메뉴 건너뛰기




Volumn 34, Issue 8, 2006, Pages

Hydroxyl radical footprinting in vivo: Mapping macromolecular structures with synchrotron radiation

Author keywords

[No Author keywords available]

Indexed keywords

HYDROXYL RADICAL; RIBONUCLEASE P; RNA 16S; TRANSFER RNA; RNA;

EID: 33646841501     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkl291     Document Type: Article
Times cited : (59)

References (43)
  • 1
    • 0023754154 scopus 로고
    • In vivo and in vitro structural analysis of the rplJ mRNA leader of Escherichia coli. Protection by bound L10-L7/L12
    • Climie,S.C. and Friesen,J.D. (1988) In vivo and in vitro structural analysis of the rplJ mRNA leader of Escherichia coli. Protection by bound L10-L7/L12. J. Biol. Chem., 263, 15166-15175.
    • (1988) J. Biol. Chem. , vol.263 , pp. 15166-15175
    • Climie, S.C.1    Friesen, J.D.2
  • 2
    • 0036232115 scopus 로고    scopus 로고
    • Lead(II) as a probe for investigating RNA structure in vivo
    • Lindell,M., Romby,P. and Wagner,E.G. (2002) Lead(II) as a probe for investigating RNA structure in vivo. RNA, 8, 534-541.
    • (2002) RNA , vol.8 , pp. 534-541
    • Lindell, M.1    Romby, P.2    Wagner, E.G.3
  • 3
    • 0024814177 scopus 로고
    • Conformational alterations in the ermC transcript in vivo during induction
    • Mayford,M. and Weisblum,B. (1989) Conformational alterations in the ermC transcript in vivo during induction. EMBO J., 8, 4307-4314.
    • (1989) EMBO J. , vol.8 , pp. 4307-4314
    • Mayford, M.1    Weisblum, B.2
  • 4
    • 0029312758 scopus 로고
    • Analysis of the structure of Tetrahymena nuclear RNAs in vivo: Telomerase RNA, the self-splicing rRNA intron, and U2 snRNA
    • Zaug,A.J. and Cech,T.R. (1995) Analysis of the structure of Tetrahymena nuclear RNAs in vivo: Telomerase RNA, the self-splicing rRNA intron, and U2 snRNA. RNA, 1, 363-374.
    • (1995) RNA , vol.1 , pp. 363-374
    • Zaug, A.J.1    Cech, T.R.2
  • 5
  • 6
    • 0032519508 scopus 로고    scopus 로고
    • A chemical modification method for the structural analysis of RNA and RNA-protein complexes within living cells
    • Balzer,M. and Wagner,R. (1998) A chemical modification method for the structural analysis of RNA and RNA-protein complexes within living cells. Anal. Biochem., 256, 240-242.
    • (1998) Anal. Biochem. , vol.256 , pp. 240-242
    • Balzer, M.1    Wagner, R.2
  • 7
    • 0036712305 scopus 로고    scopus 로고
    • RNA chaperone StpA loosens interactions of the tertiary structure in the td group I intron in vivo
    • Waldsich,C., Grossberger,R. and Schroeder,R. (2002) RNA chaperone StpA loosens interactions of the tertiary structure in the td group I intron in vivo. Genes Dev., 16, 2300-2312.
    • (2002) Genes Dev. , vol.16 , pp. 2300-2312
    • Waldsich, C.1    Grossberger, R.2    Schroeder, R.3
  • 8
    • 0024474697 scopus 로고
    • KMnO4 as a probe for lac promoter DNA melting and mechanism in vivo
    • Sasse-Dwight,S. and Gralla,J.D. (1989) KMnO4 as a probe for lac promoter DNA melting and mechanism in vivo. J. Biol. Chem., 264, 8074-8081.
    • (1989) J. Biol. Chem. , vol.264 , pp. 8074-8081
    • Sasse-Dwight, S.1    Gralla, J.D.2
  • 9
    • 0035515226 scopus 로고    scopus 로고
    • A versatile in vivo footprinting technique using 1,10-phenanthroline-copper complex to study important cellular processes
    • Basak,S. and Nagaraja,V. (2001) A versatile in vivo footprinting technique using 1,10-phenanthroline-copper complex to study important cellular processes. Nucleic Acids Res., 29, E105-E105.
    • (2001) Nucleic Acids Res. , vol.29
