Effects of Locked Nucleic Acid Substitutions on the Stability of Oligonucleotide Hairpins

REFERENCES

• Kaur , H. , Wengel , J. and Maiti , S. 2008 . Thermodynamics of DNA–RNA heteroduplex formation: effects of locked nucleic acid nucleotides incorporated into the DNA strand . Biochemistry , 47 : 1218 – 1227 .
   PubMed Web of Science ®Google Scholar
• Koshkin , A. A. , Nielsen , P. , Meldgaard , M. , Rajwanshi , V. K. , Singh , S. K. and Wengel , J. 1998 . LNA (locked nucleic acid): an RNA mimic forming exceedingly stable LNA:LNA duplexes . J. Am. Chem. Soc. , 120 : 13252 – 13253 .
   Web of Science ®Google Scholar
• Kurreck , J. , Wyszko , E. , Gillen , C. and Erdmann , V. A. 2002 . Design of antisense oligonucleotides stabilized by locked nucleic acids . Nucleic Acids Res. , 30 : 1911 – 1918 .
   PubMed Web of Science ®Google Scholar
• McTigue , P. M. , Peterson , R. J. and Kahn , J. D. 2004 . Sequence-dependent thermodynamic parameters for locked nucleic acid (LNA)-DNA duplex formation . Biochemistry , 43 : 5388 – 5405 .
   PubMed Web of Science ®Google Scholar
• Kierzek , E. , Ciesielska , A. , Pasternak , K. , Mathews , D. H. , Turner , D. H. and Kierzek , R. 2005 . The influence of locked nucleic acid residues on the thermodynamic properties of 2′-O-methyl RNA/RNA heteroduplexes . Nucleic Acids Res. , 33 : 5082 – 5093 .
   PubMed Web of Science ®Google Scholar
• Kaur , H. , Arora , A. , Wengel , J. and Maiti , S. 2006 . Thermodynamic, counterion and hydration effects for the incorporation of locked nucleic acid nucleotides into DNA duplexes . Biochemistry , 45 : 7347 – 7344 .
   PubMed Web of Science ®Google Scholar
• Pasternak , A. , Kierzek , E. , Pasternak , K. , Fratczak , A. , Turner , D. H. and Kierzek , R. 2008 . The thermodynamics of 3′-terminal pyrene and guanosine for the design of isoenergetic 2′-O-methyl-RNA-LNA chimeric oligonucleotide probes of RNA structure . Biochemistry , 47 : 1249 – 1258 .
   PubMed Web of Science ®Google Scholar
• Bruylants , G. , Boccongelli , M. , Snoussi , K. and Bartik , K. 2009 . Comparison of the thermodynamics and base-pair dynamics of a full LNA:DNA duplex and of the isosequential DNA:DNA duplex . Biochemistry , 48 : 8473 – 8482 .
   PubMed Web of Science ®Google Scholar
• Kierzek , E. , Pasternak , A. , Pasternak , K. , Gdaniec , Z. , Yildirim , I. , Turner , D. H. and Kierzek , R. 2009 . Contributions of stacking, preorganization, and hydrogen bonding to the thermodynamic stability of duplexes between RNA and 2′-O-methyl RNA with locked nucleic acids . Biochemistry , 48 : 4377 – 4387 .
   PubMed Web of Science ®Google Scholar
• Julien , K. R. , Sumita , M. , Chen , P. , Laird-Offringa , I. A. and Hoogstraten , C. G. 2008 . Conformationally restricted nucleotides as a probe of structure-function relationships in RNA . RNA , 14 : 1632 – 1643 .
   PubMed Web of Science ®Google Scholar
• Heus , H. A. and Pardi , A. 1991 . Structural features that give rise to the unusual stability of RNA hairpins containing GNRA loops . Science , 253 : 191
   PubMed Web of Science ®Google Scholar
• SantaLucia , J. , Kierzek , R. and Turner , D. H. 1992 . Context dependence of hydrogen bond free energy revealed by substitutions in an RNA hairpin . Science , 256 : 217 – 219 .
