ArticleNucleic acids research2001
Strong minor groove base conservation in sequence logos implies DNA distortion or base flipping during replication and transcription initiation.
Article in Nucleic acids research, 2001. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Who cites it
38 citing papers in PubMed.
- Dynamic alternative DNA structures in biology and disease.Nature reviews. Genetics · 2023Review
- Article
- Energy Landscapes for Base-Flipping in a Model DNA Duplex.The journal of physical chemistry. B · 2022Article
- Dynamics of 5R-Tg Base Flipping in DNA Duplexes Based on Simulations─Agreement with Experiments and Beyond.Journal of chemical information and modeling · 2022Article
- Article
- An Evolutionary/Biochemical Connection between Promoter- and Primer-Dependent Polymerases Revealed by Systematic Evolution of Ligands by Exponential Enrichment.Journal of bacteriology · 2018Article
- Genome-Wide Transcriptional Regulation and Chromosome Structural Arrangement by GalR inFrontiers in molecular biosciences · 2016Article
- Analysis of DevR regulated genes in Mycobacterium tuberculosis.Systems and synthetic biology · 2014Article
- Plasmid R6K replication control.Plasmid · 2013Review
- Self-organization and entropy reduction in a living cell.Bio Systems · 2013Article
- A flexible integrative approach based on random forest improves prediction of transcription factor binding sites.Nucleic acids research · 2012Article
- Probing the informational and regulatory plasticity of a transcription factor DNA-binding domain.PLoS genetics · 2012Article
- Structural basis for promoter-10 element recognition by the bacterial RNA polymerase σ subunit.Cell · 2011Article
- Comparing binding site information to binding affinity reveals that Crp/DNA complexes have several distinct binding conformers.Nucleic acids research · 2011Article
- Molecular determinants of origin discrimination by Orc1 initiators in archaea.Nucleic acids research · 2011Article
- 70% efficiency of bistate molecular machines explained by information theory, high dimensional geometry and evolutionary convergence.Nucleic acids research · 2010Article
- A brief review of molecular information theory.Nano communication networks · 2010Article
- DNA-Destabilizing Agents as an Alternative Approach for Targeting DNA: Mechanisms of Action and Cellular Consequences.Journal of nucleic acids · 2010Article
- Data Compression Concepts and Algorithms and their Applications to Bioinformatics.Entropy (Basel, Switzerland) · 2010Article
- THAP proteins target specific DNA sites through bipartite recognition of adjacent major and minor grooves.Nature structural & molecular biology · 2010Article
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1 author.
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No grant is acknowledged in the PubMed record.
Abstract
The sequence logo for DNA binding sites of the bacteriophage P1 replication protein RepA shows unusually high sequence conservation ( approximately 2 bits) at a minor groove that faces RepA. However, B-form DNA can support only 1 bit of sequence conservation via contacts into the minor groove. The high conservation in RepA sites therefore implies a distorted DNA helix with direct or indirect contacts to the protein. Here I show that a high minor groove conservation signature also appears in sequence logos of sites for other replication origin binding proteins (Rts1, DnaA, P4 alpha, EBNA1, ORC) and promoter binding proteins (sigma(70), sigma(D) factors). This finding implies that DNA binding proteins generally use non-B-form DNA distortion such as base flipping to initiate replication and transcription.
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