Regiospecific solid-phase synthesis of branched oligonucleotides. Effect of vicinal 2',5'- (or 2',3'-) and 3',5'-phosphodiester linkages on the formation of hairpin DNA

Bioconjugate Chemistry
R S Braich, M J Damha

Abstract

A general procedure for the solid-phase regiospecific synthesis of branched oligonucleotides (bNA) analogues using readily available phosphoramidite reagents has been developed. The key feature of this method is use of the solid-phase phosphoramidite procedure to assemble linear oligonucleotide sequences and sequential removal of the phosphate (beta-cyanoethyl or methyl) and silyl protecting groups without detaching the nascent oligonucleotide from the solid support. Conversion of the phosphate backbone into the more stable phosphodiester linkages allows for removal of the 2'-O-tert-butyldimethylsilyl protecting group without cleavage or isomerization at the branch point. This method allows for the formation of branched oligonucleotides with sequences of arbitrary base composition, length, and orientation around the branch point junction, including a "Y"-shaped octadecamer d(TACTA)-rA[2',5'd(GTATGT)]3',5'd(CAAGTT). Studies to explore structural effects in the use of a branched adenosine as replacement for nucleotide loops in duplex and triplex DNA are also described. Branched oligonucleotides of the type rA[2',5'dCndA10-5']3',5'dCndT10-3' and rA[2',5'dCn3',3'dA10-5']3',5'dCnT10-3' form hairpin duplexes with thermal stability co...Continue Reading

References

Jan 1, 1995·Annual Review of Biophysics and Biomolecular Structure·G Varani
Apr 23, 1993·Science·I Amato

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Citations

Jan 24, 1998·Journal of Biomolecular Structure & Dynamics·S RobidouxM J Damha
Jan 24, 1998·Journal of Biomolecular Structure & Dynamics·S Robidoux, M J Damha
Apr 5, 2011·Journal of Nucleic Acids·Anna AviñóRamon Eritja
Jan 31, 2003·Organic Letters·Sandra Carriero, Masad J Damha
Sep 21, 2001·Nucleosides, Nucleotides & Nucleic Acids·A M NoronhaP S Miller
May 17, 2005·Nucleosides, Nucleotides & Nucleic Acids·Sergey I Antsypovich, Günter von Kiedrowski
Apr 23, 2008·Current Protocols in Nucleic Acid Chemistry·Sandra Carriero, Masad J Damha
Dec 21, 2012·Current Protocols in Nucleic Acid Chemistry·Gang SunChristopher J Wilds
Jun 9, 2018·Organic & Biomolecular Chemistry·Satheesh EllipilliJennifer M Heemstra
Jan 16, 2007·Chemistry : a European Journal·Madhavaiah ChandraAndreas Marx
Apr 19, 2011·Chemistry, an Asian Journal·Richa Pathak, Andreas Marx
Jul 24, 2020·International Journal of Molecular Sciences·Olga A KrashenininaAlya G Venyaminova
Sep 10, 2014·Current Protocols in Nucleic Acid Chemistry·Kohji SeioMitsuo Sekine
Jul 27, 2001·Journal of the American Chemical Society·D M NollP S Miller
Oct 25, 2003·The Journal of Organic Chemistry·Sandra Carriero, Masad J Damha
Dec 6, 2001·Journal of the American Chemical Society·R N Hannoush, M J Damha
Mar 23, 2001·The Journal of Organic Chemistry·A P Guzaev, M Manoharan
Jun 13, 2014·RNA·Stephen M GarreyJay R Hesselberth

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