메뉴 건너뛰기




Volumn 11, Issue 3, 2005, Pages 344-354

SAFA: Semi-automated footprinting analysis software for high-throughput quantification of nucleic acid footprinting experiments

Author keywords

Electrophoresis; Footprinting; Gel; Hydroxyl radical; RNA folding; Software

Indexed keywords

HYDROXYL RADICAL;

EID: 13944278373     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: 10.1261/rna.7214405     Document Type: Article
Times cited : (270)

References (41)
  • 1
    • 0001422329 scopus 로고
    • Quantitative model for gene regulation by λ phage repressor
    • Ackers, G.K., Johnson, A.D., and Shea, M.A. 1982. Quantitative model for gene regulation by λ phage repressor. Proc. Natl. Acad. Sci. 79: 1129-1133.
    • (1982) Proc. Natl. Acad. Sci. , vol.79 , pp. 1129-1133
    • Ackers, G.K.1    Johnson, A.D.2    Shea, M.A.3
  • 2
    • 3042848954 scopus 로고    scopus 로고
    • Crystal structure of a self-splicing group I intron with both exons
    • Adams, P.L., Stahley, M.R., Kosek, A.B., Wang, J., and Strobel, S.A. 2004. Crystal structure of a self-splicing group I intron with both exons. Nature 430: 45-50.
    • (2004) Nature , vol.430 , pp. 45-50
    • Adams, P.L.1    Stahley, M.R.2    Kosek, A.B.3    Wang, J.4    Strobel, S.A.5
  • 4
    • 0022437260 scopus 로고
    • Quantitative DNase footprint titration: A method for studying protein-DNA interactions
    • -. 1986b. Quantitative DNase footprint titration: A method for studying protein-DNA interactions. Methods Enzymol. 130: 132-181.
    • (1986) Methods Enzymol. , vol.130 , pp. 132-181
  • 5
    • 0036816641 scopus 로고    scopus 로고
    • Probing the structural dynamics of nucleic acids by quantitative time-resolved and equilibrium hydroxyl radical "footprinting"
    • Brenowitz, M., Chance, M.R., Dhavan, G., and Takamoto, K. 2002. Probing the structural dynamics of nucleic acids by quantitative time-resolved and equilibrium hydroxyl radical "footprinting." Curr. Opin. Struct. Biol. 12: 648-653.
    • (2002) Curr. Opin. Struct. Biol. , vol.12 , pp. 648-653
    • Brenowitz, M.1    Chance, M.R.2    Dhavan, G.3    Takamoto, K.4
  • 6
    • 0025367254 scopus 로고
    • Self-splicing of group I introns
    • Cech, T.R. 1990. Self-splicing of group I introns. Annu. Rev. BioChem. 59: 543-568.
    • (1990) Annu. Rev. BioChem. , vol.59 , pp. 543-568
    • Cech, T.R.1
  • 7
    • 0025023607 scopus 로고
    • Iron(II)-ethylenediaminetetra-acetic acid catalyzed cleavage of RNA and DNA oligonucleotides: Similar reactivity toward single- and double-stranded forms
    • Celander, D.W. and Cech, T.R. 1990. Iron(II)-ethylenediaminetetra-acetic acid catalyzed cleavage of RNA and DNA oligonucleotides: Similar reactivity toward single- and double-stranded forms. Biochemistry 29: 1355-1361.
    • (1990) Biochemistry , vol.29 , pp. 1355-1361
    • Celander, D.W.1    Cech, T.R.2
  • 8
    • 0025963132 scopus 로고
    • Visualizing the higher order folding of a catalytic RNA molecule
    • -. 1991. Visualizing the higher order folding of a catalytic RNA molecule. Science 251: 401-407.
    • (1991) Science , vol.251 , pp. 401-407
  • 10
    • 0033787391 scopus 로고    scopus 로고
    • Ribozyme structures and mechanisms
    • Doherty, E.A. and Doudna, J.A. 2000. Ribozyme structures and mechanisms. Annu. Rev. BioChem. 69: 597-615.
