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Volumn 5, Issue 7, 2010, Pages 1312-1323

Site-specific fluorescent probing of RNA molecules by unnatural base-pair transcription for local structural conformation analysis

Author keywords

[No Author keywords available]

Indexed keywords

2 AMINO 6 (2 THIENYL)PURINE; 2 PYRROLECARBOXALDEHYDE; FLUORESCENT DYE; NUCLEOSIDE TRIPHOSPHATE; TRANSFER RNA; UNCLASSIFIED DRUG; 2-AMINO-6-(2-THIENYL)PURINE; BACTERIOPHAGE T7 RNA POLYMERASE; DNA DIRECTED RNA POLYMERASE; PURINE DERIVATIVE; PYRROLE DERIVATIVE; PYRROLE-2-CARBOXALDEHYDE; RNA; VIRUS PROTEIN;

EID: 77954306363     PISSN: 17542189     EISSN: 17502799     Source Type: Journal    
DOI: 10.1038/nprot.2010.77     Document Type: Article
Times cited : (42)

References (46)
  • 1
    • 33745786874 scopus 로고    scopus 로고
    • Recombination R-triplex: H-bonds contribution to stability as revealed with minor base substitutions for adenine
    • Shchyolkina, A.K., Kaluzhny, D.N., Arndt-Jovin, D.J., Jovin, T.M. & Zhurkin, V.B. Recombination R-triplex: H-bonds contribution to stability as revealed with minor base substitutions for adenine. Nucleic Acids Res. 34, 3239-3245 (2006).
    • (2006) Nucleic Acids Res. , vol.34 , pp. 3239-3245
    • Shchyolkina, A.K.1    Kaluzhny, D.N.2    Arndt-Jovin, D.J.3    Jovin, T.M.4    Zhurkin, V.B.5
  • 2
    • 0037432340 scopus 로고    scopus 로고
    • Role of a heterogeneous free state in the formation of a specifc RNA-theophylline complex
    • Jucker, F.M., Phillips, R.M., McCallum, S.A. & Pardi, A. Role of a heterogeneous free state in the formation of a specifc RNA-theophylline complex. Biochemistry 42, 2560-2567 (2003).
    • (2003) Biochemistry , vol.42 , pp. 2560-2567
    • Jucker, F.M.1    Phillips, R.M.2    McCallum, S.A.3    Pardi, A.4
  • 3
    • 70350639272 scopus 로고    scopus 로고
    • High density labeling of polymerase chain reaction products with the fuorescent base analogue tCo
    • Stengel, G., Urban, M., Purse, B.W. & Kuchta, R.D. High density labeling of polymerase chain reaction products with the fuorescent base analogue tCo. Anal. Chem. 81, 9079-9085 (2009).
    • (2009) Anal. Chem. , vol.81 , pp. 9079-9085
    • Stengel, G.1    Urban, M.2    Purse, B.W.3    Kuchta, R.D.4
  • 4
    • 76149108425 scopus 로고    scopus 로고
    • Incorporation of the fuorescent ribonucleotide analogue tCTP by T7 RNA polymerase
    • Stengel, G., Urban, M., Purse, B.W. & Kuchta, R.D. Incorporation of the fuorescent ribonucleotide analogue tCTP by T7 RNA polymerase. Anal. Chem. 82, 1082-1089 (2010).
    • (2010) Anal. Chem. , vol.82 , pp. 1082-1089
    • Stengel, G.1    Urban, M.2    Purse, B.W.3    Kuchta, R.D.4
  • 5
    • 60149088502 scopus 로고    scopus 로고
    • Structural rearrangements linked to global folding pathways of the Azoarcus group i ribozyme
    • Chauhan, S., Behrouzi, R., Rangan, P. & Woodson, S.A. Structural rearrangements linked to global folding pathways of the Azoarcus group I ribozyme. J. Mol. Biol. 386, 1167-1178 (2009).
    • (2009) J. Mol. Biol. , vol.386 , pp. 1167-1178
    • Chauhan, S.1    Behrouzi, R.2    Rangan, P.3    Woodson, S.A.4
  • 6
    • 68349148711 scopus 로고    scopus 로고
    • The use of 2-aminopurine fuorescence to study DNA polymerase function
    • Reha-Krantz, L.J. The use of 2-aminopurine fuorescence to study DNA polymerase function. Methods Mol. Biol. 521, 381-396 (2009).
