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

• Published in: RNA (Cambridge) Vol. 26; no. 9; pp. 1118 - 1130
• Main Authors: Pickard, Martha Anne G, Brylow, Karl B, Cisco, Lily A, Anecelle, Matthew R, Pershun, Mackenzie L, Chandrasekaran, Arun Richard, Halvorsen, Ken, Gleghorn, Michael L
• Format: Journal Article
• Language: English
• Published: United States Cold Spring Harbor Laboratory Press 01.09.2020
• Subjects: Ammonium; Base Pairing - genetics; Deoxyribonucleic acid; DNA; DNA - genetics; Melting; Nucleic Acid Conformation; Oligonucleotides - genetics; Poly A - genetics; Poly(A); poly(A); polyadenylic; nanoswitch; parallel; LNA; adenine
• ISSN: 1355-8382; 1469-9001
• DOI: 10.1261/rna.075408.120

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.