    • Basak, S.1    Nagaraja, V.2
  • 10
    • 16244389281 scopus 로고    scopus 로고
    • Mapping nucleic acid structure by hydroxyl radical cleavage
    • Tullius,T.D. and Greenbaum,J.A. (2005) Mapping nucleic acid structure by hydroxyl radical cleavage. Curr. Opin. Chem. Biol., 9, 127-134.
    • (2005) Curr. Opin. Chem. Biol. , vol.9 , pp. 127-134
    • Tullius, T.D.1    Greenbaum, J.A.2
  • 11
    • 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. (1998) 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
  • 12
    • 0002193871 scopus 로고
    • Primary products in radiation chemistry
    • Farhatazis,I. and Rodgers,M.A. (eds), VCH Publications, TX
    • Klassen,N.V. (1987) Primary products in radiation chemistry. In Farhatazis,I. and Rodgers,M.A. (eds), Radiation Chemistry: Principles and Applications. VCH Publications, TX, pp. 29-61.
    • (1987) Radiation Chemistry: Principles and Applications , pp. 29-61
    • Klassen, N.V.1
  • 13
    • 0022461871 scopus 로고
    • Characterization of free radical-induced base damage in DNA at biologically relevant levels
    • Dizdaroglu,M. and Bergtold,D.S. (1986) Characterization of free radical-induced base damage in DNA at biologically relevant levels. Anal. Biochem., 156, 182-188.
    • (1986) Anal. Biochem. , vol.156 , pp. 182-188
    • Dizdaroglu, M.1    Bergtold, D.S.2
  • 14
    • 0026295112 scopus 로고
    • The chemistry of free-radical-mediated DNA damage
    • Discussion 317-221
    • von Sonntag,C. (1991) The chemistry of free-radical-mediated DNA damage. Basic Life Sci., 58, 287-317; Discussion 317-221.
    • (1991) Basic Life Sci. , vol.58 , pp. 287-317
    • von Sonntag, C.1
  • 15
    • 0032544035 scopus 로고    scopus 로고
    • DNA strand breaking by the hydroxyl radical is governed by the accessible surface areas of the hydrogen atoms of the DNA backbone
    • Balasubramanian,B., Pogozelski,W.K. and Tullius,T.D. (1998) DNA strand breaking by the hydroxyl radical is governed by the accessible surface areas of the hydrogen atoms of the DNA backbone. Proc. Natl Acad. Sci. USA, 95, 9738-9743.
    • (1998) Proc. Natl Acad. Sci. USA , vol.95 , pp. 9738-9743
    • Balasubramanian, B.1    Pogozelski, W.K.2    Tullius, T.D.3
  • 16
    • 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
  • 19
    • 0034697671 scopus 로고    scopus 로고
    • High resolution in vivo footprinting of a protein-DNA complex using gamma radiation
    • Ottinger,L.M. and Tullius,T.D. (2000) High resolution in vivo footprinting of a protein-DNA complex using gamma radiation. J. Am. Chem. Soc., 122, 5901-5902.
    • (2000) J. Am. Chem. Soc. , vol.122 , pp. 5901-5902
    • Ottinger, L.M.1    Tullius, T.D.2
  • 20
    • 4444235862 scopus 로고    scopus 로고
    • Kinetics analysis of DNA-protein interactions by time resolved synchrotron X-ray footprinting
    • Johnson,K.A. (ed.), IRL Press at Oxford University, Oxford
    • Dhavan,G.M., Chance,M.R. and Brenowitz,M. (2003) Kinetics analysis of DNA-protein interactions by time resolved synchrotron X-ray footprinting. In Johnson,K.A. (ed.), Kinetic Analysis of Macromolecules: A Practical Approach. IRL Press at Oxford University, Oxford, pp. 75-86.
    • (2003) Kinetic Analysis of Macromolecules: A Practical Approach , pp. 75-86
    • Dhavan, G.M.1    Chance, M.R.2    Brenowitz, M.3
  • 21
    • 0016369454 scopus 로고
    • Total reconstitution of functionally active 50S ribosomal subunits from Escherichia coli
    • Nierhaus,K.H. and Dohme,F. (1974) Total reconstitution of functionally active 50S ribosomal subunits from Escherichia coli. Proc. Natl Acad. Sci. USA, 71, 4713-4717.
