Parallel poly(A) homo- and hetero-duplex formation detection with an adapted DNA nanoswitch technique.

Parallel poly(A) homo- and hetero-duplex formation detection with an adapted DNA nanoswitch technique. RNA. 2020 May 15;: Authors: Pickard MAG, Brylow KB, Cisco LA, Anecelle MR, Pershun ML, Chandrasekaran AR, Halvorsen K, Gleghorn ML Abstract Polyriboadenylic (poly(rA)) strands of sufficient length form parallel double helices in acidic and/or ammonium-containing conditions. Poly(rA) duplexes in acidic conditions are held together by A+-A+ base-pairing also involving base interactions with the phosphate backbone. Traditional UV-melting studies of parallel poly(A) duplexes have typically examined homo-duplex formation of a single nucleic acid species in solution. We have adapted a technique utilizing a DNA nanoswitch that detects interaction of two different strands either with similar or differing lengths or modifications. Our method detected parallel duplex formation as a function of length, chemical modifications, and pH, and at a sensitivity that required over 100 fold less concentration of sample than prior UV-melting methods. While parallel polyriboadenylic acid and poly-2'-O-methyl-adenylic acid homo-duplexes formed, we did not detect homo-duplexes of polydeoxyriboadenylic acid strands or poly-locked nucleic acid (LNA)-adenylic strands. Importantly however, a poly-locked nucleic acid (LNA)-adenylic strand, as well as a poly-2'-O-methyl-adenylic strand formed a hetero-duplex with a polyriboadenylic strand. Overall, our work vali...
Source: RNA - Category: Genetics & Stem Cells Authors: Tags: RNA Source Type: research