   PubMed Web of Science ®Google Scholar
• Antao , V. P. , Lai , S. Y. and Tinoco , I. 1991 . A thermodynamic study of unusually stable RNA and DNA hairpins . Nucleic Acids Res. , 19 : 5901 – 5905 .
   PubMed Web of Science ®Google Scholar
• Hirao , I. , Nishimura , Y. , Tagawa , Y. , Watanabe , K. and Miura , K. 1992 . Extraordinarily stable mini-hairpins: electrophoretical and thermal properties of the various sequence variants of d(GCGAAAGC) and their effect on DNA sequencing . Nucleic Acids Res. , 20 : 3891 – 3896 .
   PubMed Web of Science ®Google Scholar
• Ormond , T. K. , Spear , D. , Stoll , J. , Mackey , M. A. and St. John , P. M. 2006 . Increase in hybridization rates with oligodeoxyribonucleotides containing locked nucleic acids . J. Biomol. Struct. Dyn. , 24 : 171 – 182 .
   PubMed Web of Science ®Google Scholar
• Shvadchak , S. , Sanglier , S. , Roci , S. , Villa , P. , Haiech , J. , Hibert , M. , Dorsselaer , A. v. , Mely , Y. and Rocquigny , H. d. 2009 . Identification by high throughput screening of small compounds inhibiting the nucleic acid destabilization activity of the HIV-1 nucleocapsid protein . Biochimie , 91 : 916 – 923 .
   PubMed Web of Science ®Google Scholar
• DeStefano , J. J. and Titilope , O. 2006 . Poliovirus protein 3AB displays nucleic acid chaperone and helix-destabilizing activities . J. Virol. , 80 : 1662 – 1671 .
   PubMed Web of Science ®Google Scholar
• Cruceanu , M. , Urbaneja , M. A. , Hixson , C. V. , Johnson , D. G. , Datta , S. A. , Fivash , M. J. , Stephen , A. G. , Fisher , R. J. , Gorelick , R. J. , Casas-Finet , J. R. , Rein , A. , Rouzina , I. and Williams , M. C. 2006 . Nucleic acid binding and chaperone properties of HIV-1 Gag and nucleocapsid proteins . Nucleic Acids Res. , 34 : 593 – 605 .
   PubMed Web of Science ®Google Scholar
• SantaLucia , J. and Allawi , H. T. 1997 . Thermodynamics and NMR of internal GT mismatches in DNA . Biochemistry , 36 : 10581 – 10594 .
   PubMed Web of Science ®Google Scholar
• Cavaluzzi , M. J. and Borer , P. N. 2004 . Revised UV extinction coefficients for nucleoside-5′-monophosphates and unpaired DNA and RNA . Nucleic Acids Res. , 32 : e13/11 – e13/19 .
   Web of Science ®Google Scholar
• Warshaw , M. M. , Cantor , C. R. and Shapiro , H. 1970 . Oligonucleotide interactions. 3. Circular dichroism studies of the conformation of deoxyoligonucleotides . Biopolymers , 9 : 1059 – 1077 .
   PubMed Web of Science ®Google Scholar
• Blake , R. D. and Delcourt , S. G. 1996 . Thermodynamic effects of formamide on DNA stability . Nucleic Acids Res. , 24 : 2095 – 2103 .
   PubMed Web of Science ®Google Scholar
• Bloomfield , V. A. , Crothers , D. M. and Tinoco , I. 2000 . Nucleic Acids: Structure, Properties, and Functions , Sausalito , CA : University Science Books .
   Google Scholar
• Albergo , D. D. , Marky , L. A. , Breslauer , K. J. and Turner , D. H. 1981 . Thermodynamics of (dG-dC)3 double helix formation in water and deuterium oxide . Biochemistry , 20 : 1409 – 1413 .
