Structural Aspects of the Antiparallel and Parallel Duplexes Formed by DNA, 2'-O-Methyl RNA and RNA Oligonucleotides

PLoS One. 2015 Nov 18;10(11):e0143354. doi: 10.1371/journal.pone.0143354. eCollection 2015.

Abstract

This study investigated the influence of the nature of oligonucleotides on the abilities to form antiparallel and parallel duplexes. Base pairing of homopurine DNA, 2'-O-MeRNA and RNA oligonucleotides with respective homopyrimidine DNA, 2'-O-MeRNA and RNA as well as chimeric oligonucleotides containing LNA resulted in the formation of 18 various duplexes. UV melting, circular dichroism and fluorescence studies revealed the influence of nucleotide composition on duplex structure and thermal stability depending on the buffer pH value. Most duplexes simultaneously adopted both orientations. However, at pH 5.0, parallel duplexes were more favorable. Moreover, the presence of LNA nucleotides within a homopyrimidine strand favored the formation of parallel duplexes.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Circular Dichroism
  • DNA / chemistry*
  • Hydrogen-Ion Concentration
  • Oligonucleotides / chemistry*
  • RNA / chemistry*

Substances

  • Oligonucleotides
  • RNA
  • DNA

Grants and funding

This work was supported by National Science Center grants: UMO-2011/03/B/NZ1/00576, UMO-2011/03/B/ST5/01098, UMO-2013/08/A/ST5/00295 to RK, and UMO-2013/08/M/NZ1/01062 to EK. This publication was also supported by the Polish Ministry of Science and Higher Education, under the KNOW program.