Computational Approaches to the Detection and Analysis of Sequences with Intramolecular G-Quadruplex Forming Potential
Sequences with the potential to form intramolecular G-quadruplexes (G4-structures) are found in highly nonrandom distributions in the genomes of diverse organisms. These sequences are associated with nucleic acid metabolic processes ranging from transcription and translation to recombination and telomere function. Here we review different computational methods for identifying potential G4-forming sequences and provide protocols for their implementation. We also discuss methods for assessing the significance and specificity of associations between the sequences and different biological functions.
Key wordsG-quadruplex G4-DNA Bioinformatics Computational biology
We thank Jay Johnson, Kajia Cao, Marina Kozak, Alex Chavez, Jasmine Smith, and Qijun Chen for advice and discussions. This work was supported by NIH grants R01-AG021521, P01-AG031862, and a U. Penn Institute on Aging Pilot Grant.