Molecular thermodynamics of LNA:LNA base pairs and the hyperstabilizing effect of 5′‐proximal LNA:DNA base pairs

Locked nucleic acids (LNAs) can greatly enhance duplex DNA stability, and are therefore creating opportunities to improve therapeutics, as well as PCR‐based disease and pathogen diagnostics. Realizing the full potential of LNAs will require better understanding of their contributions to duplex stability, and the ability to predict their hydridization thermodynamics. Melting thermodynamics data for a large set of diverse duplexes containing LNAs in one or both strands are presented. Those data reveal that LNAs, when present on both strands, can stabilize a duplex not only through direct interaction with their base‐pair partner, but also through nonlocal hyperstablization effects created by LNA:LNA base pairs and/or specific patterns of oppositely oriented LNA:DNA base pairs. The data are, therefore, used to extend a thermodynamic model previously developed in our lab to permit accurate prediction of melting temperatures for duplexes bearing LNA substitutions within both strands using a classic group‐contribution approach. © 2015 American Institute of Chemical Engineers AIChE J, 61: 2711–2731, 2015