title: Thermodynamic, counterion, and hydration effects for the incorporation of locked nucleic acid nucleotides into DNA duplexes.
abstract: 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. LNA-modified oligonucleotides are known to exhibit enhanced hybridization affinity toward complementary DNA and RNA. In this work, we have evaluated the hybridization thermodynamics of a series of LNA-substituted DNA octamers, modified to various extents by one to three LNA substitutions, introduced at either adenine (5'-AGCACCAG) or thymine (5'-TGCTCCTG) nucleotides. To understand the energetics, counterion effects, and the hydration contribution of the incorporation of LNA modification, a combination of spectroscopic and calorimetric techniques was used. The CD spectra of the corresponding duplexes showed that the modified duplexes adopt an A-type conformation. UV and DSC melting studies revealed that each type of duplex unfolds in a two-state transition. A complete thermodynamic profile at 5 degrees C indicated that the net effect of modification on thermodynamic parameters might be positional and that the neighboring bases flanking the modification might influence the favorable formation of the modified duplexes. Furthermore, relative to the formation of the unmodified reference duplexes, the formation of modified duplexes is accompanied by a higher uptake of counterions and a lower uptake of water molecules.
authors.affiliation: Institute of Genomics and Integrative Biology, CSIR, Mall Road, Delhi 110 007, India.
authors.forename: Harleen
authors.initials: H
authors.lastname: Kaur
authors.forename: Amit
authors.initials: A
authors.lastname: Arora
authors.forename: Jesper
authors.initials: J
authors.lastname: Wengel
authors.forename: Souvik
authors.initials: S
authors.lastname: Maiti
mesh_terms: D001483:Base Sequence; D002152:Calorimetry, Differential Scanning; D002942:Circular Dichroism; D004247:DNA / Q000737:chemistry*; D009693:Nucleic Acid Hybridization; D009696:Nucleic Acids / Q000737:chemistry*; D009711:Nucleotides / Q000737:chemistry*; D013056:Spectrophotometry, Ultraviolet; D013816:Thermodynamics
chemical_list: D009696:Nucleic Acids; D009711:Nucleotides; D004247:DNA