    • (2000) Annu. Rev. BioChem. , vol.69 , pp. 597-615
    • Doherty, E.A.1    Doudna, J.A.2
  • 11
    • 0032712864 scopus 로고    scopus 로고
    • DNA sequencing by capillary electrophoresis
    • Dolnik, V. 1999. DNA sequencing by capillary electrophoresis (review). J. Biochem. Biophys. Methods 41: 103-119.
    • (1999) J. Biochem. Biophys. Methods , vol.41 , pp. 103-119
    • Dolnik, V.1
  • 13
    • 0031978181 scopus 로고    scopus 로고
    • Base-calling of automated sequencer traces using phred. II. Error probabilities
    • Ewing, B. and Green, P. 1998. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 8: 186-194.
    • (1998) Genome Res. , vol.8 , pp. 186-194
    • Ewing, B.1    Green, P.2
  • 14
    • 0031955518 scopus 로고    scopus 로고
    • Base-calling of automated sequencer traces using phred. I. Accuracy assessment
    • Ewing, B., Hillier, L., Wendl, M.C., and Green, P. 1998. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 8: 175-185.
    • (1998) Genome Res. , vol.8 , pp. 175-185
    • Ewing, B.1    Hillier, L.2    Wendl, M.C.3    Green, P.4
  • 15
    • 0028107359 scopus 로고
    • Solution structure of the 3′-end of brome mosaic virus genomic RNAs. Conformational mimicry with canonical tRNAs
    • Felden, B., Florentz, C., Giege, R., and Westhof, E. 1994. Solution structure of the 3′-end of brome mosaic virus genomic RNAs. Conformational mimicry with canonical tRNAs. J. Mol. Biol. 235: 508-531.
    • (1994) J. Mol. Biol. , vol.235 , pp. 508-531
    • Felden, B.1    Florentz, C.2    Giege, R.3    Westhof, E.4
  • 16
    • 0029890903 scopus 로고    scopus 로고
    • Usefulness of functional and structural solution data for the modeling of tRNA-like structures
    • Felden, B., Florentz, C., Westhof, E., and Giege, R. 1996. Usefulness of functional and structural solution data for the modeling of tRNA-like structures. Pharm. Acta Helv. 71: 3-9.
    • (1996) Pharm. Acta Helv. , vol.71 , pp. 3-9
    • Felden, B.1    Florentz, C.2    Westhof, E.3    Giege, R.4
  • 17
    • 0032515936 scopus 로고    scopus 로고
    • Hydroxyl radical footprinting of DNA complexes of the ets domain of PU.1 and its comparison to the crystal structure
    • Gross, P., Arrowsmith, C.H., and Macgregor Jr., R.B. 1998a. Hydroxyl radical footprinting of DNA complexes of the ets domain of PU.1 and its comparison to the crystal structure. Biochemistry 37: 5129-5135.
    • (1998) Biochemistry , vol.37 , pp. 5129-5135
    • Gross, P.1    Arrowsmith, C.H.2    Macgregor Jr., R.B.3
  • 18
    • 0344193601 scopus 로고    scopus 로고
    • Quantitative hydroxyl radical footprinting reveals cooperative interactions between DNA-binding subdomains of PU.1 and IRF4
    • Gross, P., Yee, A.A., Arrowsmith, C.H., and Macgregor, R.B., Jr. 1998b. Quantitative hydroxyl radical footprinting reveals cooperative interactions between DNA-binding subdomains of PU.1 and IRF4. Biochemistry 37: 9802-9811.
    • (1998) Biochemistry , vol.37 , pp. 9802-9811
    • Gross, P.1    Yee, A.A.2    Arrowsmith, C.H.3    Macgregor Jr., R.B.4
  • 19
    • 0037388234 scopus 로고    scopus 로고
    • Gapped DNA is anisotropically bent
    • Guo, H. and Tullius, T.D. 2003. Gapped DNA is anisotropically bent. Proc. Natl. Acad. Sci. 100: 3743-3747.
