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

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.

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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.