Mass spectral characterization of a protein-nucleic acid photocrosslink

Protein Science

Volumn 8, Issue 12, 1999, Pages 2806-2812

  Golden, Mace C ^a,b,c   Resing, Katheryn A ^a   Collins, Brian D ^b   Willis, Michael C ^b   Koch, Tad H ^a  

^a UNIVERSITY OF COLORADO   (United States)

^b GILEAD SCIENCES   (United States)

^c UNITED STATES AIR FORCE ACADEMY   (United States)

Author keywords

Bromodeoxyuridine; Mass spectrometry; Photocrosslinking; Sequencing

Indexed keywords

ALKALINE PHOSPHATASE; BASIC FIBROBLAST GROWTH FACTOR; BROXURIDINE; HEPARIN; NUCLEIC ACID; OLIGONUCLEOTIDE; PHOSPHODIESTERASE; SINGLE STRANDED DNA; SNAKE VENOM; TRYPSIN; URACIL;

ARTICLE; CROSS LINKING; DNA SEQUENCE; EXCIMER LASER; MASS SPECTROMETRY; PEPTIDE ANALYSIS; PHOTOCHEMISTRY; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL;

SERPENTES;

EID: 0033435101     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.8.12.2806     Document Type: Article

References (31)

1. Allen T, Wick K, Matthews K. 1991. Identification of amino acids in lac repressor protein cross-linked to operator DNA specifically substituted with bromodeoxyuridine. J Biol Chem 266:6113-6119.
2. Baird A, Klagsbrun M. 1991. The fibroblast growth factor family. Cancer Cells 3:239-243.
3. Bennett SK, Jensen ON, Barofsky DF, Mosbaugh DW. 1994. UV-catalyzed cross-linking of Escherichia coli uracil-DNA glycosylase to DNA. J Biol Chem 269:21870-21879.
4. Biemann K. 1990a. Nomenclature for peptide fragment ions. Methods Enzymol 193:886-887.
5. Biemann K. 1990b. Sequencing of peptides by tandem mass spectrometry and high-energy collision-induced dissociation. Methods Enzymol 193:455-479.
6. Connor DA, Falick AM, Shetlar MD. 1998a. UV light-induced cross-linking of nucleosides, nucleotides and a dinucleotide to the carboxy-terminal heptad repeat peptide of RNA polymerase II as studied by mass spectrometry. Photochem Photobiol 68:1-8.
7. Connor DA, Falick AM, Young MC, Shetlar MD. 1998b. Probing the binding region of the single-stranded DNA-binding domain of rat DNA polymerase β using nanosecond-pulse laser-induced cross-linking and mass spectrometry. Photochem Photobiol 68:299-308.
8. Dietz TM, Koch TH. 1987. Photochemical coupling of 5-bromouracil to tryptophan, tyrosine and histidine, peptide-like derivatives in aqueous fluid solution. Photochem Photobiol 46:971-978.
9. Dietz TM, Koch TH. 1989. Photochemical reduction of 5-bromouracil by cysteine derivatives and coupling of 5-bromouracil to cystine derivatives. Photochem Photobiol 49:121-129.
10. Faham S, Hileman RE, Fromm JR, Linhardt RJ, Rees DC. 1996. Heparin structure and interactions with basic fibroblast growth factor. Science 271:1116-1120.
11. Gott JM, M CW, Koch TH, Uhlenbeck OC. 1991. A specific UV-induced RNA-protein crosslink using 5-bromouracil-substituted RNA. Biochemistry 30:6290-6295.
12. Hicke BJ, Willis MC, Koch TH, Cech TR. 1994. Telomeric protein-DNA point contacts identified by photocrosslinking using 5-bromodeoxyuridine. Biochemistry 33:3364-3373.
13. Horvath MP, Schweiker VL, Bevilacqua JM, Ruggles JA, Schultz SC. 1998. Crystal structure of the Oxytricha nova telomere and binding protein complexed with single strand DNA. Cell 95:963-974.
14. Jensen KB, Atkinson BL, Willis MC, Koch TH, Gold L. 1995. Using in vitro selection to direct the covalent attachment of human immunodeficiency virus type 1 Rev protein to high-affinity RNA ligands. Proc Natl Acad Sci USA 92:12220-12224.
