Design of LNA probes that improve mismatch discrimination

Nucleic Acids Research

Volumn 34, Issue 8, 2006, Pages

  You, Yong ^a   Moreira, Bernardo G ^a   Behlke, Mark A ^a   Owczarzy, Richard ^a  

^a INTEGRATED DNA TECHNOLOGIES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

2 AMINOPURINE; DOUBLE STRANDED DNA; GUANINE NUCLEOTIDE; LOCKED NUCLEIC ACID; SODIUM ION; ANTISENSE OLIGONUCLEOTIDE; DNA; MAGNESIUM; SODIUM;

ARTICLE; BASE MISPAIRING; BASE PAIRING; CONTROLLED STUDY; DNA DENATURATION; DNA FLANKING REGION; DNA MODIFICATION; DNA PROBE; DNA SEQUENCE; FLUORESCENCE ANALYSIS; INTERMETHOD COMPARISON; MOLECULAR INTERACTION; NUCLEIC ACID PROBE; PRIORITY JOURNAL; CHEMISTRY; FLUORESCENCE; STANDARD; TEMPERATURE;

2-AMINOPURINE; BASE PAIR MISMATCH; DNA; FLUORESCENCE; MAGNESIUM; NUCLEIC ACID DENATURATION; NUCLEIC ACID PROBES; OLIGONUCLEOTIDES, ANTISENSE; SODIUM; TEMPERATURE;

EID: 33646849284     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkl175     Document Type: Article

References (36)

