ArticleProceedings of the National Academy of Sciences of the United States of America1998
Structural code for DNA recognition revealed in crystal structures of papillomavirus E2-DNA targets.
Article in Proceedings of the National Academy of Sciences of the United States of America, 1998. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
31 citing papers in PubMed, 112 citations in OpenAlex.
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- Binding of transcription factor GabR to DNA requires recognition of DNA shape at a location distinct from its cognate binding site.Nucleic acids research · 2016Article
- Single-stranded DNA within nanopores: conformational dynamics and implications for sequencing; a molecular dynamics simulation study.Biophysical journal · 2012Article
- Signatures of DNA flexibility, interactions and sequence-related structural variations in classical X-ray diffraction patterns.Nucleic acids research · 2011Article
- Molecular dynamics simulations of DNA within a nanopore: arginine-phosphate tethering and a binding/sliding mechanism for translocation.Biochemistry · 2011Article
- Differential stability of DNA crossovers in solution mediated by divalent cations.Nucleic acids research · 2010Article
- Origins of specificity in protein-DNA recognition.Annual review of biochemistry · 2010Review
- Signatures of protein-DNA recognition in free DNA binding sites.Journal of molecular biology · 2009Article
- Crystallographic analysis of a sex-specific enhancer element: sequence-dependent DNA structure, hydration, and dynamics.Journal of molecular biology · 2009Article
- Evolutionary and biophysical relationships among the papillomavirus E2 proteins.Frontiers in bioscience (Landmark edition) · 2009Review
- Magnitude and direction of DNA bending induced by screw-axis orientation: influence of sequence, mismatches and abasic sites.Nucleic acids research · 2008Article
- Comprehensive comparison of the interaction of the E2 master regulator with its cognate target DNA sites in 73 human papillomavirus types by sequence statistics.Nucleic acids research · 2008Article
- Overview of the structure of all-AT oligonucleotides: organization in helices and packing interactions.Biophysical journal · 2006Article
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Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
Abstract
Transcriptional regulation in papillomaviruses depends on sequence-specific binding of the regulatory protein E2 to several sites in the viral genome. Crystal structures of bovine papillomavirus E2 DNA targets reveal a conformational variant of B-DNA characterized by a roll-induced writhe and helical repeat of 10.5 bp per turn. A comparison between the free and the protein-bound DNA demonstrates that the intrinsic structure of the DNA regions contacted directly by the protein and the deformability of the DNA region that is not contacted by the protein are critical for sequence-specific protein/DNA recognition and hence for gene-regulatory signals in the viral system. We show that the selection of dinucleotide or longer segments with appropriate conformational characteristics, when positioned at correct intervals along the DNA helix, can constitute a structural code for DNA recognition by regulatory proteins. This structural code facilitates the formation of a complementary protein-DNA interface that can be further specified by hydrogen bonds and nonpolar interactions between the protein amino acids and the DNA bases.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.