Effects of locked nucleic acid substitutions on the stability of oligonucleotide hairpins

Nucleosides, Nucleotides and Nucleic Acids

Volumn 31, Issue 1, 2012, Pages 28-41

  Hull, Chelsea ^a   Szewcyk, Corinne ^a   St John, Pamela M ^a  

^a STATE UNIVERSITY OF NEW YORK   (United States)

Author keywords

LNA; modified oligonucleotides; nucleid acid structure; physical properties

Indexed keywords

DNA HYBRID; DOUBLE STRANDED DNA; FORMAMIDE;

ARTICLE; CONTROLLED STUDY; DNA HAIRPIN; DNA HYBRIDIZATION; DNA STRUCTURE; ENTHALPY; ENTROPY; HIGH RESOLUTION MELTING ANALYSIS; NUCLEIC ACID BASE SUBSTITUTION; RNA HYBRIDIZATION; ULTRAVIOLET SPECTROSCOPY;

DNA; FORMAMIDES; INVERTED REPEAT SEQUENCES; NUCLEIC ACID CONFORMATION; OLIGONUCLEOTIDES; RNA; RNA STABILITY; SPECTRUM ANALYSIS; THERMODYNAMICS; TRANSITION TEMPERATURE;

RNA VIRUSES;

EID: 84856868603     PISSN: 15257770     EISSN: 15322335     Source Type: Journal    
DOI: 10.1080/15257770.2011.639826     Document Type: Article

References (37)

