Rapid oligonucleotide-templated fluorogenic tetrazine ligations

Nucleic Acids Research

Volumn 41, Issue 15, 2013, Pages

  Šečkute, Jolita ^a   Yang, Jun ^a   Devaraj, Neal K ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; COMPLEMENTARY RNA; FLUORESCENT DYE; FLUOROPHORE; METHYL CYCLOPROPYLENE DIENOPHILE DERIVATIVE; OLIGONUCLEOTIDE; PROPYLENE; TETRAZINE DERIVATIVE; UNCLASSIFIED DRUG;

ARTICLE; CHEMICAL REACTION KINETICS; CHEMICAL STRUCTURE; CONTROLLED STUDY; CYCLOADDITION; DNA DETERMINATION; DNA HYBRIDIZATION; DNA MODIFICATION; DNA PROBE; DNA SEQUENCE; DNA TEMPLATE; FLUORESCENCE; PRIORITY JOURNAL; RNA ANALYSIS; RNA SEQUENCE;

BASE SEQUENCE; CULTURE MEDIA; CYCLOADDITION REACTION; CYCLOPROPANES; FLUORESCENCE; FLUORESCENT DYES; HELA CELLS; HUMANS; NUCLEIC ACID HYBRIDIZATION; OLIGONUCLEOTIDE PROBES; OLIGONUCLEOTIDES, ANTISENSE; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS, DNA; SEQUENCE ANALYSIS, RNA;

EID: 84883485838     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt540     Document Type: Article

References (56)