    • (2003) Proc. Natl. Acad. Sci. , vol.100 , pp. 3743-3747
    • Guo, H.1    Tullius, T.D.2
  • 20
    • 0028883219 scopus 로고
    • Directed hydroxyl radical probing of 16S rRNA using Fe(II) tethered to ribosomal protein S4
    • Heilek, G.M., Marusak, R., Meares, C.F., and Noller, H.F. 1995. Directed hydroxyl radical probing of 16S rRNA using Fe(II) tethered to ribosomal protein S4. Proc. Natl. Acad. Sci. 92: 1113-1116.
    • (1995) Proc. Natl. Acad. Sci. , vol.92 , pp. 1113-1116
    • Heilek, G.M.1    Marusak, R.2    Meares, C.F.3    Noller, H.F.4
  • 21
    • 0007208716 scopus 로고
    • Interactions between DNA-bound repressers govern regulation by the λ phage repressor
    • Johnson, A.D., Meyer, B.J., and Ptashne, M. 1979. Interactions between DNA-bound repressers govern regulation by the λ phage repressor. Proc. Natl. Acad. Sci. 76: 5061-5065.
    • (1979) Proc. Natl. Acad. Sci. , vol.76 , pp. 5061-5065
    • Johnson, A.D.1    Meyer, B.J.2    Ptashne, M.3
  • 22
    • 0033962573 scopus 로고    scopus 로고
    • Calculation of the relative geometry of tRNAs in the ribosome from directed hydroxyl-radical probing data
    • Joseph, S., Whirl, M.L., Kondo, D., Noller, H.F., and Altman, R.B. 2000. Calculation of the relative geometry of tRNAs in the ribosome from directed hydroxyl-radical probing data. RNA 6: 220-232.
    • (2000) RNA , vol.6 , pp. 220-232
    • Joseph, S.1    Whirl, M.L.2    Kondo, D.3    Noller, H.F.4    Altman, R.B.5
  • 23
    • 0024359787 scopus 로고
    • Defining the inside and outside of a catalytic RNA molecule
    • Latham, J.A. and Cech, T.R. 1989. Defining the inside and outside of a catalytic RNA molecule. Science 245: 276-282.
    • (1989) Science , vol.245 , pp. 276-282
    • Latham, J.A.1    Cech, T.R.2
  • 24
    • 0030898046 scopus 로고    scopus 로고
    • Comparing two-dimensional electrophoretic gel images across the Internet
    • Lemkin, P.F. 1997. Comparing two-dimensional electrophoretic gel images across the Internet. Electrophoresis 18: 461-470.
    • (1997) Electrophoresis , vol.18 , pp. 461-470
    • Lemkin, P.F.1
  • 25
    • 0032603145 scopus 로고    scopus 로고
    • Comparing 2-D electrophoretic gels across Internet databases
    • Lemkin, P.F. and Thornwall, G. 1999. Comparing 2-D electrophoretic gels across Internet databases. Methods Mol. Biol. 112: 393-410.
    • (1999) Methods Mol. Biol. , vol.112 , pp. 393-410
    • Lemkin, P.F.1    Thornwall, G.2
  • 26
    • 0032736946 scopus 로고    scopus 로고
    • Flicker image comparison of 2-D gel images for putative protein identification using the 2DWG meta-database
    • -. 1999. Flicker image comparison of 2-D gel images for putative protein identification using the 2DWG meta-database. Mol. Biotechnol. 12: 159-172.
    • (1999) Mol. Biotechnol. , vol.12 , pp. 159-172
  • 27
    • 3242694499 scopus 로고    scopus 로고
    • Mapping protein-ligand interactions by hydroxyl-radical protein footprinting
    • Loizos, N. 2004. Mapping protein-ligand interactions by hydroxyl-radical protein footprinting. Methods Mol. Biol. 261: 199-210.
