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Tuning the hybridization properties of modified oligonucleotides: from flexible to conformationally constrained phosphonate internucleotide linkages
O. Páv, I. Barvík, R. Liboska, M. Petrová, O. Šimák, Š. Rosenbergová, P. Novák, M. Buděšínský, I. Rosenberg,
Language English Country Great Britain
Document type Journal Article
Grant support
NV15-31604A
MZ0
CEP Register
PubMed
27995239
DOI
10.1039/c6ob02571d
Knihovny.cz E-resources
- MeSH
- Nucleic Acid Hybridization MeSH
- Magnetic Resonance Spectroscopy MeSH
- Molecular Conformation MeSH
- Oligonucleotides chemistry MeSH
- Organophosphonates chemistry MeSH
- Molecular Dynamics Simulation MeSH
- Publication type
- Journal Article MeSH
The concept of conformational restriction leading to the preorganization of modified strands has proven to be successful and has afforded nucleic acid analogues with many interesting properties suitable for various biochemical applications. We utilized this concept to prepare a set of constrained oligonucleotides derived from 1,4-dioxane and 1,3-dioxolane-locked nucleoside phosphonates and evaluated their hybridization affinities towards their complementary RNA strands. With an increase of ΔTmper modification up to +5.2 °C, the hybridization experiments revealed the (S)-2',3'-O-phosphonomethylidene internucleotide linkage as one of the most Tm-increasing modifications reported to date. Moreover, we introduced a novel prediction tool for the pre-selection of potentially interesting chemical modifications of oligonucleotides.
References provided by Crossref.org
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- $a Páv, Ondřej $u Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí 2, 16610 Prague, Czech Republic. ivan.rosenberg@uochb.cas.cz.
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- $a The concept of conformational restriction leading to the preorganization of modified strands has proven to be successful and has afforded nucleic acid analogues with many interesting properties suitable for various biochemical applications. We utilized this concept to prepare a set of constrained oligonucleotides derived from 1,4-dioxane and 1,3-dioxolane-locked nucleoside phosphonates and evaluated their hybridization affinities towards their complementary RNA strands. With an increase of ΔTmper modification up to +5.2 °C, the hybridization experiments revealed the (S)-2',3'-O-phosphonomethylidene internucleotide linkage as one of the most Tm-increasing modifications reported to date. Moreover, we introduced a novel prediction tool for the pre-selection of potentially interesting chemical modifications of oligonucleotides.
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