1. Stojanovic,M.N., de Prada,P. and Landry,D.W. (2001) Catalytic molecular beacons. ChemBioChem, 2, 411-415
2. Liu,J., Cao,Z. and Lu,Y. (2009) Functional nucleic acid sensors. Chem. Rev., 109, 1948-1998
3. Dave,N. and Liu,J. (2010) Fast molecular beacon hybridization in organic solvents with improved target specificity. J. Phys. Chem. B., 114, 15694-15699
4. Armitage,B.A. (2011) Imaging of RNA in live cells. Curr. Opin. Chem. Biol., 15, 806-812
5. Chen,A.K., Davydenko,O., Behlke,M.A. and Tsourkas,A. (2010) Ratiometric bimolecular beacons for the sensitive detection of RNA in single living cells. Nucleic Acids Res., 38, e148
6. Silverman,A.P. and Kool,E.T. (2006) Detecting RNA and DNA with templated chemical reactions. Chem. Rev., 106, 3775-3789
7. Wang,K., Tang,Z., Yang,C.J., Kim,Y., Fang,X., Li,W., Wu,Y., Medley,C.D., Cao,Z., Li,J. et al. (2009) Molecular engineering of DNA: molecular beacons. Angew Chem. Int. Ed. Engl., 48, 856-870
8. Marti,A.A., Jockusch,S., Stevens,N., Ju,J. and Turro,N.J. (2007) Fluorescent hybridization probes for sensitive and selective DNA and RNA detection. Acc. Chem. Res., 40, 402-409
9. Tsourkas,A., Behlke,M.A., Rose,S.D. and Bao,G. (2003) Hybridization kinetics and thermodynamics of molecular beacons. Nucleic Acids Res., 31, 1319-1330
10. Guo,J., Ju,J. and Turro,N.J. (2012) Fluorescent hybridization probes for nucleic acid detection. Anal. Bioanal. Chem., 402, 3115-3125
11. Tyagi,S. (2009) Imaging intracellular RNA distribution and dynamics in living cells. Nat. Methods, 6, 331-338
12. Mhlanga,M.M., Vargas,D.Y., Fung,C.W., Kramer,F.R. and Tyagi,S. (2005) tRNA-linked molecular beacons for imaging mRNAs in the cytoplasm of living cells. Nucleic Acids Res., 33, 1902-1912
13. Gryaznov,S.M., Schultz,R., Chaturvedi,S.K. and Letsinger,R.L. (1994) Enhancement of selectivity in recognition of nucleic acids via chemical autoligation. Nucleic Acids Res., 22, 2366-2369
14. Kumar,R., El-Sagheer,A., Tumpane,J., Lincoln,P., Wilhelmsson,L.M. and Brown,T. (2007) Template-directed oligonucleotide strand ligation, covalent intramolecular DNA circularization and catenation using click chemistry. J. Am. Chem. Soc., 129, 6859-6864
15. Kolpashchikov,D.M. (2006) A binary DNA probe for highly specific nucleic Acid recognition. J. Am. Chem. Soc., 128, 10625-10628
16. Socher,E., Jarikote,D.V., Knoll,A., Roglin,L., Burmeister,J. and Seitz,O. (2008) FIT probes: peptide nucleic acid probes with a fluorescent base surrogate enable real-time DNA quantification and single nucleotide polymorphism discovery. Anal. Biochem., 375, 318-330
17. Okamoto,A. (2011) ECHO probes: a concept of fluorescence control for practical nucleic acid sensing. Chem. Soc. Rev., 40, 5815-5828
18. Rohatgi,R., Bartel,D.P. and Szostak,J.W. (1996) Nonenzymatic, template-directed ligation of oligoribonucleotides is highly regioselective for the formation of 30-50 phosphodiester bonds. J. Am. Chem. Soc., 118, 3340-3344
19. Sarkar,T., Conwell,C.C., Harvey,L.C., Santai,C.T. and Hud,N.V. (2005) Condensation of oligonucleotides assembled into nicked and gapped duplexes: potential structures for oligonucleotide delivery. Nucleic Acids Res., 33, 143-151
20. Bruick,R.K., Dawson,P.E., Kent,S.B., Usman,N. and Joyce,G.F. (1996) Template-directed ligation of peptides to oligonucleotides. Chem. Biol., 3, 49-56
21. Peng,X., Li,H. and Seidman,M. (2010) A template-mediated clickclick reaction: PNA-DNA, PNA-PNA (or peptide) ligation, and single nucleotide discrimination. Eur. J. Org. Chem., 2010, 4194-4197
22. Peelen,D. and Smith,L.M. (2005) Immobilization of aminemodified oligonucleotides on aldehyde-terminated alkanethiol monolayers on gold. Langmuir, 21, 266-271
23. Xu,Y., Karalkar,N.B. and Kool,E.T. (2001) Nonenzymatic autoligation in direct three-color detection of RNA and DNA point mutations. Nat. Biotechnol., 19, 148-152
24. Sando,S. and Kool,E.T. (2002) Quencher as leaving group: efficient detection of DNA-joining reactions. J. Am. Chem. Soc., 124, 2096-2097
25. Silverman,A.P. and Kool,E.T. (2005) Quenched probes for highly specific detection of cellular RNAs. Trends Biotechnol., 23, 225-230
26. Shibata,A., Abe,H. and Ito,Y. (2012) Oligonucleotide-templated reactions for sensing nucleic acids. Molecules, 17, 2446-2463
27. El-Sagheer,A.H. and Brown,T. (2010) Click chemistry with DNA. Chem. Soc. Rev., 39, 1388-1405
28. Gorska,K., Keklikoglou,I., Tschulena,U. and Winssinger,N. (2011) Rapid fluorescence imaging of miRNAs in human cells using templated Staudinger reaction. Chem. Sci., 2, 1969
29. Furukawa,K., Abe,H., Tamura,Y., Yoshimoto,R., Yoshida,M., Tsuneda,S. and Ito,Y. (2011) Fluorescence detection of intron lariat RNA with reduction-triggered fluorescent probes. Angew. Chem. Int. Ed. Engl., 50, 12020-12023
30. Chen,X.H., Roloff,A. and Seitz,O. (2012) Consecutive signal amplification for DNA detection based on de novo fluorophore synthesis and host-guest chemistry. Angew. Chem. Int. Ed. Engl., 51, 4479-4483
