Fluorescent intercalator displacement replacement (FIDR) assay: Determination of relative thermodynamic and kinetic parameters in triplex formation-a case study using triplex-forming LNAs

Nucleic Acids Research

Volumn 40, Issue 21, 2012, Pages

  Sau, Sujay P ^a   Kumar, Pawan ^a,b   Sharma, Pawan K ^b   Hrdlicka, Patrick J ^a  

^a UNIVERSITY OF IDAHO   (United States)

^b KURUKSHETRA UNIVERSITY   (India)

Author keywords

[No Author keywords available]

Indexed keywords

ALPHA L LOCKED NUCLEIC ACID; C5 (3 AMINOPROPYN 1 YL) LOCKED NUCLEIC ACID; DOUBLE STRANDED DNA; ETHIDIUM; LOCKED NUCLEIC ACID; MONOMER; OLIGONUCLEOTIDE; PYRIMIDINE; TRIPLEX FORMING OLIGONUCLEOTIDE; UNCLASSIFIED DRUG;

ANALYTICAL PARAMETERS; ARTICLE; ASSAY; BINDING AFFINITY; BINDING KINETICS; CHEMICAL ANALYSIS; CHEMICAL STRUCTURE; CONFORMATION; DISSOCIATION; FLUORESCENT INTERCALATOR DISPLACEMENT REPLACEMENT ASSAY; GENE TARGETING; PRIORITY JOURNAL; THERMODYNAMICS;

DNA; ETHIDIUM; FLUORESCENT DYES; FLUOROMETRY; INTERCALATING AGENTS; KINETICS; MODELS, CHEMICAL; OLIGONUCLEOTIDES; THERMODYNAMICS;

EID: 84870610462     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks729     Document Type: Article

References (54)

