Highly prevalent putative quadruplex sequence motifs in human DNA

By Alan K. Todd, Matthew Johnston, Stephen Neidle. Nucleic Acids Research, 2005

907 citations recorded by the source corpus.

We report here the results of a systematic search for the existence and prevalence of potential intramolecular G-quadruplex forming sequences in the human genome. We have also examined the tendency for particular sequences of ‘loop’ regions to occur in particular positions with respect to the G-tracts in a quadruplex. Using arithmetic ratio and probability techniques we have discovered frequent and systematic occurrence of certain sequence types, the most prominent being a potential quadruplex containing CCTGT in the first ‘loop’ position. Being able to highlight types of potential quadruplex sequences in G-rich regions is an important step in searching for biologically relevant sequences and finding their function.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/e072830ac3aceda6496282f0825ca6dcc76eb252

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Citations in the corpus

Circular dichroism and conformational polymorphism of DNA (2009, background): “Particular genomic regions, especially in gene promoters, have a potential to form quadruplexes (82,83), which are believed to form in vivo and affect cellular processes (79).”
QGRS Mapper: a web-based server for predicting G-quadruplexes in nucleotide sequences (2006, background): “Although, G-quadruplexes have been surveyed in the human genome with such techniques (34,35), there are no known user-friendly computational tools easily accessible to the public.”
Small molecule-induced DNA damage identifies alternative DNA structures in human genes (2012, neutral): “G-quadruplex nucleic acids may provide structural variations in the genom”
Prevalence of quadruplexes in the human genome (2005, positive): “Many of these have single-base loops, a trend also observed in an independent study by our collaborators ( 30 ).”
Quadruplex DNA: sequence, topology and structure (2006, background): “A potential loop sequence in this quadruplex region has the sequence AGGA in common with one of the c-kit sequences (90); this sequence was predicted (18) to have a high frequency of occurrence.”
Making the Bend: DNA Tertiary Structure and Protein-DNA Interactions (2014, background): “In vivo, sequences giving rise to quadruplexes have been identified in G-rich eukaryotic telomeres and promoter regions [67–70].”
Targeting G-quadruplexes in gene promoters: a novel anticancer strategy? (2011, background): “The advancement in our understanding of the biophysical principles that link G-quadruplex formation in vitro with oligonucleotide sequences has provided a rational basis for constructing algorithms that predict sequences that are likely to fold into intramolecular G-quadruplexe”
G-quadruplexes in promoters throughout the human genome (2006, background): “However, the role of quadruplexes outside telomeric regions is still unclear, although the quadruplex motif is prevalent in the human genome, (9,10) with an average incidence of 1 quadruplex every 10 000 bases.”
The Structure and Function of DNA G-Quadruplexes (2020, methodology): “Based on biophysical studies on different G4 structures, algorithms using sequence motifs such as GR3NxGR3NxGR3NxGR3 were developed and deployed to predict putative G4 structures in genomic DNA [14,15].”