1. Ugozzoli,L.A., Latorra,D., Puckett,R., Arar,K. and Hamby,K. (2004) Real-time genotyping with oligonucleotide probes containing locked nucleic acids. Anal. Biochem., 324, 143-152.
2. Johnson,M.P., Haupt,L.M. and Griffiths,L.R. (2004) Locked nucleic acid (LNA) single nucleotide polymorphism (SNP) genotype analysis and validation using real-time PCR. Nucleic Acids Res., 32, e55.
3. Wang,L., Blasic,J.R.,Jr, Holden,M.J. and Pires,R. (2005) Sensitivity comparison of real-time PCR probe designs on a model DNA plasmid. Anal. Biochem., 344, 257-265.
4. Chou,L.-S., Meadows,C., Wittwer,C.T. and Lyon,E. (2005) Unlabeled oligonucleotide probes modified with locked nucleic acids for improved mismatch discrimination in genotyping by melting analysis. BioTechniques, 39, 644-647.
5. Mouritzen,P., Nielsen,A.T., Pfundheller,H.M., Choleva,Y., Kongsbak,L. and Møller,S. (2003) Single nucleotide polymorphism genotyping using locked nucleic acid (LNA™). Expert Rev. Mol. Diagn., 3, 27-38.
6. Kauppinen,S., Nielsen,P.S., Mouritzen,P., Nielsen,A.T., Vissing,H., Møller,S. and Ramsing,N.B. (2003) LNA microarrays in genomics. PharmaGenomics, 3, 24-34.
7. Braasch,D.A., Jensen,S., Liu,Y., Kaur,K., Arar,K., White,M.A. and Corey,D.R. (2003) RNA interference in mammalian cells by chemically-modified RNA. Biochemistry, 42, 7967-7975.
8. Braasch,D.A., Liu,Y. and Corey,D.R. (2002) Antisense inhibition of gene expression in cells by oligonucleotides incorporating locked nucleic acids: Effect of mRNA target sequence and chimera design. Nucleic Acids Res., 30, 5160-5167.
9. Du,H., Strohsahl,C.M., Camera,J., Miller,B.L. and Krauss,T.D. (2005) Sensitivity and specificity of metal surface-immobilized 'molecular beacon' biosensors. J. Am. Chem. Soc., 127, 7932-7940.
10. Koshkin,A.A., Singh,S.K., Nielsen,P., Rajwanshi,V.K., Kumar,R., Meldgaard,M., Olsen,C.E. and Wengel,J. (1998) LNA (Locked Nucleic Acids): Synthesis of the adenine, cytosine, guanine, 5-methylcytosine, thymine and uracil bicyclonucleoside monomers, oligomerisation, and unprecedented nucleic acid recognition. Tetrahedron, 54, 3607-3630.
11. Tolstrup,N., Nielsen,P.S., Kolberg,J.G., Frankel,A.M., Vissing,H. and Kauppinen,S. (2003) OligoDesign: Optimal design of LNA (locked nucleic acid) oligonucleotide capture probes for gene expression profiling. Nucleic Acids Res., 31, 3758-3762.
12. 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.
13. Ørum,H., Jakobsen,M.H., Koch,T., Vuust,J. and Borre,M.B. (1999) Detection of the factor V Leiden mutation by direct allele-specific hybridization of PCR amplicons to photoimmobilized locked nucleic acids. Clin. Chem., 45, 1898-1905.
14. Simeonov,A. and Nikiforov,T.T. (2002) Single nucleotide polymorphism genotyping using short, fluorescently labeled locked nucleic acid (LNA) probes and fluorescence polarization detection. Nucleic Acids Res., 30, e91.
15. 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.
16. Frieden,M., Hansen,H.F. and Koch,T. (2003) Nuclease stability of LNA oligonucleotides and LNA-DNA chimeras. Nucleosides Nucleotides Nucleic Acids, 22, 1041-1043.
17. Wahlestedt,C., Salmi,P., Good,L., Kela,J., Johnsson,T., Hökfelt,T., Broberger,C., Porreca,F., Lai,J., Ren,K. et al. (2000) Potent and nontoxic antisense oligonucleotides containing locked nucleic acids. Proc. Natl Acad. Sci. USA., 97, 5633-5638.
18. Moreira,B.G., You,Y., Behlke,M.A. and Owczarzy,R. (2005) Effects of fluorescent dyes, quenchers, and dangling ends on DNA duplex stability. Biochem. Biophys. Res. Commun., 327, 473-484.
19. Owczarzy,R., You,Y., Moreira,B.G., Manthey,J.A., Huang,L., Behlke,M.A. and Walder,J.A. (2004) Effects of sodium ions on DNA duplex oligomers: improved predictions of melting temperatures. Biochemistry, 43, 3537-3554.
20. Fasman,G.D. (1975) Handbook of Biochemistry and Molecular Biology. CRC Press, Cleveland, Ohio, Vol. I, pp. 589.
21. Kaiser,J.F. and Reed,W.A. (1977) Data smoothing using low-pass digital filters. Rev. Sci. Instrum., 48, 1447-1457.
22. Owczarzy,R. (2005) Melting temperatures of nucleic acids: Discrepancies in analysis. Biophys. Chem., 117, 207-215.
23. Petersen,M., Nielsen,C.B., Nielsen,K.E., Jensen,G.A., Bondensgaard,K., Singh,S.K., Rajwanshi,V.K., Koshkin,A.A., Dahl,B.M., Wengel,J. et al. (2000) The conformations of locked nucleic acids (LNA). J. Mol. Recognit., 13, 44-53.
24. LGC): D(GCAGAAGCAG) duplex containing four locked nucleotides. Bioconjugate Chem., 11, 228-238.
25. Anderson,C.F. and Record,M.T.,Jr (1995) Salt-nucleic acid interactions. Annu. Rev. Phys. Chem., 46, 657-700.
26. Petersheim,M. and Turner,D.H. (1983) Base-stacking and base-pairing contributions to helix stability: Thermodynamics of double-helix formation with CCGG, CCGGp, CCGGAp, ACCGGp, CCGGUp, and ACCGGUp. Biochemistry, 22, 256-263.
27. Rachofsky,E.L., Osman,R. and Ross,J.B.A. (2001) Probing structure and dynamics of DNA with 2-aminopurine: Effects of local environment on fluorescence. Biochemistry, 40, 946-956.
28. Jean,J.M. and Hall,K.B. (2001) 2-Aminopurine fluorescence quenching and lifetimes: Role of base stacking. Proc. Natl Acad. Sci. USA., 98, 37-41.
29. Eritja,R., Kaplan,B.E., Mhaskar,D., Sowers,L.C., Petruska,J. and Goodman,M.F. (1986) Synthesis and properties of defined DNA oligomers containing base mispairs involving 2-aminopurine. Nucleic Acids Res., 14, 5869-5884.
30. Law,S.M., Eritja,R., Goodman,M.F. and Breslauer,K.J. (1996) Spectroscopic and calorimetric characterizations of DNA duplexes containing 2-aminopurine. Biochemistry, 35, 12329-12337.
31. Egli,M., Minasov,G., Tereshko,V., Pallan,P.S., Teplova,M., Inamati,G.B., Lesnik,E.A., Owens,S.R., Ross,B.S., Prakash,T.P. et al. (2005) Probing the influence of stereoelectronic effects on the biophysical properties of oligonucleotides: Comprehensive analysis of the RNA affinity, nuclease resistance, and crystal structure of ten 2′-O-ribonucleic acid modifications. Biochemistry, 44, 9045-9057.
32. SantaLucia,J.,Jr and Hicks,D. (2004) The thermodynamics of DNA structural motifs. Annu. Rev. Biophys. Biomol. Struct., 33, 415-440.
33. Urakawa,H., Noble,P.A., Fantroussi,S.E., Kelly,J.J. and Stahl,D.A. (2002) Single-base-pair discrimination of terminal mismatches by using oligonucleotide microarrays and neural network analyses. Appl. Environ. Microbiol., 68, 235-244.
34. Letowski,J., Brousseau,R. and Masson,L. (2004) Designing better probes: effect of probe size, mismatch position and number on hybridization in DNA oligonucleotide microarrays. J. Microbiol. Meth., 57, 269-278.
35. 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.
36. 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.