1. Mukherjee, A. and Vasquez, K.M. (2011) Triplex technology in studies of DNA damage, DNA repair and mutagenesis. Biochimie, 93, 1197-1208.
2. Ghosh, I., Stains, C.I., Ooi, A.T. and Segal, D.J. (2006) Direct detection of double-stranded DNA: molecular methods and applications for DNA diagnostics. Mol. BioSyst., 2, 551-560. (Pubitemid 44583903)
3. Dervan, P.B., Doss, R.M. and Marques, M.A. (2005) Programmable DNA binding oligomers for control of transcription. Curr. Med. Chem. Anti-Cancer Agents, 5, 373-387. (Pubitemid 40974811)
4. Nielsen, P.E. (2010) Peptide nucleic acids (PNA) in chemical biology and drug discovery. Chem. Biodiversity, 7, 786-804.
5. Rapireddy, S., Bahal, R. and Ly, D.H. (2011) Strand invasion of mixed-sequence, double-helical B-DNA by g-peptide nucleic acids containing G-clamp nucleobases under physiological conditions. Biochemistry, 50, 3913-3918.
6. Lohse, J., Dahl, O. and Nielsen, P.E. (1999) Double duplex invasion by peptide nucleic acid: a general principle for sequence-specific targeting of double-stranded DNA, Proc. Natl Acad. Sci. USA, 96, 11804-11808. (Pubitemid 29502813)
7. Ishizuka, T., Yoshida, J., Yamamoto, Y., Sumaoka, J., Tedeschi, T., Corradini, R., Sforza, S. and Komiyama, M. (2008) Chiral introduction of positive charges to PNA for double-duplex invasion to versatile sequences. Nucleic Acids Res., 36, 1464-1471. (Pubitemid 351426100)
8. Beane, R., Gabillet, S., Montaillier, C., Arar, K. and Corey, D.R. (2008) Recognition of chromosomal DNA inside cells by locked nucleic acids. Biochemistry, 47, 13147-13149.
9. Sau, S.P., Kumar, T.S. and Hrdlicka, P.J. (2010) Invader LNA: efficient targeting of short double stranded DNA. Org. Biomol. Chem., 8, 2028-2036.
10. Duca, M., Vekhoff, P., Oussedik, K., Halby, L. and Arimondo, P.B. (2008) The triple helix: 50 years later, the outcome. Nucleic Acids Res., 36, 5123-5138.
11. Puri, N., Majumdar, A., Cuenoud, B., Miller, P.S. and Seidman, M.M. (2004) Importance of clustered 20-O-(2-aminoethyl) residues for the gene targeting activity of triple helix-forming oligonucleotides. Biochemistry, 43, 1343-1351. (Pubitemid 38176533)
12. Mergny, J.-L. and Lacroix, L. (2003) Analysis of thermal melting curves. Oligonucleotides, 13, 515-537. (Pubitemid 38296149)
13. Rusling, D.A., Broughton-Head, V.J., Tuck, A., Khairallah, H., Osborne, S.D., Brown, T. and Fox, K.R. (2008) Kinetic studies on the formation of DNA triplexes containing the nucleoside analogue 20-O-(2-aminoethyl)-5-(3-amino-1- propynyl)uridine. Org. Biomol. Chem., 6, 122-129. (Pubitemid 350255966)
14. Rougee, M., Faucon, B., Mergny, J.-L., Barcelo, F., Giovannangeli, C., Garestier, T. and Helène, C. (1992) Kinetics and thermodynamics of triple-helix formation: effects of ionic strength and mismatches. Biochemistry, 31, 9269-9278.
15. Protozanova, E. and Macgregor, R.B. (1996) Kinetic footprinting of DNA triplex formation. Anal. Biochem., 243, 92-99. (Pubitemid 26418581)
16. Paes, H. and Fox, K.R. (1997) Kinetic studies on the formation of intermolecular triple helices. Nucleic Acids Res., 25, 3269-3274. (Pubitemid 27338686)
17. Bates, P.J., Dosanjh, H.S., Kumar, S., Jenkins, T.C., Laughton, C.A. and Neidle, S. (1995) Detection and kinetic studies of triplex formation by oligodeoxynucleotides using real-time biomolecular interaction analysis (BIA). Nucleic Acids Res., 23, 3627-3632.
18. Torigoe, H., Hari, Y., Sekiguchi, M., Obika, S. and Imanishi, T. (2001) 20-O, 40-C-methylene bridged nucleic acid modification promotes pyrimidine motif triplex DNA formation at physiological pH: thermodynamic and kinetic studies. J. Biol. Chem., 276, 2354-2360.
19. Xodo, L.E. (1995) Kinetic analysis of triple-helix formation by pyrimidine oligodeoxynucleotides and duplex DNA. Eur. J. Biochem., 228, 918-926.
20. Yang, M., Ghosh, S.S. and Millar, D.P. (1994) Direct measurement of thermodynamic and kinetic parameters of DNA triple helix formation by fluorescence spectroscopy. Biochemistry, 33, 15329-15337.
