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Molecular models for intrastrand DNA G-quadruplexes

Federico Fogolari12*, Haritha Haridas1, Alessandra Corazza12, Paolo Viglino12, Davide Corà3, Michele Caselle3, Gennaro Esposito12 and Luigi E Xodo1

Author Affiliations

1 Dipartimento di Scienze e Tecnologie Biomediche, Università di Udine, Piazzale Kolbe 4 - 33100 Udine, Italy

2 Istituto Nazionale Biostrutture e Biosistemi, Viale Medaglie d'Oro 305, 00136 Roma, Italy

3 Dipartimento di Fisica Teorica Università di Torino, Via P. Giuria 1 10125 Torino, Italy

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BMC Structural Biology 2009, 9:64  doi:10.1186/1472-6807-9-64

Published: 7 October 2009



Independent surveys of human gene promoter regions have demonstrated an overrepresentation of G3Xn1G3Xn2G3Xn3G3 motifs which are known to be capable of forming intrastrand quadruple helix structures. In spite of the widely recognized importance of G-quadruplex structures in gene regulation and growing interest around this unusual DNA structure, there are at present only few such structures available in the Nucleic Acid Database. In the present work we generate by molecular modeling feasible G-quadruplex structures which may be useful for interpretation of experimental data.


We have used all quadruplex DNA structures deposited in the Nucleic Acid Database in order to select a list of fragments entailing a strand of three adjacent G's paired with another strand of three adjacent G's separated by a loop of one to four residues. These fragments were further clustered and representative fragments were finally selected. Further fragments were generated by assemblying the two strands of each fragment with loops from different fragments whenever the anchor G's were superimposable. The fragments were used to assemble G quadruplex based on a superimposability criterion.


Molecular models have been generated for a large number of G3Xn1G3Xn2G3Xn3G3 sequences. For a given sequence not all topologies are possible with the available repertoire of fragments due to steric hindrance and low superimposability. Since all molecular models are generated by fragments coming from observed quadruplex structures, molecular models are in principle reliable and may be used for interpretation of experimental data. Some examples of applications are given.