Name: David D Dunlap, Ph.D. Title: Adjunct Assistant Professor Cell Biology Email: firstname.lastname@example.org Phone: 4047273951
Address:Department of Cell Biology, Emory University School of Medicine , 615 Michael Street , Atlanta , GA , 30322
Chromatin folding and dynamics
My laboratory is engaged in research on the folding and dynamics of "chromatin", which in a broad sense might be defined as genomic DNA with associated proteins, ions, and small molecules. DNA is an extraordinarily stiff polymer, and yet it bends and can become tightly coiled as a result of interactions with proteins and ions that reduce the extreme negative charge borne by the phosphates along the helical backbone of the polymer. Flexibility increases with the salt concentration, which screens the repulsions between phosphates, and bends have been shown to result from asymmetric neutralization of phosphates. My laboratory uses scanning force microscopy and recently has shown that the flexibility of DNA increases dramatically on positively charged surfaces prepared with polyamines. Natural polyamines (putrescine, spermidine, spermine) are ubiquitous, positively charged, small molecules that interact with a variety of other molecules in the cell, including nucleic acids, phospholipids and proteins. Polyamines are essential for normal cell growth and differentiation, and proper concentrations appear to be required for cell survival prior to gastrulation. This requirement may reflect the fact that enhanced flexibility of DNA certainly contributes to facilitate the wrapping of it around positive charge bearing histone octamers to form stable nucleosomes, the fundamental units of eurkaryotic chromatin. Scanning force microscopy provides a convenient platform upon which to investigate the parameters governing chromatin structure.
I also collaborate with chemists and physicists to design experiments aimed at characterizing the extent and duration of protein-mediated DNA loops or condensates as a function of DNA supercoiling and binding site specificity and spacing. Using fluorescence microscopy, tethered particle motion, and nano-particle manipulation techniques, we study the topology of single DNA molecules as a result of the activity of proteins that regulate transcription of chromatin. These proteins generate nano-Newton-scale forces that we can measure and/or apply in single molecule experiments to reveal mechanochemical details of these interactions.
Juhi Ojha, Gunasingh Masilamoni, David Dunlap, Ross A. Udoff, and Anil G. Cashikar (2011): Sequestration of Toxic Oligomers by HspB1 as a Cytoprotective Mechanism. Molecular and Cellular Biology 31:3146-57
Laura Finzi and David Dunlap (2010): Single-molecule approaches to probe the structure, kinetics, and thermodynamics of nucleoprotein complexes that regulate transcription. Journal of Molecular Biology 285:18973-8
Haowei Wang, Laura Finzi, Dale E.A. Lewis, and David Dunlap (2009): AFM studies of lambda repressor oligomers securing DNA loops. Current Pharmaceutical Biotechnology 10:494-501
Chiara Zurla, Carlo Manzo, David Dunlap, Dale E.A. Lewis, Sankar Adhya, and Laura Finzi (2009): Direct demonstration and quantification of long-range DNA looping by the lambda bacteriophage repressor. Nucleic Acids Research 37:2789-2795
Giuseppe Lia, Szabolcs Semsey, Dale Lewis, Sankar Adhya, David Bensimon, David Dunlap, and Laura Finzi (2008): The antiparallel loops in gal DNA. Nucleic Acids Research 36:4204-4210
Giuseppe Lia, Marco Indrieri, Tom Owen-Hughes, Laura Finzi, Alessandro Podesta’, Paolo Milani, and David Dunlap (2008): ATP-dependent looping of DNA by ISWI. Journal of Biophotonics 4:280-286
Rosalinda F. Guerra, Laura Imperadori, Roberto Mantovani, David D. Dunlap, and Laura Finzi (2007): DNA Compaction by the Nuclear Factor-Y. Biophysical Journal 93:176
Chiara Zurla Tomas Samuely, Giovanni Bertoni, Francesco Valle, Giovanni Dietler, Laura Finzi and David D. Dunlap (2007): Integration Host Factor alters LacI-induced DNA looping. Biophysical Chemistry 128:245
John F. Beausang, Chiara Zurla, Carlo Manzo, David Dunlap, Laura Finzi, and Philip C. Nelson (2007): DNA Looping Kinetics Analyzed Using Diffusive Hidden Markov Model. Biophysical Journal 92:L64
Philip C. Nelson, Chiara Zurla, Doriano Brogioli, John F. Beausang, Laura Finzi, and David Dunlap (2006): Tethered Particle Motion as a Diagnostic of DNA Tether Length. Journal of Physical Chemistry B 110:17260