    • (2009) Methods Mol. Biol. , vol.521 , pp. 381-396
    • Reha-Krantz, L.J.1
  • 7
    • 67849103980 scopus 로고    scopus 로고
    • Nucleic acid base analog FRET-pair facilitating detailed structural measurements in nucleic acid containing systems
    • Borjesson, K. et al. Nucleic acid base analog FRET-pair facilitating detailed structural measurements in nucleic acid containing systems. J. Am. Chem. Soc. 131, 4288-4293 (2009).
    • (2009) J. Am. Chem. Soc. , vol.131 , pp. 4288-4293
    • Borjesson, K.1
  • 8
    • 41149092164 scopus 로고    scopus 로고
    • Fluorescence of size-expanded DNA bases: Reporting on DNA sequence and structure with an unnatural genetic set
    • Krueger, A.T. & Kool, E.T. Fluorescence of size-expanded DNA bases: reporting on DNA sequence and structure with an unnatural genetic set. J. Am. Chem. Soc. 130, 3989-3999 (2008).
    • (2008) J. Am. Chem. Soc. , vol.130 , pp. 3989-3999
    • Krueger, A.T.1    Kool, E.T.2
  • 9
    • 67651163670 scopus 로고    scopus 로고
    • Highly effcient incorporation of the fuorescent nucleotide analogs tC and tCo by Klenow fragment
    • Sandin, P. et al. Highly effcient incorporation of the fuorescent nucleotide analogs tC and tCo by Klenow fragment. Nucleic Acids Res. 37, 3924-3933 (2009).
    • (2009) Nucleic Acids Res. , vol.37 , pp. 3924-3933
    • Sandin, P.1
  • 10
    • 68249131738 scopus 로고    scopus 로고
    • Ambivalent incorporation of the fuorescent cytosine analogues tC and tCo by human DNA polymerase alpha and Klenow fragment
    • Stengel, G., Purse, B.W., Wilhelmsson, L.M., Urban, M. & Kuchta, R.D. Ambivalent incorporation of the fuorescent cytosine analogues tC and tCo by human DNA polymerase alpha and Klenow fragment. Biochemistry 48, 7547-7555 (2009).
    • (2009) Biochemistry , vol.48 , pp. 7547-7555
    • Stengel, G.1    Purse, B.W.2    Wilhelmsson, L.M.3    Urban, M.4    Kuchta, R.D.5
  • 11
    • 33751016032 scopus 로고    scopus 로고
    • Fluorescent DNA base replacements: Reporters and sensors for biological systems
    • Wilson, J.N. & Kool, E.T. Fluorescent DNA base replacements: reporters and sensors for biological systems. Org. Biomol. Chem. 4, 4265-4274 (2006).
    • (2006) Org. Biomol. Chem. , vol.4 , pp. 4265-4274
    • Wilson, J.N.1    Kool, E.T.2
  • 12
    • 72249111306 scopus 로고    scopus 로고
    • FRET enabled real time detection of RNA-small molecule binding
    • Xie, Y., Dix, A.V. & Tor, Y. FRET enabled real time detection of RNA-small molecule binding. J. Am. Chem. Soc. 131, 17605-17614 (2009).
    • (2009) J. Am. Chem. Soc. , vol.131 , pp. 17605-17614
    • Xie, Y.1    Dix, A.V.2    Tor, Y.3
  • 13
    • 54249091527 scopus 로고    scopus 로고
    • Characterization of two adenosine analogs as fuorescence probes in RNA
    • Zhao, Y., Knee, J.L. & Baranger, A.M. Characterization of two adenosine analogs as fuorescence probes in RNA. Bioorg. Chem. 36, 271-277 (2008).
    • (2008) Bioorg. Chem. , vol.36 , pp. 271-277
    • Zhao, Y.1    Knee, J.L.2    Baranger, A.M.3
  • 14
    • 28344451166 scopus 로고    scopus 로고
    • Optimizing splinted ligation of highly structured small RNAs
    • Kurschat, W.C., Muller, J., Wombacher, R. & Helm, M. Optimizing splinted ligation of highly structured small RNAs. RNA 11, 1909-1914 (2005).
    • (2005) RNA , vol.11 , pp. 1909-1914
    • Kurschat, W.C.1    Muller, J.2    Wombacher, R.3    Helm, M.4
  • 15
    • 0033638325 scopus 로고    scopus 로고
    • Synthetically modifed DNAs as substrates for polymerases
    • Kool, E.T. Synthetically modifed DNAs as substrates for polymerases. Curr. Opin. Chem. Biol. 4, 602-608 (2000).
