Research Article: Structural Aspects of the Antiparallel and Parallel Duplexes Formed by DNA, 2’-O-Methyl RNA and RNA Oligonucleotides

Date Published: November 18, 2015

Publisher: Public Library of Science

Author(s): Marta Szabat, Tomasz Pedzinski, Tomasz Czapik, Elzbieta Kierzek, Ryszard Kierzek, Rakesh N. Veedu.


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.

Partial Text

DNA exists as a right-handed, double-stranded structure, which is classified as a B helix. RNA also appears as a right-handed structure (A helix). However, in native RNA, double-stranded helical regions are short (on average 5–7 base pairs long). Moreover, RNA contains many structural motifs disrupting its helical structure, such as various types of single and multinucleotide mismatches, internal loops, hairpins, bulge loops, terminal unpaired regions and multibranch [1]. Some specific sequences under certain conditions can form a left-handed helical structure [2]. The transition from one structure to another occurs depending on the base sequence, humidity, type and concentration of cations and anions, temperature and pH value. Although double helical structures are the most common structures, nucleic acids can form triplexes or quadruplexes in parallel and antiparallel strand orientations [3–5].

Combination of synthetic chemistry, thermodynamic UV-melting analysis, circular dichroism and fluorescence spectroscopies has allowed to obtain a global view of formation parallel and antiparallel duplexes by unmodified and modified DNA, 2’-O-Me RNA and RNA oligonucleotides. The present results demonstrate that homo- and heteroduplexes could be characterized by those biophysical methods to search theirs antiparallel and parallel orientation. However, very limited number of this type of the investigations published in literature makes unambiguous conclusions difficult. Herein the results concern CD spectra, broad thermodynamic studies and also fluorescence analyzes of 18 various duplexes.