15. Jensen ON, Barofsky DF, Young MC, vonHippel PH, Swenson S, Seifried SE. 1993. Direct observation of UV-crosslinked protein-nucleic acid complexes by matrix-assisted laser desorption ionization mass spectrometry. Rapid Common Mass Spectrom 7:496-501.
16. Jensen ON, Barofsky DF, Young MC, vonHippel PH, Swenson S, Seifried SE. 1994. Mass spectrometric protocol for the analysis of UV-crosslinked protein-nucleic acid complexes. In: Techniques in protein chemistry V. New York: Academic Press. pp 27-37.
17. Jensen ON, Kulkarni S, Aldrich JV, Barofsky DF. 1996. Characterization of peptide-oligonucleotide heteroconjugates by mass spectrometry. Nucleic Acids Res 24:3866-3872.
18. McLuckey SA, Habibi-Goudarzi S. 1993. Decomposition of multiply charged oligonucleotide anions. J Am Chem Soc 115:12085-12095.
19. Meisenheimer KM, Koch TH. 1997. Photocross-linking of nucleic acids to associated proteins. Crit Rev Biochem Mol Biol 32:101-140.
20. Meisenheimer KM, Meisenheimer PL, Koch TH. 1999. Nucleoprotein photocrosslinking using halopyrimidine-substituted RNAs. Methods Enzymol. Forthcoming.
21. Moy FJ, Seddon AP, Böhlen P, Powers R. 1996. High-resolution solution structure of basic fibroblast growth factor determined by multidimensional heteronuclear magnetic resonance spectroscopy. Biochemistry 35:13552-13561.
22. Norris CL, Meisenheimer KM, Koch TH. 1997. Mechanistic studies relevant to bromouridine enhanced nulcleoprotein photocrosslinking. Possible involvement of an excited tyrosine residue of the protein. Photochem Photobiol 65:201-207.
23. Rapraeger AC, Krufka A, Olwin B. 1991. Requirement of Heparan sulfate for bFGF-mediated fibroblast growth and myoblast differentiation. Science 252:1705-1708.
24. Sambrook J, Fritsch EF, Maniatis T. 1989. Molecular cloning. Plainview, New York: Cold Spring Harbor Laboratory Press.
25. Stump WT, Hall KB. 1995. Crosslinking of an iodo-uridine-RNA hairpin to a single site on the human U1A N-terminal RNA binding domain. RNA 1:55-63.
26. Tanner NK, Hanna MM, Abelson J. 1988. Binding interactions between yeast tRNA ligase and a precursor transfer ribonucleic acid containing two photo-reactive uridine analogues. Biochemistry 27:8852-8861.
27. Tuerk C, Gold L. 1990. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249:505-510.
28. Urlaub H, Thiede B, Müller E-C, Brimacombe R, Wittmann-Liebold B. 1997. Identification and sequence analysis of contact sites between ribosomal proteins and rRNA in Escherichia coli 30 S subunits by a new approach using matrix-assisted laser desorption/ionization mass spectrometry combined with N-terminal microsequencing. J Biol Chem 272:14547-14555.
29. Vlodavsky I, Bar-Shavit R, Ishai-Michaeli R, Bashkin P, Fuks Z. 1991. Extracellular sequestration and release of fibroblast growth factor: a regulatory mechanism? Trends Biochem Sci 16:268-271.
30. Wilm M, Shevchenko A, Houthaeve T, Breit S, Schweigerer L, Fotsis T, Mann M. 1996. Femtomole sequencing of proteins from polyacrylamide gels by nano-electrospray mass spectrometry. Nature 379:466-469.
31. Wong DL, Pavlovich JG, Reich NO. 1998. Electrospray ionization mass spectrometric characterization of photocrosslinked DNA-EcoR1 DNA methyltransferase complexes. Nucleic Acids Res 26:645-649.