G-quadruplex prediction in E. coli genome reveals a conserved putative G-quadruplex-Hairpin-Duplex switch


Kaplan O. I. , Berber B., Hekim N., Doluca O.

NUCLEIC ACIDS RESEARCH, vol.44, no.19, pp.9083-9095, 2016 (Journal Indexed in SCI) identifier

  • Publication Type: Article / Article
  • Volume: 44 Issue: 19
  • Publication Date: 2016
  • Doi Number: 10.1093/nar/gkw769
  • Title of Journal : NUCLEIC ACIDS RESEARCH
  • Page Numbers: pp.9083-9095

Abstract

Many studies show that short non-coding sequences are widely conserved among regulatory elements. More and more conserved sequences are being discovered since the development of next generation sequencing technology. A common approach to identify conserved sequences with regulatory roles relies on topological changes such as hairpin formation at the DNA or RNA level. G-quadruplexes, non-canonical nucleic acid topologies with little established biological roles, are increasingly considered for conserved regulatory element discovery. Since the tertiary structure of G-quadruplexes is strongly dependent on the loop sequence which is disregarded by the generally accepted algorithm, we hypothesized that G-quadruplexes with similar topology and, indirectly, similar interaction patterns, can be determined using phylogenetic clustering based on differences in the loop sequences. Phylogenetic analysis of 52 G-quadruplex forming sequences in the Escherichia coli genome revealed two conserved G-quadruplex motifs with a potential regulatory role. Further analysis revealed that both motifs tend to form hairpins and G quadruplexes, as supported by circular dichroism studies. The phylogenetic analysis as described in this work can greatly improve the discovery of functional G-quadruplex structures and may explain unknown regulatory patterns.