    • (1974) Proc. Natl Acad. Sci. USA , vol.71 , pp. 4713-4717
    • Nierhaus, K.H.1    Dohme, F.2
  • 22
    • 0033534197 scopus 로고    scopus 로고
    • Nucleotides in 16S rRNA protected by the association of 30S and 50S ribosomal subunits
    • Merryman,C., Moazed,D., McWhirter,J. and Noller,H.F. (1999) Nucleotides in 16S rRNA protected by the association of 30S and 50S ribosomal subunits. J. Mol. Biol., 285, 97-105.
    • (1999) J. Mol. Biol. , vol.285 , pp. 97-105
    • Merryman, C.1    Moazed, D.2    McWhirter, J.3    Noller, H.F.4
  • 23
    • 0022470564 scopus 로고
    • Rapid chemical probing of conformation in 16 S ribosomal RNA and 30 S ribosomal subunits using primer extension
    • Moazed,D., Stern,S. and Noller,H.F. (1986) Rapid chemical probing of conformation in 16 S ribosomal RNA and 30 S ribosomal subunits using primer extension. J. Mol. Biol., 187, 399-416.
    • (1986) J. Mol. Biol. , vol.187 , pp. 399-416
    • Moazed, D.1    Stern, S.2    Noller, H.F.3
  • 24
    • 0003098935 scopus 로고    scopus 로고
    • Footprinting and modification-interference analysis of binding sites on RNA
    • Smith,C.W.J. (ed.), Oxford University Press, NY
    • Merryman,C. and Noller,H.F. (1998) Footprinting and modification-interference analysis of binding sites on RNA. In Smith,C.W.J. (ed.), RNA-Protein Interactions. Oxford University Press, NY, pp. 237-253.
    • (1998) RNA-Protein Interactions , pp. 237-253
    • Merryman, C.1    Noller, H.F.2
  • 25
    • 24044530426 scopus 로고    scopus 로고
    • Lead(II) cleavage analysis of RNase P RNA in vivo
    • Lindell,M., Brannvall,M., Wagner,E.G. and Kirsebom,L.A. (2005) Lead(II) cleavage analysis of RNase P RNA in vivo. RNA, 11, 1348-1354.
    • (2005) RNA , vol.11 , pp. 1348-1354
    • Lindell, M.1    Brannvall, M.2    Wagner, E.G.3    Kirsebom, L.A.4
  • 27
    • 0001073978 scopus 로고
    • A resolution-sensitive procedure for comparing protein surfaces and its application to the comparison of antigen-combining sites
    • Gerstein,M. (1992) A resolution-sensitive procedure for comparing protein surfaces and its application to the comparison of antigen-combining sites. Acta Cryst. A, 48, 271-276.
    • (1992) Acta Cryst. A , vol.48 , pp. 271-276
    • Gerstein, M.1
  • 28
    • 0021202164 scopus 로고
    • Freezing of living cells: Mechanisms and implications
    • Mazur,P. (1984) Freezing of living cells: Mechanisms and implications. Am. J. Physiol., 247, C125-142.
    • (1984) Am. J. Physiol. , vol.247
    • Mazur, P.1
  • 29
    • 0029143136 scopus 로고
    • Thiazolidine prodrugs of cysteamine and cysteine as radioprotective agents
    • Roberts,J.C., Koch,K.E., Detrick,S.R., Warters,R.L. and Lubec,G. (1995) Thiazolidine prodrugs of cysteamine and cysteine as radioprotective agents. Radiat. Res., 143, 203-213.
    • (1995) Radiat. Res. , vol.143 , pp. 203-213
    • Roberts, J.C.1    Koch, K.E.2    Detrick, S.R.3    Warters, R.L.4    Lubec, G.5
  • 30
    • 0026526993 scopus 로고
    • Free radicals from irradiated lyophilized DNA: Influence of water of hydration
    • Huttermann,J., Rohrig,M. and Kohnlein,W. (1992) Free radicals from irradiated lyophilized DNA: Influence of water of hydration. Int. J. Radiat. Biol., 61, 299-313.
    • (1992) Int. J. Radiat. Biol. , vol.61 , pp. 299-313
    • Huttermann, J.1    Rohrig, M.2    Kohnlein, W.3
  • 31
    • 0030228822 scopus 로고    scopus 로고
    • Damage induced by hydroxyl radicals generated in the hydration layer of gamma-irradiated frozen aqueous solution of DNA
