Parallel poly(A) homo- and hetero-duplex formation detection with an adapted DNA nanoswitch technique
- Martha Anne G. Pickard1,
- Karl B. Brylow1,
- Lily A. Cisco1,3,
- Matthew R. Anecelle1,
- Mackenzie L. Pershun1,
- Arun Richard Chandrasekaran2,
- Ken Halvorsen2 and
- Michael L. Gleghorn1
- 1School of Chemistry and Materials Science, Rochester Institute of Technology, Rochester, New York 14623, USA
- 2The RNA Institute, University at Albany, State University of New York, Albany, New York 12222, USA
- Corresponding author: mlgsch{at}rit.edu
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 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.
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Article is online at http://www.rnajournal.org/cgi/doi/10.1261/rna.075408.120.
- Received March 14, 2020.
- Accepted May 4, 2020.
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