Formation of G-wires, bimolecular and tetramolecular quadruplex: Cation-induced structural polymorphs of G-rich DNA sequence of human SYTX gene

Biopolymers. 2018 May;109(5):e23115. doi: 10.1002/bip.23115. Epub 2018 Apr 19.

Abstract

An exceptional property of auto-folding into a range of intra- as well as intermolecular quadruplexes by guanine-rich oligomers (GROs) of promoters, telomeres and various other genomic locations is still one of the most attractive areas of research at present times. The main reason for this attention is due to their established in vivo existence and biological relevance. Herein, the structural status of a 20-nt long G-rich sequence with two G5 stretches (SG20) is investigated using various biophysical and biochemical techniques. Bioinformatics analysis suggested the presence of a 17-nt stretch of this SG20 sequence in the intronic region of human SYTX (Synaptotagmin 10) gene. The SYTX gene helps in sensing out the Ca2+ ion, causing its intake in the pre-synaptic neuron. A range of various topologies like bimolecular, tetramolecular and guanine-wires (nano-wires) was exhibited by the studied sequence, as a function of cations (Na+ /K+ ) concentration. UV-thermal denaturation, gel electrophoresis, and circular dichroism (CD) spectroscopy showed correlations and established a cation-dependent structural switch. The G-wire formation, in the presence of K+ , may further be explored for its possible relevance in nano-biotechnological applications.

Keywords: G-wire; bimolecular quadruplex; circular dichroism of DNA; guanine-quadruplex; polyacrylamide gel electrophoresis; structural polymorphism.

MeSH terms

  • Base Sequence
  • Calcium / chemistry*
  • Cations, Divalent
  • Cations, Monovalent
  • Computational Biology
  • G-Quadruplexes*
  • Gene Expression
  • Guanine / chemistry
  • Humans
  • Oligonucleotides / chemistry
  • Potassium / chemistry*
  • Sodium / chemistry*
  • Synaptotagmins / chemistry*
  • Synaptotagmins / genetics

Substances

  • Cations, Divalent
  • Cations, Monovalent
  • Oligonucleotides
  • SYT10 protein, human
  • Synaptotagmins
  • Guanine
  • Sodium
  • Potassium
  • Calcium