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.
Highlights
DNA exists as a right-handed, double-stranded structure, which is classified as a B helix
All oligonucleotides were synthesized on a MerMade12 (BioAutomation) synthesizer using standard phosphoramidite chemistry [30]
Thermodynamic data for model DNA and RNA duplexes are summarized in S1 Table
Summary
DNA exists as a right-handed, double-stranded structure, which is classified as a B helix. RNA appears as a right-handed structure (A helix). In native RNA, double-stranded helical regions are short (on average 5–7 base pairs long). 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. Double helical structures are the most common structures, nucleic acids can form triplexes or quadruplexes in parallel and antiparallel strand orientations [3,4,5]
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