbenzamidine-Ru(ii) complexes with chiral selectivity.Chemical science · 2019Article
- The crystal structure of AcrR from Mycobacterium tuberculosis reveals a one-component transcriptional regulation mechanism.FEBS open bio · 2019Article
- Structural study to analyze the DNA-binding properties of DsrC protein from the dsr operon of sulfur-oxidizing bacterium Allochromatium vinosum.Journal of molecular modeling · 2019Article
- How methyl-sugar interactions determine DNA structure and flexibility.Nucleic acids research · 2019Article
- Interdependent Sequence Selectivity and Diastereoselectivity in the Alkylation of DNA by Decarbamoylmitomycin C.Chemistry (Weinheim an der Bergstrasse, Germany) · 2018Article
- Dynamics of water and ions around DNA: What is so special about them?Journal of biosciences · 2018Review
- Conformational rearrangement of 1,2-d(GG) intrastrand cis-diammineplatinum crosslinked DNA is driven by counter-ion penetration within the minor groove of the modified site.Journal of molecular modeling · 2017Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe B-DNA major and minor groove dimensions are crucial for DNA-protein interactions. It has long been thought that the groove dimensions depend on the DNA sequence, however this relationship has remained elusive. Here, our aim is to elucidate how the DNA sequence intrinsically shapes the grooves. METHODOLOGY/PRINCIPAL
findingsThe present study is based on the analysis of datasets of free and protein-bound DNA crystal structures, and from a compilation of NMR (31)P chemical shifts measured on free DNA in solution on a broad range of representative sequences. The (31)P chemical shifts can be interpreted in terms of the BI↔BII backbone conformations and dynamics. The grooves width and depth of free and protein-bound DNA are found to be clearly related to the BI/BII backbone conformational states. The DNA propensity to undergo BI↔BII backbone transitions is highly sequence-dependent and can be quantified at the dinucleotide level. This dual relationship, between DNA sequence and backbone behavior on one hand, and backbone behavior and groove dimensions on the other hand, allows to decipher the link between DNA sequence and groove dimensions. It also firmly establishes that proteins take advantage of the intrinsic DNA groove properties. CONCLUSIONS/SIGNIFICANCE: The study provides a general framework explaining how the DNA sequence shapes the groove dimensions in free and protein-bound DNA, with far-reaching implications for DNA-protein indirect readout in both specific and non specific interactions.
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