   PubMed Web of Science ®Google Scholar
• Xodo , L. E. , Manzini , G. , Quadrifoglio , F. , Marel , G. A.v.d. and Boom , J. H.v. 1988 . Oligodeoxynucleotide folding in solution: loop size and stability of B-hairpins . Biochemistry , 27 : 6321 – 6326 .
   PubMed Web of Science ®Google Scholar
• Owczarzy , R. 2005 . Melting temperatures of nucleic acids: discrepancies in analysis . Biophys. Chem. , 117 : 207 – 215 .
   PubMed Web of Science ®Google Scholar
• Freier , S. M. , Albergo , D. D. and Turner , D. H. 1983 . Solvent effects on the dynamics of (dG-dC)3 . Biopolymers , 22 : 1107 – 1131 .
   PubMed Web of Science ®Google Scholar
• Breslauer , K. , Sturtevant , J. and Tinoco , I. 1975 . Calorimetric and spectroscopic investigation of the helix-to-coil transition of a ribo-oligonucleotide: rA7U7 . J. Mol. Biol. , 99 : 549 – 565 .
   PubMed Web of Science ®Google Scholar
• Searle , M. S. and Williams , D. H. 1993 . On the stability of nucleic acid structures in solution: enthalpy–entropy compensations, internal rotations and reversibility . Nucleic Acids Res. , 21 : 2051 – 2056 .
   PubMed Web of Science ®Google Scholar
• Breslauer , K. J. 1994 . Extracting thermodynamic data from equilibrium melting curves for oligonucleotide order-disorder transitions . Methods Mol. Biol. , 26 : 347 – 372 .
   PubMedGoogle Scholar
• Nielsen , C. B. , Singh , S. K. , Wengel , J. and Jacobsen , J. P. 1999 . The solution structure of a locked nucleic acid (LNA) hybridized to DNA . J. Biomol. Struct. Dyn. , 17 : 175 – 191 .
   PubMed Web of Science ®Google Scholar
• Nielsen , K. E. , Singh , S. K. , Wengel , J. and Jacosbsen , J. P. 2000 . Solution structure of an LNA hybridized to DNA: NMR study of the d(CT(L)GCT(L)T(L)GC):d(GCAGAAGCAG) duplex containing four locked nucleotides . Bioconjug. Chem. , 11 : 228 – 238 .
   PubMed Web of Science ®Google Scholar
• Petersen , M. , Bondensgaard , K. , Wengel , J. and Jacobsen , J. P. 2002 . Locked nucleic acid (LNA) recognition of RNA: NMR solution structures of LNA:RNA hybrids . J. Am. Chem. Soc. , 124 : 5974 – 5982 .
   PubMed Web of Science ®Google Scholar
• Xodo , L. E. , Manzini , G. , Quadrifoglio , F. , Marel , G. A.v.d. and Boom , J. H.v. 1988 . The B-Z conformational transition in folded oligodeoxynucleotides: loop size and stability of Z-hairpins . Biochemistry , 27 : 6327 – 6331 .
   PubMed Web of Science ®Google Scholar
• Leulliot , N. , Baumruk , V. , Abdelkafi , M. , Turpin , P.-Y. , Namane , A. , Gouyette , C. , Huynh-Dinh , T. and Ghomi , M. 1999 . Unusual nucleotide conformations in GNRA and UNCG type tetraloops hairpins: evidence from Raman markers assignments . Nucleic Acids Res. , 27 : 1398 – 1404 .
   PubMed Web of Science ®Google Scholar
• Moody , E. M. , Feerrar , J. C. and Bevilacqua , P. C. 2004 . Evidence that folding of an RNA tetraloop hairpin is less cooperative than its DNA counterpart . Biochemistry , 43 : 7992
   PubMed Web of Science ®Google Scholar
• Xia , T. , SantaLucia , J. , Burkard , M. E. , Kierzek , R. , Schroeder , S. J. , Jiao , X. , Cox , C. and Turner , D. H. 1998 . Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson–Crick base pairs . Biochemistry , 37 : 14719 – 14735 .
   PubMed Web of Science ®Google Scholar