title: 2D meets 4G: G-quadruplexes in RNA secondary structure prediction.
abstract: G-quadruplexes are abundant locally stable structural elements in nucleic acids. The combinatorial theory of RNA structures and the dynamic programming algorithms for RNA secondary structure prediction are extended here to incorporate G-quadruplexes using a simple but plausible energy model. With preliminary energy parameters, we find that the overwhelming majority of putative quadruplex-forming sequences in the human genome are likely to fold into canonical secondary structures instead. Stable G-quadruplexes are strongly enriched, however, in the 5'UTR of protein coding mRNAs.
authors: University of Vienna, Vienna.
authors: Ronny
authors: R
authors: Lorenz
authors: University of Leipzig, Leipzig.
authors: Stephan H
authors: SH
authors: Bernhart
authors: Max Planck Institute for Mathematics in the Sciences, Leipzig and University of Leipzig, Leipzig.
authors: Jing
authors: J
authors: Qin
authors: University of Vienna, Vienna.
authors: Christian
authors: C
authors: Höner zu Siederdissen
authors: University of Vienna, Vienna and Center for Genomic Regulation (CRG), Barcelona.
authors: Andrea
authors: A
authors: Tanzer
authors: University of Vienna, Vienna.
authors: Fabian
authors: F
authors: Amman
authors: University of Vienna, Vienna and University of Copenhagen.
authors: Ivo L
authors: IL
authors: Hofacker
authors: University of Leipzig, Leipzig, Max Planck Institute for Mathematics in the Sciences, Leipzig, Fraunhofer Institute for CellTherapy and Immunology and University of Copenhagen.
authors: Peter F
authors: PF
authors: Stadler
mesh_terms: D020121:5' Untranslated Regions; D001483:Base Sequence; D019295:Computational Biology; D054856:G-Quadruplexes; D006801:Humans; D009690:Nucleic Acid Conformation; D059370:RNA Folding; D012333:RNA, Messenger / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA; D013816:Thermodynamics
chemical_list: D020121:5' Untranslated Regions; D012333:RNA, Messenger