1. Kaur, H.; Wengel, J.; Maiti, S. Thermodynamics of DNA-RNA heteroduplex formation: effects of locked nucleic acid nucleotides incorporated into the DNA strand. Biochemistry 2008, 47, 1218-1227. (Pubitemid 351161878)
2. Koshkin, A.A.; Nielsen, P.; Meldgaard, M.; Rajwanshi, V.K.; Singh, S.K.; Wengel, J. LNA (locked nucleic acid): an RNA mimic forming exceedingly stable LNA:LNA duplexes. J. Am. Chem. Soc. 1998, 120, 13252-13253. (Pubitemid 29024087)
3. Kurreck, J.; Wyszko, E.; Gillen, C.; Erdmann, V.A. Design of antisense oligonucleotides stabilized by locked nucleic acids. Nucleic Acids Res. 2002, 30, 1911-1918. (Pubitemid 34537585)
4. McTigue, P.M.; Peterson, R.J.; Kahn, J.D. Sequence-dependent thermodynamic parameters for locked nucleic acid (LNA)-DNA duplex formation. Biochemistry 2004, 43, 5388-5405. (Pubitemid 38620931)
5. Kierzek, E.; Ciesielska, A.; Pasternak, K.; Mathews, D.H.; Turner, D.H.; Kierzek, R. The influence of locked nucleic acid residues on the thermodynamic properties of 2′-O-methyl RNA/RNA heteroduplexes. Nucleic Acids Res. 2005, 33, 5082-5093. (Pubitemid 41487816)
6. Kaur, H.; Arora, A.; Wengel, J.; Maiti, S. Thermodynamic, counterion and hydration effects for the incorporation of locked nucleic acid nucleotides into DNA duplexes. Biochemistry 2006, 45, 7347-7344.
7. Pasternak, A.; Kierzek, E.; Pasternak, K.; Fratczak, A.; Turner, D.H.; Kierzek, R. 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 2008, 47, 1249-1258. (Pubitemid 351198702)
8. Bruylants, G.; Boccongelli, M.; Snoussi, K.; Bartik, K. Comparison of the thermodynamics and basepair dynamics of a full LNA:DNA duplex and of the isosequential DNA:DNA duplex. Biochemistry 2009, 48, 8473-8482.
9. Kierzek, E.; Pasternak, A.; Pasternak, K.; Gdaniec, Z.; Yildirim, I.; Turner, D.H.; Kierzek, R. 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 2009, 48, 4377-4387.
10. Julien, K.R.; Sumita, M.; Chen, P.; Laird-Offringa, I.A.; Hoogstraten, C.G. Conformationally restricted nucleotides as a probe of structure-function relationships in RNA. RNA 2008, 14, 1632-1643.
11. Heus, H.A.; Pardi, A. Structural features that give rise to the unusual stability of RNA hairpins containing GNRA loops. Science 1991, 253, 191.
12. SantaLucia, J.; Kierzek, R.; Turner, D.H. Context dependence of hydrogen bond free energy revealed by substitutions in an RNA hairpin. Science 1992, 256, 217-219.
13. Antao, V.P.; Lai, S.Y.; Tinoco, I. A thermodynamic study of unusually stable RNA and DNA hairpins. Nucleic Acids Res. 1991, 19, 5901-5905. (Pubitemid 21913002)
14. Hirao, I.; Nishimura, Y.; Tagawa, Y.; Watanabe, K.; Miura, K. 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. 1992, 20, 3891-3896.
15. Ormond, T.K.; Spear, D.; Stoll, J.; Mackey, M.A.; St. John, P.M. Increase in hybridization rates with oligodeoxyribonucleotides containing locked nucleic acids. J. Biomol. Struct. Dyn. 2006, 24, 171-182. (Pubitemid 44570213)
16. Shvadchak, S.; Sanglier, S.; Roci, S.; Villa, P.; Haiech, J.; Hibert, M.; Dorsselaer, A.v.; Mely, Y.; Rocquigny, H.d. Identification by high throughput screening of small compounds inhibiting the nucleic acid destabilization activity of the HIV-1 nucleocapsid protein. Biochimie 2009, 91, 916-923.
17. DeStefano, J.J.; Titilope, O. Poliovirus protein 3AB displays nucleic acid chaperone and helixdestabilizing activities. J. Virol. 2006, 80, 1662-1671. (Pubitemid 43228708)
18. 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.;Williams, M.C. Nucleic acid binding and chaperone properties of HIV-1 Gag and nucleocapsid proteins. Nucleic Acids Res. 2006, 34, 593-605. (Pubitemid 43240247)
19. SantaLucia, J.; Allawi, H.T. Thermodynamics and NMR of internal GT mismatches in DNA. Biochemistry 1997, 36, 10581-10594. (Pubitemid 27374152)
20. Cavaluzzi, M.J.; Borer, P.N. Revised UV extinction coefficients for nucleoside-5′-monophosphates and unpaired DNA and RNA. Nucleic Acids Res. 2004, 32, e13/11-e13/19.
21. Warshaw, M.M.; Cantor, C.R.; Shapiro, H. Oligonucleotide interactions. 3. Circular dichroism studies of the conformation of deoxyoligonucleotides. Biopolymers 1970, 9, 1059-1077.
22. Blake, R.D.; Delcourt, S.G. Thermodynamic effects of formamide on DNA stability. Nucleic Acids Res. 1996, 24, 2095-2103. (Pubitemid 26174552)
23. Bloomfield, V.A.; Crothers, D.M.; Tinoco, I. Nucleic Acids: Structure, Properties, and Functions, University Science Books, Sausalito, CA, 2000.
24. Albergo, D.D.; Marky, L.A.; Breslauer, K.J.; Turner, D.H. Thermodynamics of (dG-dC)3 double helix formation in water and deuterium oxide. Biochemistry 1981, 20, 1409-1413.
25. Xodo, L.E.; Manzini, G.; Quadrifoglio, F.;Marel, G.A.v.d.; Boom, J.H.v. Oligodeoxynucleotide folding in solution: loop size and stability of B-hairpins. Biochemistry 1988, 27, 6321-6326.
26. Owczarzy, R. Melting temperatures of nucleic acids: discrepancies in analysis. Biophys. Chem. 2005, 117, 207-215. (Pubitemid 41253595)
27. Freier, S.M.; Albergo, D.D.; Turner, D.H. Solvent effects on the dynamics of (dG-dC)3. Biopolymers 1983, 22, 1107-1131.
28. Breslauer, K.; Sturtevant, J.; Tinoco, I. Calorimetric and spectroscopic investigation of the helix-tocoil transition of a ribo-oligonucleotide: rA7U7. J. Mol. Biol. 1975, 99, 549-565.
29. Searle, M.S.; Williams, D.H. On the stability of nucleic acid structures in solution: enthalpy-entropy compensations, internal rotations and reversibility. Nucleic Acids Res. 1993, 21, 2051-2056. (Pubitemid 23160720)
30. Breslauer, K.J. Extracting thermodynamic data from equilibrium melting curves for oligonucleotide order-disorder transitions. Methods Mol. Biol. 1994, 26, 347-372.
31. Nielsen, C.B.; Singh, S.K.; Wengel, J.; Jacobsen, J.P. The solution structure of a locked nucleic acid (LNA) hybridized to DNA. J. Biomol. Struct. Dyn. 1999, 17, 175-191. (Pubitemid 29510977)
32. Nielsen, K.E.; Singh, S.K.; Wengel, J.; Jacosbsen, J.P. 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. 2000, 11, 228-238. (Pubitemid 30174490)
33. Petersen, M.; Bondensgaard, K.; Wengel, J.; Jacobsen, J.P. Locked nucleic acid (LNA) recognition of RNA: NMR solution structures of LNA:RNA hybrids. J. Am. Chem. Soc. 2002, 124, 5974-5982. (Pubitemid 34555398)
34. Xodo, L.E.; Manzini, G.; Quadrifoglio, F.; Marel, G.A.v.d.; Boom, J.H.v. The B-Z conformational transition in folded oligodeoxynucleotides: loop size and stability of Z-hairpins. Biochemistry 1988, 27, 6327-6331.
35. Leulliot, N.; Baumruk, V.; Abdelkafi, M.; Turpin, P.-Y.; Namane, A.; Gouyette, C.; Huynh-Dinh, T.; Ghomi, M. Unusual nucleotide conformations in GNRA and UNCG type tetraloops hairpins: evidence from Raman markers assignments. Nucleic Acids Res. 1999, 27, 1398-1404. (Pubitemid 29206453)
36. Moody, E.M.; Feerrar, J.C.; Bevilacqua, P.C. Evidence that folding of an RNA tetraloop hairpin is less cooperative than its DNA counterpart. Biochemistry 2004, 43, 7992.
37. Xia, T.; SantaLucia, J.; Burkard, M.E.; Kierzek, R.; Schroeder, S.J.; Jiao, X.; Cox, C.; Turner, D.H. Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs. Biochemistry 1998, 37, 14719-14735. (Pubitemid 28487580)