Computational Approaches to the Detection and Analysis of Sequences with Intramolecular G-Quadruplex Forming Potential

  • Paul Ryvkin
  • Steve G. Hershman
  • Li-San WangEmail author
  • F. Brad Johnson
Part of the Methods in Molecular Biology book series (MIMB, volume 608)


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 words

G-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.


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Copyright information

© Humana Press, a part of Springer Science+Business Media, LLC 2010

Authors and Affiliations

  • Paul Ryvkin
    • 1
  • Steve G. Hershman
    • 2
  • Li-San Wang
    • 3
    Email author
  • F. Brad Johnson
    • 4
  1. 1.Department of Pathology and Laboratory Medicine, Penn Center for Bioinformatics, and Graduate Group in Genomics and Computational BiologyUniversity of Pennsylvania School of MedicinePhiladelphiaUSA
  2. 2.Department of Pathology and Laboratory MedicineUniversity of Pennsylvania School of MedicinePhiladelphiaUSA
  3. 3.Department of Pathology and Laboratory Medicine, Institute on Aging, Penn Center for Bioinformatics, and Graduate Group in Genomics and Computational BiologyUniversity of Pennsylvania School of MedicinePhiladelphiaUSA
  4. 4.Department of Pathology and Laboratory Medicine, Institute on AgingUniversity of Pennsylvania School of MedicinePhiladelphiaUSA

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