21. Tse, W.C. and Boger, D.L. (2004) A fluorescent intercalator displacement assay for establishing DNA binding selectivity and affinity. Acc. Chem. Res., 37, 61-69.
22. Lewis, M.A. and Long, E.C. (2006) Fluorescent intercalator displacement analyses of DNA binding by the peptide-derived natural products netropsin, actinomycin and bleomycin. Bioorg. Med. Chem., 14, 3481-3490.
23. Krishnamurthy, M., Schirle, N.T. and Beal, P.A. (2008) Screening helix-threading peptides for RNA binding using a thiazole orange displacement assay. Bioorg. Med. Chem., 16, 8914-8921.
24. Hauschild, K.E., Stover, J.S., Boger, D.L. and Ansari, A.Z. (2009) CSI-FID: high throughput label-free detection of DNA binding molecules. Bioorg. Med. Chem. Lett., 19, 3779-3782.
25. Yeung, B.K.S., Tse, W.C. and Boger, D.L. (2003) Determination of binding affinities of triplex forming oligonucleotides using a fluorescent intercalator displacement (FID) assay. Bioorg. Med. Chem. Lett., 13, 3801-3804. (Pubitemid 37206511)
26. Kaur, H., Babu, B.R. and Maiti, S. (2007) Perspectives on chemistry and therapeutic applications of Locked Nucleic Acid (LNA). Chem. Rev., 107, 4672-4697. (Pubitemid 350225863)
27. 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. (Pubitemid 28108183)
28. Obika, S., Hari, Y., Sugimoto, T., Sekiguchi, M. and Imanishi, T. (2000) Triplex-forming enhancement with high sequence selectivity by single 20-O, 40-C-methylene bridged nucleic acid (20, 40-BNA) modification. Tetrahedron Lett., 41, 8923-8927.
29. Sensen, M.D., Kvn L., Bryld, T., Ha? kansson, A.E., Verbeure, B., Gaubert, G., Herdewijn, P. and Wengel, J. (2002) a-L-ribo-configured locked nucleic acid (a-L-LNA): synthesis and properties. J. Am. Chem. Soc., 124, 2164-2176. (Pubitemid 34267102)
30. Obika, S., Uneda, T., Sugimoto, T., Nanbu, D., Minami, T., Doi, T. and Imanishi, T. (2001) 20-O, 40-C-methylene bridged nucleic acid (20, 40-BNA). Bioorg. Med. Chem., 9, 1001-1011.
31. S?ensen, J.J., Nielsen, J.T. and Petersen, M. (2004) Solution structure of a dsDNA:LNA triplex. Nucleic Acids Res., 32, 6078-6085. (Pubitemid 40074002)
32. Sun, B.-W., Babu, B.R., S?ensen, M.D., Zakrzewska, K., Wengel, J. and Sun, J.-S. (2004) Sequence and pH effects of LNA-containing triple helix-forming oligonucleotides: physical chemistry, biochemistry and modeling studies. Biochemistry, 43, 4160-4169. (Pubitemid 38445636)
33. Brunet, E., Alberti, P., Perrouault, L., Babu, R., Wengel, J. and Giovannangeli, C. (2005) Exploring cellular activity of locked nucleic acid-modified triplex-forming oligonucleotides and defining its molecular basis. J. Biol. Chem., 280, 20076-20085. (Pubitemid 41379537)
34. Kumar, N., Nielsen, K.E., Maiti, S. and Petersen, M. (2006) Triplex formation with alpha-L-LNA (alpha-L-ribo-configured locked nucleic acid). J. Am. Chem. Soc., 128, 14-15. (Pubitemid 43100827)
35. Torigoe, H., Rahman, S.M.A., Takuma, H., Sato, N., Imanishi, T., Obika, S. and Sasaki, K. (2011) 20-O, 40-C-aminomethylene-bridged nucleic acid modification with enhancement of nuclease resistance promotes pyrimidine motif triplex nucleic acid formation at physiological pH. Chem. Eur. J., 17, 2742-2751.
36. Rahman, S.M.A., Seki, S., Obika, S., Haitani, S., Miyashita, K. and Imanishi, T. (2007) Highly stable pyrimidine-motif triplex formation at physiological pH values by a bridged nucleic acid analogue. Angew. Chem. Int. Ed., 46, 4306-4309. (Pubitemid 47040827)
37. Hland, T., Kumar, S., Babu, B.R., Umemoto, T., Albaek, N., Sharma, P.K., Nielsen, P. and Wengel, J. (2007) LNA (locked nucleic acid) and analogs as triplex-forming oligonucleotides. Org. Biomol. Chem., 5, 2375-2379. (Pubitemid 47133392)
38. Koizumi, M., Morita, K., Daigo, M., Tsutsumi, S., Abe, K., Obika, S. and Imanishi, T. (2003) Triplex formation with 20-O, 40-C-ethylene-bridged nucleic acids (ENA) having C30-endo conformation at physiological pH. Nucleic Acids Res., 31, 3267-3273. (Pubitemid 37441786)
