Unusual Thermal Stability of RNA/[R P-PS]-DNA/RNA Triplexes Containing a Homopurine DNA Strand

Homopurine deoxyribonucleoside phosphorothioates, as short as hexanucleotides and possessing all internucleotide linkages of R P configuration, form a triple helix with two RNA or 2′-OMe-RNA strands, with Watson-Crick and Hoogsteen complementarity. Melting temperature and fluorescence quenching expe...

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Bibliographic Details
Published in:Biophysical journal 2007-04, Vol.92 (7), p.2507-2515
Main Authors: Guga, Piotr, Boczkowska, Małgorzata, Janicka, Magdalena, Maciaszek, Anna, Kuberski, Sławomir, Stec, Wojciech J.
Format: Article
Language:English
Subjects:
Binding Sites
Biochemistry
Chemical synthesis
Computer Simulation
Deoxyribonucleic acid
DNA
DNA - chemistry
DNA-Binding Proteins - chemistry
Drug Stability
Models, Chemical
Netropsin - chemistry
Nucleic Acid Denaturation
Nucleic Acids
Protein Binding
Purines - chemistry
Ribonucleic acid
RNA
RNA - chemistry
Temperature
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Summary:Homopurine deoxyribonucleoside phosphorothioates, as short as hexanucleotides and possessing all internucleotide linkages of R P configuration, form a triple helix with two RNA or 2′-OMe-RNA strands, with Watson-Crick and Hoogsteen complementarity. Melting temperature and fluorescence quenching experiments strongly suggest that the Hoogsteen RNA strand is parallel to the homopurine [R P-PS]-oligomer. Remarkably, these triplexes are thermally more stable than complexes formed by unmodified homopurine DNA molecules of the same sequence. The triplexes formed by phosphorothioate DNA dodecamers containing 4–6 dG residues are thermally stable at pH 7.4, although their stability increases significantly at pH 5.3. FTIR measurements suggest participation of the C 2-carbonyl group of the pyrimidines in the stabilization of the triplex structure. Formation of triple-helix complexes with exogenously delivered PS-oligos may become useful for the reduction of RNA accessibility in vivo and, hence, selective suppression/inhibition of the translation process.
ISSN:0006-3495
1542-0086
DOI:10.1529/biophysj.106.099283