ReviewCurrent opinion in structural biology2011
DNA shape, genetic codes, and evolution.
Review in Current opinion in structural biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
22 citing papers in PubMed, 43 citations in OpenAlex.
- Binding to the DNA Minor Groove by Heterocyclic Dications: from AT Specific to GC Recognition Compounds.Current protocols · 2023Review
- Article
- Intrinsic DNA topology as a prioritization metric in genomic fine-mapping studies.Nucleic acids research · 2020Article
- Structure-mechanics statistical learning unravels the linkage between local rigidity and global flexibility in nucleic acids.Chemical science · 2020Article
- Conserved Critical Evolutionary Gene Structures in Orthologs.Journal of molecular evolution · 2019Article
- Triplet-Based Codon Organization Optimizes the Impact of Synonymous Mutation on Nucleic Acid Molecular Dynamics.Journal of molecular evolution · 2018Article
- Recruitment of CRISPR-Cas systems by Tn7-like transposons.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Evidence of selection for an accessible nucleosomal array in human.BMC genomics · 2016Article
- GBshape: a genome browser database for DNA shape annotations.Nucleic acids research · 2015Article
- Operator recognition by the ROK transcription factor family members, NagC and Mlc.Nucleic acids research · 2015Article
- Crosstalk between the HpArsRS two-component system and HpNikR is necessary for maximal activation of urease transcription.Frontiers in microbiology · 2015Article
- Absence of a simple code: how transcription factors read the genome.Trends in biochemical sciences · 2014Review
- DNA dynamics and single-molecule biology.Chemical reviews · 2014Review
- Synonymous codon bias and functional constraint on GC3-related DNA backbone dynamics in the prokaryotic nucleoid.Nucleic acids research · 2014Article
- TFBSshape: a motif database for DNA shape features of transcription factor binding sites.Nucleic acids research · 2014Article
- Binding of nucleoid-associated protein fis to DNA is regulated by DNA breathing dynamics.PLoS computational biology · 2013Article
- Binding to the DNA minor groove by heterocyclic dications: from AT-specific monomers to GC recognition with dimers.Current protocols in nucleic acid chemistry · 2012Review
- Computational models for large-scale simulations of facilitated diffusion.Molecular bioSystems · 2012Review
- Functional specificity of a protein-DNA complex mediated by two arginines bound to the minor groove.Journal of bacteriology · 2012Article
- Codons support the maintenance of intrinsic DNA polymer flexibility over evolutionary timescales.Genome biology and evolution · 2012Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 2 institutions in 1 country.
Funding
Abstract
Although the three-letter genetic code that maps nucleotide sequence to protein sequence is well known, there must exist other codes that are embedded in the human genome. Recent work points to sequence-dependent variation in DNA shape as one mechanism by which regulatory and other information could be encoded in DNA. Recent advances include the discovery of shape-dependent recognition of DNA that depends on minor groove width and electrostatics, the existence of overlapping codes in protein-coding regions of the genome, and evolutionary selection for compensatory changes in nucleotide composition that facilitate nucleosome occupancy. It is becoming clear that DNA shape is important to biological function, and therefore will be subject to evolutionary constraint.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.