    • (2000) Curr. Opin. Chem. Biol. , vol.4 , pp. 602-608
    • Kool, E.T.1
  • 16
    • 0035942246 scopus 로고    scopus 로고
    • Unnatural base pairs for specifc transcription
    • Ohtsuki, T. et al. Unnatural base pairs for specifc transcription. Proc. Natl Acad. Sci. USA 98, 4922-4925 (2001).
    • (2001) Proc. Natl Acad. Sci. USA , vol.98 , pp. 4922-4925
    • Ohtsuki, T.1
  • 18
    • 0344851941 scopus 로고    scopus 로고
    • Beyond A C, G and T: Augmenting nature's alphabet
    • Henry, A.A. & Romesberg, F.E. Beyond A, C, G and T: augmenting nature's alphabet. Curr. Opin. Chem. Biol. 7, 727-733 (2003).
    • (2003) Curr. Opin. Chem. Biol. , vol.7 , pp. 727-733
    • Henry, A.A.1    Romesberg, F.E.2
  • 19
    • 1142306164 scopus 로고    scopus 로고
    • Site-Specific Incorporation of a Photo-Crosslinking Component into RNA by T7 Transcription Mediated by Unnatural Base Pairs
    • DOI 10.1016/S1074-5521(03)00295-3
    • Kimoto, M. et al. Site-specifc incorporation of a photo-crosslinking component into RNA by T7 transcription mediated by unnatural base pairs. Chem. Biol. 11, 47-55 (2004). (Pubitemid 38203989)
    • (2004) Chemistry and Biology , vol.11 , Issue.1 , pp. 47-55
    • Kimoto, M.1    Endo, M.2    Mitsui, T.3    Okuni, T.4    Hirao, I.5    Yokoyama, S.6
  • 21
    • 26444610292 scopus 로고    scopus 로고
    • Site-specifc biotinylation of RNA molecules by transcription using unnatural base pairs
    • Moriyama, K., Kimoto, M., Mitsui, T., Yokoyama, S. & Hirao, I. Site-specifc biotinylation of RNA molecules by transcription using unnatural base pairs. Nucleic Acids Res. 33, e129 (2005).
    • (2005) Nucleic Acids Res. , vol.33
    • Moriyama, K.1    Kimoto, M.2    Mitsui, T.3    Yokoyama, S.4    Hirao, I.5
  • 22
    • 33846393737 scopus 로고    scopus 로고
    • Unnatural base pair systems for DNA/RNA-based biotechnology
    • Hirao, I. Unnatural base pair systems for DNA/RNA-based biotechnology. Curr. Opin. Chem. Biol. 10, 622-627 (2006).
    • (2006) Curr. Opin. Chem. Biol. , vol.10 , pp. 622-627
    • Hirao, I.1
  • 23
    • 33746521883 scopus 로고    scopus 로고
    • Placing extra components into RNA by specifc transcription using unnatural base pair systems
    • Hirao, I. Placing extra components into RNA by specifc transcription using unnatural base pair systems. Biotechniques 40, 711-717 (2006).
    • (2006) Biotechniques , vol.40 , pp. 711-717
    • Hirao, I.1
  • 24
    • 33747762272 scopus 로고    scopus 로고
    • An unnatural hydrophobic base pair system: Site-specifc incorporation of nucleotide analogs into DNA and RNA
    • Hirao, I. et al. An unnatural hydrophobic base pair system: site-specifc incorporation of nucleotide analogs into DNA and RNA. Nat. Methods 3, 729-735 (2006).
    • (2006) Nat. Methods , vol.3 , pp. 729-735
    • Hirao, I.1
  • 25
    • 34548757334 scopus 로고    scopus 로고
    • Fluorescent probing for RNA molecules by an unnatural base-pair system
    • Kimoto, M. et al. Fluorescent probing for RNA molecules by an unnatural base-pair system. Nucleic Acids Res. 35, 5360-5369 (2007).
    • (2007) Nucleic Acids Res. , vol.35 , pp. 5360-5369
    • Kimoto, M.1
  • 26
    • 70549098251 scopus 로고    scopus 로고
    • Non-natural nucleic acids for synthetic biology
    • Appella, D.H. Non-natural nucleic acids for synthetic biology. Curr. Opin. Chem. Biol. 13, 687-696 (2009).
    • (2009) Curr. Opin. Chem. Biol. , vol.13 , pp. 687-696
    • Appella, D.H.1
  • 27
    • 59649091247 scopus 로고    scopus 로고
    • An unnatural base pair system for effcient PCR amplifcation and functionalization of DNA molecules
    • Kimoto, M., Kawai, R., Mitsui, T., Yokoyama, S. & Hirao, I. An unnatural base pair system for effcient PCR amplifcation and functionalization of DNA molecules. Nucleic Acids Res. 37, e14 (2009).
