Thermodynamic, counterion and hydration effects for the incorporation of locked nucleic acid (LNA) nucleotides in duplex.

A Locked Nucleic Acid (LNA) monomer is a conformationally restricted nucleotide analogue with an extra 2'-O, 4'-C-methylene bridge added to the ribose ring that is known to exhibit enhanced hybridization affinity towards complementary DNA and RNA, however the underlying thermodynamic basis for this observation are poorly understood. We have evaluated the influence of LNA residues on hybridization thermodynamics, counterions and hydration of DNADNA and DNARNA heteroduplex using spectroscopic and calorimetric techniques. Thermodynamic analysis for duplex formation using UV and differential scanning calorimetry suggested that LNA-induced stabilization results from a large, favorable increase in the enthalpy of hybridization that compensates for the unfavorable entropy change. The heat capacity change, Delta C(p), accompanying the duplex formation, obtained through DSC, has also been reported and has been used to furnish thermodynamic parameters at 37 degrees C. Furthermore, it was observed that relative to the formation of unmodified duplex, the formation of LNA-modified duplexes was accompanied by a higher uptake of counterions and a lower uptake of water molecules.