    • (2004) Methods Mol. Biol. , vol.261 , pp. 199-210
    • Loizos, N.1
  • 28
    • 0034680558 scopus 로고    scopus 로고
    • A detailed interpretation of OH radical footprints in a TBP-DNA complex reveals the role of dynamics in the mechanism of sequence-specific binding
    • Pastor, N., Weinstein, H., Jamison, E., and Brenowitz, M. 2000. A detailed interpretation of OH radical footprints in a TBP-DNA complex reveals the role of dynamics in the mechanism of sequence-specific binding. J. Mol. Biol. 304: 55-68.
    • (2000) J. Mol. Biol. , vol.304 , pp. 55-68
    • Pastor, N.1    Weinstein, H.2    Jamison, E.3    Brenowitz, M.4
  • 29
    • 0030570441 scopus 로고    scopus 로고
    • Sequence-specific DNA binding of the phage Mu C protein: Footprinting analysis reveals altered DNA conformation upon protein binding
    • Ramesh, V. and Nagaraja, V. 1996. Sequence-specific DNA binding of the phage Mu C protein: Footprinting analysis reveals altered DNA conformation upon protein binding. J. Mol. Biol. 260: 22-33.
    • (1996) J. Mol. Biol. , vol.260 , pp. 22-33
    • Ramesh, V.1    Nagaraja, V.2
  • 30
    • 0031566962 scopus 로고    scopus 로고
    • Time-resolved synchrotron X-ray "footprinting," a new approach to the study of nucleic acid structure and function: Application to protein-DNA interactions and RNA folding
    • Sclavi, B., Woodson, S., Sullivan, M., Chance, M.R., and Brenowitz, M. 1997. Time-resolved synchrotron X-ray "footprinting," a new approach to the study of nucleic acid structure and function: Application to protein-DNA interactions and RNA folding. J. Mol. Biol. 266: 144-159.
    • (1997) J. Mol. Biol. , vol.266 , pp. 144-159
    • Sclavi, B.1    Woodson, S.2    Sullivan, M.3    Chance, M.R.4    Brenowitz, M.5
  • 31
    • 0032549780 scopus 로고    scopus 로고
    • RNA folding at millisecond intervals by synchrotron hydroxyl radical footprinting
    • Sclavi, B., Sullivan, M., Chance, M.R., Brenowitz, M., and Woodson, S.A. 1998a. RNA folding at millisecond intervals by synchrotron hydroxyl radical footprinting. Science 279: 1940-1943.
    • (1998) Science , vol.279 , pp. 1940-1943
    • Sclavi, B.1    Sullivan, M.2    Chance, M.R.3    Brenowitz, M.4    Woodson, S.A.5
  • 32
    • 0032319210 scopus 로고    scopus 로고
    • Following the folding of RNA with time-resolved synchrotron X-ray footprinting
    • Sclavi, B., Woodson, S., Sullivan, M., Chance, M., and Brenowitz, M. 1998b. Following the folding of RNA with time-resolved synchrotron X-ray footprinting. Methods Enzymol. 295: 379-402.
    • (1998) Methods Enzymol. , vol.295 , pp. 379-402
    • Sclavi, B.1    Woodson, S.2    Sullivan, M.3    Chance, M.4    Brenowitz, M.5
  • 33
    • 0030742832 scopus 로고    scopus 로고
    • Quantitative analysis of electrophoresis data: Novel curve fitting methodology and its application to the determination of a protein-DNA binding constant
    • Shadle, S.E., Allen, D.F., Guo, H., Pogozelski, W.K., Bashkin, J.S., and Tullius, T.D. 1997. Quantitative analysis of electrophoresis data: Novel curve fitting methodology and its application to the determination of a protein-DNA binding constant. Nucleic Acids Res. 25: 850-860.
    • (1997) Nucleic Acids Res. , vol.25 , pp. 850-860
    • Shadle, S.E.1    Allen, D.F.2    Guo, H.3    Pogozelski, W.K.4    Bashkin, J.S.5    Tullius, T.D.6
  • 34
    • 0027997554 scopus 로고
    • DNA conformational changes associated with the cooperative binding of cI-repressor of bacteriophage λ to OR
    • Strahs, D. and Brenowitz, M. 1994. DNA conformational changes associated with the cooperative binding of cI-repressor of bacteriophage λ to OR. J. Mol. Biol. 244: 494-510.
