DNA is a locally inflexible polymer. Nonetheless, the intrinsic inflexibility of DNA is somehow overcome in cells, allowing the constant folding and looping of DNA for storage and gene expression. It is fundamentally important to understand how DNA flexibility is enhanced in healthy, and diseased cells. HMGB proteins are abundant non-histone proteins in eukaryotic chromatin. HMGB proteins are thought to function as architectural factors that enhance DNA bending and twisting. We seek to better understand, both the molecular mechanism of HMGB proteins, and the functional role of HMGB proteins in gene expression in living cells.
Four specific aims are proposed. 1. Characterization of HMGB mechanism by single molecule experiments. We will test if HMGB proteins cause transient flexible hinges in DNA. 2. Analysis of DNA collapse by cationic protein domains. We will test if HMGB proteins can use cationic domains to cause DNA collapse. 3. Analysis of facilitated DNA looping in bacteria. We will test if HMGB proteins can stabilize bacterial repression loops and substitute for bacterial architectural DNA binding proteins. 4. Analysis of the effect of HMGB proteins on transcription activator position effects in yeast. We will test if HMGB proteins stabilize DNA regulatory loops in yeast. Lav description: The instructions for building living things are coded in recipes (genes) within the cell cookbook (DNA). Very long DNA molecules are difficult to sharply bend and twist, but must nonetheless be folded into many shapes in order to function in cells. By understanding the cell proteins that make DNA flexible, we will learn about tools that may be used to artificially regulate disease genes.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM075965-04
Application #
7686153
Study Section
Macromolecular Structure and Function B Study Section (MSFB)
Program Officer
Preusch, Peter C
Project Start
2006-09-25
Project End
2011-08-31
Budget Start
2009-09-01
Budget End
2011-08-31
Support Year
4
Fiscal Year
2009
Total Cost
$309,924
Indirect Cost
Name
Mayo Clinic, Rochester
Department
Type
DUNS #
006471700
City
Rochester
State
MN
Country
United States
Zip Code
55905
Peters, Justin P; Kowal, Ewa A; Pallan, Pradeep S et al. (2018) Comparative analysis of inosine-substituted duplex DNA by circular dichroism and X-ray crystallography. J Biomol Struct Dyn 36:2753-2772
Murugesapillai, Divakaran; Bouaziz, Serge; Maher, L James et al. (2017) Accurate nanoscale flexibility measurement of DNA and DNA-protein complexes by atomic force microscopy in liquid. Nanoscale 9:11327-11337
Uchida, Akira; Murugesapillai, Divakaran; Kastner, Markus et al. (2017) Unexpected sequences and structures of mtDNA required for efficient transcription from the first heavy-strand promoter. Elife 6:
Murugesapillai, Divakaran; McCauley, Micah J; Maher 3rd, L James et al. (2017) Single-molecule studies of high-mobility group B architectural DNA bending proteins. Biophys Rev 9:17-40
Mogil, Lauren S; Becker, Nicole A; Maher 3rd, L James (2016) Supercoiling Effects on Short-Range DNA Looping in E. coli. PLoS One 11:e0165306
Becker, Nicole A; Maher 3rd, L James (2015) High-resolution mapping of architectural DNA binding protein facilitation of a DNA repression loop in Escherichia coli. Proc Natl Acad Sci U S A 112:7177-82
Stellwagen, Nancy C; Peters, Justin P; Dong, Qian et al. (2014) The free solution mobility of DNA and other analytes varies as the logarithm of the fractional negative charge. Electrophoresis 35:1855-63
Murugesapillai, Divakaran; McCauley, Micah J; Huo, Ran et al. (2014) DNA bridging and looping by HMO1 provides a mechanism for stabilizing nucleosome-free chromatin. Nucleic Acids Res 42:8996-9004
Becker, Nicole A; Greiner, Alexander M; Peters, Justin P et al. (2014) Bacterial promoter repression by DNA looping without protein-protein binding competition. Nucleic Acids Res 42:5495-504
Peters, Justin P; Mogil, Lauren S; McCauley, Micah J et al. (2014) Mechanical properties of base-modified DNA are not strictly determined by base stacking or electrostatic interactions. Biophys J 107:448-459

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