31. Meguellati,K., Koripelly,G. and Ladame,S. (2010) DNAtemplated synthesis of trimethine cyanine dyes: a versatile fluorogenic reaction for sensing G-quadruplex formation. Angew Chem. Int. Ed. Engl., 49, 2738-2742
32. Sando,S., Abe,H. and Kool,E.T. (2004) Quenched auto-ligating DNAs: multicolor identification of nucleic acids at single nucleotide resolution. J. Am. Chem. Soc., 126, 1081-1087
33. Devaraj,N.K., Hilderbrand,S., Upadhyay,R., Mazitschek,R. and Weissleder,R. (2010) Bioorthogonal turn-on probes for imaging small molecules inside living cells. Angew. Chem. Int. Ed. Engl., 49, 2869-2872
34. Devaraj,N.K. and Weissleder,R. (2011) Biomedical applications of tetrazine cycloadditions. Acc. Chem. Res., 44, 816-827
35. Liu,D.S., Tangpeerachaikul,A., Selvaraj,R., Taylor,M.T., Fox,J.M. and Ting,A.Y. (2012) Diels-Alder cycloaddition for fluorophore targeting to specific proteins inside living cells. J. Am. Chem. Soc., 134, 792-795
36. Plass,T., Milles,S., Koehler,C., Szymanski,J., Mueller,R., Wiessler,M., Schultz,C. and Lemke,E.A. (2012) Amino acids for Diels-Alder reactions in living cells. Angew. Chem. Int. Ed. Engl., 51, 4166-4170
37. Dumas-Verdes,C., Miomandre,F., Lepicier,E., Galangau,O., Vu,T.T., Clavier,G., Meallet-Renault,R. and Audebert,P. (2010) BODIPY-Tetrazine multichromophoric derivatives. Eur. J. Org. Chem., 2010, 2525-2535
38. Budin,G., Yang,K.S., Reiner,T. and Weissleder,R. (2011) Bioorthogonal probes for polo-like kinase 1 imaging and quantification. Angew. Chem. Int. Ed. Engl., 50, 9378-9381
39. Lang,K., Davis,L., Torres-Kolbus,J., Chou,C., Deiters,A. and Chin,J.W. (2012) Genetically encoded norbornene directs sitespecific cellular protein labelling via a rapid bioorthogonal reaction. Nat. Chem., 4, 298-304
40. Yang,J., Seckute,J., Cole,C.M. and Devaraj,N.K. (2012) Live-cell imaging of cyclopropene tags with fluorogenic tetrazine cycloadditions. Angew. Chem. Int. Ed. Engl., 51, 7476-7479
41. Sletten,E.M. and Bertozzi,C.R. (2011) From mechanism to mouse: a tale of two bioorthogonal reactions. Acc. Chem. Res., 44, 666-676
42. Blackman,M.L., Royzen,M. and Fox,J.M. (2008) Tetrazine ligation: fast bioconjugation based on inverse-electron-demand diels-alder reactivity. J. Am. Chem. Soc., 130, 13518-13519
43. Devaraj,N.K., Weissleder,R. and Hilderbrand,S.A. (2008) Tetrazine-based cycloadditions: application to pretargeted live cell imaging. Bioconjug. Chem., 19, 2297-2299
44. van Dijk,M. and Bonvin,A.M. (2009) 3D-DART: a DNA structure modelling server. Nucleic Acids Res., 37, W235-W239
45. Banks,J.L., Beard,H.S., Cao,Y., Cho,A.E., Damm,W., Farid,R., Felts,A.K., Halgren,T.A., Mainz,D.T., Maple,J.R. et al. (2005) Integrated modeling program, applied chemical theory (IMPACT). J. Comput. Chem., 26, 1752-1780
46. Yang,J., Karver,M.R., Li,W., Sahu,S. and Devaraj,N.K. (2012) Metal-catalyzed one-pot synthesis of tetrazines directly from aliphatic nitriles and hydrazine. Angew. Chem. Int. Ed. Engl., 51, 5222-5225
47. Karver,M.R., Weissleder,R. and Hilderbrand,S.A. (2011) Synthesis and evaluation of a series of 1,2,4,5-tetrazines for bioorthogonal conjugation. Bioconjug. Chem., 22, 2263-2270
48. Cacciapaglia,R., Di Stefano,S. and Mandolini,L. (2004) Effective molarities in supramolecular catalysis of two-substrate reactions. Acc. Chem. Res., 37, 113-122
49. Li,X. and Liu,D.R. (2004) DNA-templated organic synthesis: nature's strategy for controlling chemical reactivity applied to synthetic molecules. Angew. Chem. Int. Ed. Engl., 43, 4848-4870
50. Landegren,U., Kaiser,R., Sanders,J. and Hood,L. (1988) A ligasemediated gene detection technique. Science, 241, 1077-1080
51. Ellenberger,T. and Tomkinson,A.E. (2008) Eukaryotic DNA ligases: structural and functional insights. Annu. Rev. Biochem., 77, 313-338
52. Chen,X., Ballin,J.D., Della-Maria,J., Tsai,M.S., White,E.J., Tomkinson,A.E. and Wilson,G.M. (2009) Distinct kinetics of human DNA ligases I, IIIalpha, IIIbeta, and IV reveal direct DNA sensing ability and differential physiological functions in DNA repair. DNA Repair, 8, 961-968
53. Herschlag,D. (1991) Implications of ribozyme kinetics for targeting the cleavage of specific RNA molecules in vivo: more isn't always better. Proc. Natl Acad. Sci. USA, 88, 6921-6925
54. Elghanian,R., Storhoff,J.J., Mucic,R.C., Letsinger,R.L. and Mirkin,C.A. (1997) Selective colorimetric detection of polynucleotides based on the distance-dependent optical properties of gold nanoparticles. Science, 277, 1078-1081
55. Xu,Y. and Kool,E.T. (1999) High sequence fidelity in a nonenzymatic DNA autoligation reaction. Nucleic Acids Res., 27, 875-881
56. Darzacq,X., Shav-Tal,Y., de Turris,V., Brody,Y., Shenoy,S.M., Phair,R.D. and Singer,R.H. (2007) In vivo dynamics of RNA polymerase II transcription. Nat. Struct. Mol. Biol., 14, 796-806