Abstract

We are continuing to explore the densitometric analysis of ?OH footprint autoradiograms. One approach that was explored during the past year is a ?band-by-band? fitting analysis originally developed in our laboratory for thermodynamic studies using ?OH and 5-phenyl-phenanthroline as probes of DNA conformation that occur in sequence-specific protein-DNA interactions. Implementation of these protocols have been greatly facilitated by the development by Dr. Thomas Tullius and his co-workers of a band-fitting program (GelExplorer) with an interactive graphical interface interactive that runs within the IRIS Explorer environment. The results obtained by this procedure for the DNA containing a ?TATA Box? (the binding site of the eukaryotic transcription factor TBP) shows that the decrease in Hthe relative band densities for the sequence ?AAAA? is consistent with Hthe assumption of an altered configuration by this sequence. Similar Hdata sets obtained at temperatures from 15 - 45 ?C are being compared Hwith solvent accessibility calculations of this DNA obtained from Hmolecular dynamics calculations. The goal of this project is to correlate changes in DNA conformation with the temperature dependencies of the thermodynamics and kinetics of DNA binding by TBP. H?OH cleavage data sets have been obtained for a number of different H?TATA box? sequences that display unique thermodynamic and kinetic Hsignatures.

  Funding Agency

Agency
National Institute of Health (NIH)
Institute
National Center for Research Resources (NCRR)
Type
Biotechnology Resource Grants (P41)
Project #
5P41RR001633-20
Application #
6618354
Study Section
Project Start
2002-09-01
Project End
2003-08-31
Budget Start
Budget End
Support Year
20
Fiscal Year
2002
Total Cost
Indirect Cost

  Institution

Name
Albert Einstein College of Medicine
Department
Type
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
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
Swisher, Jennifer F; Su, Linhui J; Brenowitz, Michael et al. (2002) Productive folding to the native state by a group II intron ribozyme. J Mol Biol 315:297-310
Dhavan, Gauri M; Crothers, Donald M; Chance, Mark R et al. (2002) Concerted binding and bending of DNA by Escherichia coli integration host factor. J Mol Biol 315:1027-37

Showing the most recent 10 out of 68 publications