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

Autor:	Pickard MAG; School of Chemistry and Materials Science, Rochester Institute of Technology, Rochester, New York 14623, USA., Brylow KB; School of Chemistry and Materials Science, Rochester Institute of Technology, Rochester, New York 14623, USA., Cisco LA; School of Chemistry and Materials Science, Rochester Institute of Technology, Rochester, New York 14623, USA., Anecelle MR; School of Chemistry and Materials Science, Rochester Institute of Technology, Rochester, New York 14623, USA., Pershun ML; School of Chemistry and Materials Science, Rochester Institute of Technology, Rochester, New York 14623, USA., Chandrasekaran AR; The RNA Institute, University at Albany, State University of New York, Albany, New York 12222, USA., Halvorsen K; The RNA Institute, University at Albany, State University of New York, Albany, New York 12222, USA., Gleghorn ML; School of Chemistry and Materials Science, Rochester Institute of Technology, Rochester, New York 14623, USA.
Jazyk:	angličtina
Zdroj:	RNA (New York, N.Y.) [RNA] 2020 Sep; Vol. 26 (9), pp. 1118-1130. Date of Electronic Publication: 2020 May 15.
DOI:	10.1261/rna.075408.120
Abstrakt:	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 validates a new tool for studying parallel duplexes and reveals fundamental properties of poly(A) parallel duplex formation. Parallel duplexes may find use in DNA nanotechnology and in molecular biology applications such as a potential poly(rA) tail capture tool as an alternative to traditional oligo(dT) based purification. (© 2020 Pickard et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.)
Databáze:	MEDLINE
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