Time Resolved Synchrotron Xray Footprinting of Nucleic Acids

Chance, Mark R.

Abstract

Hydroxyl radicals (*OH) can cleave the phosphodiester backbone of nucleic acids and are valuable reagents in the study of nucleic acid structure and protein-nucleic acid interactions through """"""""footprinting"""""""" studies. Irradiation of solutions by high flux """"""""white light"""""""" x-ray beams based on bending magnet beamlines at the National Synchrotron Light Source (NSLS) yields sufficient concentrations of *OH so that quantitative nuclease protection (""""""""foot-printing"""""""") studies of DNA and RNA can be conducted with 10 - 20 msec x-ray exposure. The utility of this timescale for nucleic acid cleavage is demonstrated by synchrotron x-ray time-resolved """"""""footprinting"""""""" analyses of the Mg2+ -dependent folding of the Tetrahymena thermo-philia L-21 Sca I ribozyme RNA. Since RNA folding progress curves over timescales from msec to minutes have been obtained for 25 regions of the ribozyme, this research provides an unprecedented structural kinetic picture of the folding of a large macromolecule. Synchro-tron x-ray """"""""footprinting"""""""" is a new approach of general applicability for the study of time-re-solved structural changes of nucleic acid conformation and protein-nucleic acid complexes.

Funding Agency

• Agency: National Institute of Health (NIH)
• Institute: National Center for Research Resources (NCRR)
• Type: Biotechnology Resource Grants (P41)
• Project #: 5P41RR001633-20
• Application #: 6618339
• Project Start: 2002-09-01
• Project End: 2003-08-31
• Support Year: 20
• Fiscal Year: 2002

Institution

• Name: Albert Einstein College of Medicine
• DUNS #: 009095365
• City: Bronx
• State: NY
• Country: United States
• Zip Code: 10461

Publications

Vongsvivut, Jitraporn; Fernandez, Jason; Ekgasit, Sanong et al. (2004) Characterization of supported cylinder-planar germanium waveguide sensors with synchrotron infrared radiation. Appl Spectrosc 58:143-51

Masip, Lluis; Pan, Jonathan L; Haldar, Suranjana et al. (2004) An engineered pathway for the formation of protein disulfide bonds. Science 303:1185-9

Huang, Raymond Y; Miller, Lisa M; Carlson, Cathy S et al. (2003) In situ chemistry of osteoporosis revealed by synchrotron infrared microspectroscopy. Bone 33:514-21

Rashidzadeh, Hassan; Khrapunov, Sergei; Chance, Mark R et al. (2003) Solution structure and interdomain interactions of the Saccharomyces cerevisiae ""TATA binding protein"" (TBP) probed by radiolytic protein footprinting. Biochemistry 42:3655-65

Uchida, Takeshi; Takamoto, Keiji; He, Qin et al. (2003) Multiple monovalent ion-dependent pathways for the folding of the L-21 Tetrahymena thermophila ribozyme. J Mol Biol 328:463-78

Taylor, Colleen M; Watton, Stephen P; Bryngelson, Peter A et al. (2003) Inner-sphere complexation of cobalt(II) 2,9-dimethyl-1,10-phenanthroline ([Co(neo)]2+) with commercial and sol-gel derived silica gel surfaces. Inorg Chem 42:312-20

Marinkovic, N S; Huang, R; Bromberg, P et al. (2002) Center for Synchrotron Biosciences' U2B beamline: an international resource for biological infrared spectroscopy. J Synchrotron Radiat 9:189-97

Huang, R Y; Miller, L M; Carlson, C S et al. (2002) Characterization of bone mineral composition in the proximal tibia of cynomolgus monkeys: effect of ovariectomy and nandrolone decanoate treatment. Bone 30:492-7

Dewan, John C; Feeling-Taylor, Angela; Puius, Yoram A et al. (2002) Structure of mutant human carbonmonoxyhemoglobin C (betaE6K) at 2.0 A resolution. Acta Crystallogr D Biol Crystallogr 58:2038-42

Kiselar, J G; Maleknia, S D; Sullivan, M et al. (2002) Hydroxyl radical probe of protein surfaces using synchrotron X-ray radiolysis and mass spectrometry. Int J Radiat Biol 78:101-14