    • (1994) J. Mol. Biol. , vol.244 , pp. 494-510
    • Strahs, D.1    Brenowitz, M.2
  • 35
    • 0033521233 scopus 로고    scopus 로고
    • No braiding of Holliday junctions in positively supercoiled DNA molecules
    • Sun, W., Mao, C., Iwasaki, H., Kemper, B., and Seeman, N.C. 1999. No braiding of Holliday junctions in positively supercoiled DNA molecules. J. Mol. Biol. 294: 683-699.
    • (1999) J. Mol. Biol. , vol.294 , pp. 683-699
    • Sun, W.1    Mao, C.2    Iwasaki, H.3    Kemper, B.4    Seeman, N.C.5
  • 36
    • 4344590128 scopus 로고    scopus 로고
    • Semi-automated, single-band peak-fitting analysis of hydroxyl radical nucleic acid footprint autoradiograms for the quantitative analysis of transitions
    • Takamoto, K., Chance, M.R., and Brenowitz, M. 2004a. Semi-automated, single-band peak-fitting analysis of hydroxyl radical nucleic acid footprint autoradiograms for the quantitative analysis of transitions. Nucleic Acids Res. 32(15): E119.
    • (2004) Nucleic Acids Res. , vol.32 , Issue.15
    • Takamoto, K.1    Chance, M.R.2    Brenowitz, M.3
  • 37
    • 6344242969 scopus 로고    scopus 로고
    • Principles of RNA compaction: Insights from the equilibrium folding pathway of the P4-P6 RNA domain in monovalent cations
    • Takamoto, K., Das, R., He, Q., Doniach, S., Brenowitz, M., Herschlag, D., Chance, M.R. 2004b. Principles of RNA compaction: Insights from the equilibrium folding pathway of the P4-P6 RNA domain in monovalent cations. J. Mol. Biol. 343(5): 1195-1206.
    • (2004) J. Mol. Biol. , vol.343 , Issue.5 , pp. 1195-1206
    • Takamoto, K.1    Das, R.2    He, Q.3    Doniach, S.4    Brenowitz, M.5    Herschlag, D.6    Chance, M.R.7
  • 39
    • 0037035555 scopus 로고    scopus 로고
    • Linkage of monovalent and divalent ion binding in the folding of the P4-P6 domain of the Tetrahymena ribozyme
    • Uchida, T., He, Q., Ralston, C.Y., Brenowitz, M., and Chance, M.R. 2002. Linkage of monovalent and divalent ion binding in the folding of the P4-P6 domain of the Tetrahymena ribozyme. Biochemistry 41: 5799-5806.
    • (2002) Biochemistry , vol.41 , pp. 5799-5806
    • Uchida, T.1    He, Q.2    Ralston, C.Y.3    Brenowitz, M.4    Chance, M.R.5
  • 40
    • 0037466333 scopus 로고    scopus 로고
    • Multiple monovalent ion-dependent pathways for the folding of the L-21 Tetrahymena thermophila ribozyme
    • Uchida, T., Takamoto, K., He, Q., Chance, M.R., and Brenowitz, M. 2003. Multiple monovalent ion-dependent pathways for the folding of the L-21 Tetrahymena thermophila ribozyme. J. Mol. Biol. 328: 463-478.
    • (2003) J. Mol. Biol. , vol.328 , pp. 463-478
    • Uchida, T.1    Takamoto, K.2    He, Q.3    Chance, M.R.4    Brenowitz, M.5
  • 41
    • 0032498266 scopus 로고    scopus 로고
    • Mapping the position of translational elongation factor EF-G in the ribosome by directed hydroxyl radical probing
    • Wilson, K.S. and Noller, H.F. 1998. Mapping the position of translational elongation factor EF-G in the ribosome by directed hydroxyl radical probing. Cell 92: 131-139.
    • (1998) Cell , vol.92 , pp. 131-139
    • Wilson, K.S.1    Noller, H.F.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.