title: Molecular models for intrastrand DNA G-quadruplexes.
abstract: BACKGROUND
  Independent surveys of human gene promoter regions have demonstrated an overrepresentation of G(3)X(n1)G3X(n2)G(3)X(n3)G(3) 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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  Molecular models have been generated for a large number of G(3)X(n1)G(3)X(n2)G3X(n3)G(3) 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.
authors.affiliation: Dipartimento di Scienze e Tecnologie Biomediche, Università di Udine, Piazzale Kolbe 4 - 33100 Udine, Italy. federico.fogolari@uniud.it
authors.forename: Federico
authors.initials: F
authors.lastname: Fogolari
authors.forename: Haritha
authors.initials: H
authors.lastname: Haridas
authors.forename: Alessandra
authors.initials: A
authors.lastname: Corazza
authors.forename: Paolo
authors.initials: P
authors.lastname: Viglino
authors.forename: Davide
authors.initials: D
authors.lastname: Corà
authors.forename: Michele
authors.initials: M
authors.lastname: Caselle
authors.forename: Gennaro
authors.initials: G
authors.lastname: Esposito
authors.forename: Luigi E
authors.initials: LE
authors.lastname: Xodo
mesh_terms: D003198:Computer Simulation; D004247:DNA / Q000737:chemistry*; D030561:Databases, Nucleic Acid; D054856:G-Quadruplexes; D006801:Humans; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D011166:Porphyrins / Q000737:chemistry; D016615:Telomere / Q000737:chemistry
chemical_list: D011166:Porphyrins; C021096:tetra(4-N-methylpyridyl)porphine; D004247:DNA