    • (2009) Nucleic Acids Res. , vol.37
    • Kimoto, M.1    Kawai, R.2    Mitsui, T.3    Yokoyama, S.4    Hirao, I.5
  • 29
    • 39549087460 scopus 로고    scopus 로고
    • Discovery, characterization, and optimization of an unnatural base pair for expansion of the genetic alphabet
    • Leconte, A.M. et al. Discovery, characterization, and optimization of an unnatural base pair for expansion of the genetic alphabet. J. Am. Chem. Soc. 130, 2336-2343 (2008).
    • (2008) J. Am. Chem. Soc. , vol.130 , pp. 2336-2343
    • Leconte, A.M.1
  • 30
    • 33947255494 scopus 로고    scopus 로고
    • Characterization of fuorescent, unnatural base pairs
    • Mitsui, T., Kimoto, M., Kawai, R., Yokoyama, S. & Hirao, I. Characterization of fuorescent, unnatural base pairs. Tetrahedron 63, 3528-3537 (2007).
    • (2007) Tetrahedron , vol.63 , pp. 3528-3537
    • Mitsui, T.1    Kimoto, M.2    Kawai, R.3    Yokoyama, S.4    Hirao, I.5
  • 31
    • 34548581964 scopus 로고    scopus 로고
    • Cytostatic evaluations of nucleoside analogs related to unnatural base pairs for a genetic expansion system
    • Kimoto, M., Moriyama, K., Yokoyama, S. & Hirao, I. Cytostatic evaluations of nucleoside analogs related to unnatural base pairs for a genetic expansion system. Bioorg. Med. Chem. Lett. 17, 5582-5585 (2007).
    • (2007) Bioorg. Med. Chem. Lett. , vol.17 , pp. 5582-5585
    • Kimoto, M.1    Moriyama, K.2    Yokoyama, S.3    Hirao, I.4
  • 32
    • 0023651444 scopus 로고
    • Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates
    • Milligan, J.F., Groebe, D.R., Witherell, G.W. & Uhlenbeck, O.C. Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates. Nucleic Acids Res. 15, 8783-8798 (1987).
    • (1987) Nucleic Acids Res. , vol.15 , pp. 8783-8798
    • Milligan, J.F.1    Groebe, D.R.2    Witherell, G.W.3    Uhlenbeck, O.C.4
  • 33
    • 0024819449 scopus 로고
    • Synthesis of small RNAs using T7 RNA polymerase
    • Milligan, J.F. & Uhlenbeck, O.C. Synthesis of small RNAs using T7 RNA polymerase. Methods Enzymol. 180, 51-62 (1989).
    • (1989) Methods Enzymol. , vol.180 , pp. 51-62
    • Milligan, J.F.1    Uhlenbeck, O.C.2
  • 34
    • 77954247857 scopus 로고    scopus 로고
    • Oligonucleotide synthesis 3rd edn. (eds. Sambrook J. & Russell D.W.) Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, USA
    • Oligonucleotide synthesis. In Molecular Cloning: A Laboratory Manual 3rd edn. Vol.2 (eds. Sambrook J. & Russell D.W.) 10.42-10.46 (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, USA, 2001).
    • (2001) Molecular Cloning: A Laboratory Manual , vol.2 , pp. 1042-1046
  • 35
    • 0023502864 scopus 로고
    • Chemical synthesis of deoxyoligonucleotides by the phosphoramidite method
    • Caruthers, M.H. et al. Chemical synthesis of deoxyoligonucleotides by the phosphoramidite method. Methods Enzymol. 154, 287-313 (1987).
    • (1987) Methods Enzymol. , vol.154 , pp. 287-313
    • Caruthers, M.H.1
  • 36
    • 0031915891 scopus 로고    scopus 로고
    • Error analysis of chemically synthesized polynucleotides
    • Hecker, K.H. & Rill, R.L. Error analysis of chemically synthesized polynucleotides. Biotechniques 24, 256-260 (1998).
    • (1998) Biotechniques , vol.24 , pp. 256-260
    • Hecker, K.H.1    Rill, R.L.2
  • 37
    • 3042820410 scopus 로고    scopus 로고
    • A simple, rapid, high-fdelity and cost-effective PCR-based two-step DNA synthesis method for long gene sequences
    • Xiong, A.S. et al. A simple, rapid, high-fdelity and cost-effective PCR-based two-step DNA synthesis method for long gene sequences. Nucleic Acids Res. 32, e98 (2004).
