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Increase in hybridization rates with oligonucleotides containing locked nucleic acids
Author(s) -
St. John Pamela Michele,
Ormond Thomas K,
Spear Daniel,
Mackey Megan A
Publication year - 2006
Publication title -
the faseb journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.709
H-Index - 277
eISSN - 1530-6860
pISSN - 0892-6638
DOI - 10.1096/fasebj.20.5.a946-c
Subject(s) - oligonucleotide , nucleic acid , nucleic acid thermodynamics , dna , reaction rate constant , nucleotide , duplex (building) , chemistry , biology , base sequence , biochemistry , gene , kinetics , physics , quantum mechanics
Locked nucleic acids (LNAs) incorporated into either stable single stranded oligonucleotides containing tetraloops or their complements have been found to increase hybridization rate constants by as much as an order of magnitude compared to the all‐DNA hybridization rate constants. Model sequences composed of 20 bases in length that can form hairpins due to a stable GAAA tetraloop were used where LNAs were substituted for the nucleotides in the loop, stem, or end regions of the strand and in the complementary strand. Substitution of the LNAs to the loop predictably raised the melting temperatures of the duplex however, the hybridization rates between the tetraloop and the complementary sequence also increased. In contrast, when LNAs were substituted in the stem, the hybridization rate constants decreased implying the formation of a more stable hairpin. Substitution of LNAs into the end region of the sequence had little affect on the hybridization rate constants although melting temperatures still showed a predictable increase. Rate constants also increased when LNAs were substituted into complementary strands of DNA tetraloops. The increase in hybridization rate constant is being attributed to changes in the structure of the stable single strands observed from gel electrophoresis studies. Partial funding for this research was made possible by the donors of the American Chemical Society Petroleum Research Fund.