39. Torigoe, H., Nakagawa, O., Imanishi, T., Obika, S. and Sasaki, K. (2012) Chemical modification of triplex-forming oligonucleotide to promote pyrimidine motif triplex formation at physiological pH. Biochimie, 94, 1032-1040.
40. Kumar, S., Hansen, M.H., Albaek, N., Steffansen, S.I., Petersen, M. and Nielsen, P. (2009) Synthesis of functionalized carbocyclic locked nucleic acid analogues by ring-closing diene and enyne metathesis and their influence on nucleic acid stability and structure. J. Org. Chem., 74, 6756-6769.
41. Bijapur, J., Keppler, M.D., Bergqvist, S., Brown, T. and Fox, K.R. (1999) 5-(1-propargylamino)-20-deoxyuridine (UP): a novel thymidine analogue for generating DNA triplexes with increased stability. Nucleic Acids Res., 27, 1802-1809. (Pubitemid 29209621)
42. Brazier, J.A., Shibata, T., Townsley, J., Taylor, B.F., Frary, E., Williams, N.H. and Williams, D.M. (2005) Amino-functionalized DNA: the properties of C5-amino-alkyl substituted 20-deoxyuridines and their application in DNA triplex formation. Nucleic Acids Res., 33, 1362-1371. (Pubitemid 41439929)
43. Lacroix, L., Lacoste, J., Reddoch, J.F., Mergny, J.-L., Levy, D.D., Seidman, M.M., Matteucci, M.D. and Glazer, P.M. (1999) Triplex formation by oligonucleotides containing 5-(1-propynyl)-20-deoxyuridine: decreased magnesium dependence and improved intracellular gene targeting. Biochemistry, 38, 1893-1901.
44. Phipps, A.K., Tarko?y, M., Schultze, P. and Feigon, J. (1998) Solution structure of an intramolecular DNA triplex containing 5-(1-propynyl)-20- deoxyuridine residues in the third strand. Biochemistry, 37, 5820-5830. (Pubitemid 28196733)
45. Li, H., Miller, P.S. and Seidman, M.M. (2008) Selectivity and affinity of DNA triplex forming oligonucleotides containing the nucleoside analogues 20-O-methyl-5-(3-amino-1-propynyl)uridine and 20-O-methyl-5-propynyluridine. Org. Biomol. Chem., 6, 4212-4217.
46. Lou, C., Xiao, Q., Brennan, L., Light, M.E., Vergara-Irigaray, N., Atkinson, E.M., Holden-Dye, L.M., Fox, K.R. and Brown, T. (2010) Synthesis and properties of triplex-forming oligonucleotides containing 20-O-(2-methoxyethyl)- 5-(3-aminoprop-1-ynyl)-uridine. Bioorg. Med. Chem., 18, 6389-6397.
47. Sollogoub, M., Darby, R.A.J., Cuenoud, B., Brown, T., Fox, K.R., Coman, D. and Russu, I.M. (2002) Stable DNA triple helix formation using oligonucleotides containing 20-aminoethoxy-5-propargylamino-U. Biochemistry, 41, 7224-7231. (Pubitemid 34602438)
48. ?tergaard, M.E., Kumar, P., Baral, B., Raible, D.J., Kumar, T.S., Anderson, B.A., Guenther, D.C., Deobald, L., Paszczynski, A.J. and Sharma, P.K. (2009) C5-functionalized LNA: unparalleled hybridization properties and enzymatic stability. ChemBioChem, 10, 2740-2743.
49. Sau, S.P., Kumar, P., Anderson, B.A., ?tergaard, M.E., Deobald, L., Paszczynski, A., Sharma, P.K. and Hrdlicka, P.J. (2009) Optimized DNA-targeting using triplex forming C5-alkynyl functionalized LNA. Chem. Commun., 6756-6758.
50. Mergny, J.-L., Collier, D., Rougee, M., Montenay-Garestier, T. and He?lène, C. (1991) Intercalation of ethidium bromide into oligonucleotide. Nucleic Acids Res., 19, 1521-1526.
51. Maher, L.J., Dervan, P.B. and Wold, B. (1990) Kinetic analysis of oligodeoxyribonucleotide-directed triple-helix formation on DNA. Biochemistry, 29, 8820-8826. (Pubitemid 20302781)
52. Sugimoto, N., Wu, P., Hara, H. and Kawamoto, Y. (2001) pH and cation effects on the properties of parallel pyrimidine motif DNA triplexes. Biochemistry, 40, 9396-9405. (Pubitemid 32730063)
53. Lee, J.S., Woodsworth, M.L., Latimer, L.J.P. and Morgan, A.R. (1984) Poly(pyrimidine) poly(purine) synthetic DNAs containing 5-methylcytosine form stable triplexes at neutral pH. Nucleic Acids Res., 12, 6603-6614.
54. Scaria, P.V. and Shafer, R.H. (1991) Binding of ethidium bromide to a DNA triple helix. Evidence for intercalation. J. Biol. Chem., 266, 5417-5423. (Pubitemid 21909510)