    • (2004) Nucleic Acids Res. , vol.32
    • Xiong, A.S.1
  • 38
    • 44749088592 scopus 로고    scopus 로고
    • Phosphoserine aminoacylation of tRNA bearing an unnatural base anticodon
    • Fukunaga, R., Harada, Y., Hirao, I. & Yokoyama, S. Phosphoserine aminoacylation of tRNA bearing an unnatural base anticodon. Biochem. Biophys. Res. Commun. 372, 480-485 (2008).
    • (2008) Biochem. Biophys. Res. Commun. , vol.372 , pp. 480-485
    • Fukunaga, R.1    Harada, Y.2    Hirao, I.3    Yokoyama, S.4
  • 39
    • 42149130929 scopus 로고    scopus 로고
    • Chemical gene synthesis: Strategies, softwares, error corrections, and applications
    • Xiong, A.S. et al. Chemical gene synthesis: strategies, softwares, error corrections, and applications. FEMS Microbiol. Rev. 32, 522-540 (2008).
    • (2008) FEMS Microbiol. Rev. , vol.32 , pp. 522-540
    • Xiong, A.S.1
  • 40
    • 0347364647 scopus 로고    scopus 로고
    • Generating a synthetic genome by whole genome assembly: PhiX174 bacteriophage from synthetic oligonucleotides
    • Smith, H.O., Hutchison, C.A. III, Pfannkoch, C. & Venter, J.C. Generating a synthetic genome by whole genome assembly: phiX174 bacteriophage from synthetic oligonucleotides. Proc. Natl Acad. Sci. USA 100, 15440-15445 (2003).
    • (2003) Proc. Natl Acad. Sci. USA , vol.100 , pp. 15440-15445
    • Smith, H.O.1    Iii, A.H.C.2    Pfannkoch, C.3    Venter, J.C.4
  • 41
    • 8144226497 scopus 로고    scopus 로고
    • Total synthesis of long DNA sequences: Synthesis of a contiguous 32-kb polyketide synthase gene cluster
    • Kodumal, S.J. et al. Total synthesis of long DNA sequences: synthesis of a contiguous 32-kb polyketide synthase gene cluster. Proc. Natl Acad. Sci. USA 101, 15573-15578 (2004).
    • (2004) Proc. Natl Acad. Sci. USA , vol.101 , pp. 15573-15578
    • Kodumal, S.J.1
  • 42
    • 0004136246 scopus 로고    scopus 로고
    • Purifcation of synthetic oligonucleotides by polyacrylamide gel electrophoresis
    • 3rd edn. (eds. Sambrook J. & Russell D.W.) Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, USA
    • Purifcation of synthetic oligonucleotides by polyacrylamide gel electrophoresis. In Molecular Cloning: A Laboratory Manual 3rd edn. Vol.2 (eds. Sambrook J. & Russell D.W.) 10.11-10.16 (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, USA, 2001).
    • (2001) Molecular Cloning: A Laboratory Manual , vol.2 , pp. 1011-1016
  • 43
    • 77954272158 scopus 로고    scopus 로고
    • Preparation of denaturing polyacrylamide gels
    • 3rd edn (eds. Sambrook J. & Russell D.W.) Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, USA
    • Preparation of denaturing polyacrylamide gels. In Molecular Cloning: A Laboratory Manual 3rd edn. Vol.2 (eds. Sambrook J. & Russell D.W.) 12.74-12.80 (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, USA, 2001).
    • (2001) Molecular Cloning: A Laboratory Manual , vol.2 , pp. 1274-1280
  • 44
    • 24344485204 scopus 로고    scopus 로고
    • Melting temperatures of nucleic acids: Discrepancies in analysis
    • Owczarzy, R. Melting temperatures of nucleic acids: discrepancies in analysis. Biophys. Chem. 117, 207-215 (2005).
    • (2005) Biophys. Chem. , vol.117 , pp. 207-215
    • Owczarzy, R.1
  • 45
    • 0034840623 scopus 로고    scopus 로고
    • A simple and effcient method to transcribe RNAs with reduced 3′ heterogeneity
    • Kao, C., Rudisser, S. & Zheng, M. A simple and effcient method to transcribe RNAs with reduced 3′ heterogeneity. Methods 23, 201-205 (2001).
    • (2001) Methods , vol.23 , pp. 201-205
    • Kao, C.1    Rudisser, S.2    Zheng, M.3


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