    • Ohshima,H., Iida,Y., Matsuda,A. and Kuwabara,M. (1996) Damage induced by hydroxyl radicals generated in the hydration layer of gamma-irradiated frozen aqueous solution of DNA. J. Radiat. Res. (Tokyo), 37, 199-207.
    • (1996) J. Radiat. Res. (Tokyo) , vol.37 , pp. 199-207
    • Ohshima, H.1    Iida, Y.2    Matsuda, A.3    Kuwabara, M.4
  • 34
    • 13844296708 scopus 로고    scopus 로고
    • Bumps in the road: How replicative DNA polymerases see DNA damage
    • Hogg,M., Wallace,S.S. and Doublie,S. (2005) Bumps in the road: How replicative DNA polymerases see DNA damage. Curr. Opin. Struct. Biol., 15, 86-93.
    • (2005) Curr. Opin. Struct. Biol. , vol.15 , pp. 86-93
    • Hogg, M.1    Wallace, S.S.2    Doublie, S.3
  • 36
    • 0036303417 scopus 로고    scopus 로고
    • Crystal structure of the 30 S ribosomal subunit from Thermus thermophilus: Structure of the proteins and their interactions with 16 S RNA
    • Brodersen,D.E., Clemons,W.M.,Jr, Carter,A.P., Wimberly,B.T. and Ramakrishnan,V. (2002) Crystal structure of the 30 S ribosomal subunit from Thermus thermophilus: Structure of the proteins and their interactions with 16 S RNA. J. Mol. Biol., 316, 725-768.
    • (2002) J. Mol. Biol. , vol.316 , pp. 725-768
    • Brodersen, D.E.1    Clemons Jr., W.M.2    Carter, A.P.3    Wimberly, B.T.4    Ramakrishnan, V.5
  • 37
    • 0021100156 scopus 로고
    • S1 nuclease mapping analysis of ribosomal RNA processing in wild type and processing deficient Escherichia coli
    • King,T.C. and Schlessinger,D. (1983) S1 nuclease mapping analysis of ribosomal RNA processing in wild type and processing deficient Escherichia coli. J. Biol. Chem., 258, 12034-12042.
    • (1983) J. Biol. Chem. , vol.258 , pp. 12034-12042
    • King, T.C.1    Schlessinger, D.2
  • 38
    • 0030598998 scopus 로고    scopus 로고
    • Growth rate regulation of 4.5 S RNA and M1 RNA the catalytic subunit of Escherichia coli RNase P
    • Dong,H., Kirsebom,L.A. and Nilsson,L. (1996) Growth rate regulation of 4.5 S RNA and M1 RNA the catalytic subunit of Escherichia coli RNase P. J. Mol. Biol., 261, 303-308.
    • (1996) J. Mol. Biol. , vol.261 , pp. 303-308
    • Dong, H.1    Kirsebom, L.A.2    Nilsson, L.3
  • 40
    • 0029866752 scopus 로고    scopus 로고
    • Mapping in three dimensions of regions in a catalytic RNA protected from attack by an Fe(II)-EDTA reagent
    • Westhof,E., Wesolowski,D. and Altman,S. (1996) Mapping in three dimensions of regions in a catalytic RNA protected from attack by an Fe(II)-EDTA reagent. J. Mol. Biol., 258, 600-613.
    • (1996) J. Mol. Biol. , vol.258 , pp. 600-613
    • Westhof, E.1    Wesolowski, D.2    Altman, S.3
  • 41
    • 0020050364 scopus 로고
    • Radiolytic pathways in gamma-irradiated DNA: Influence of chemical and conformational factors
    • Gregoli,S., Olast,M. and Bertinchamps,A. (1982) Radiolytic pathways in gamma-irradiated DNA: Influence of chemical and conformational factors. Radiat. Res., 89, 238-254.
    • (1982) Radiat. Res. , vol.89 , pp. 238-254
    • Gregoli, S.1    Olast, M.2    Bertinchamps, A.3
  • 42
    • 0033568535 scopus 로고    scopus 로고
    • Millisecond radiolytic modification of peptides by synchrotron X-rays identified by mass spectrometry
    • Maleknia,S.D., Brenowitz,M. and Chance,M.R. (1999) Millisecond radiolytic modification of peptides by synchrotron X-rays identified by mass spectrometry. Anal. Chem., 71, 3965-3973.
    • (1999) Anal. Chem. , vol.71 , pp. 3965-3973
    • Maleknia, S.D.1    Brenowitz, M.2    Chance, M.R.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.