David Dunlap

Senior Staff Scientist

Office: MSC - RM N211

Phone: 404-727-8036

Email: ddunlap@emory.edu

Additional Contact Information

Mailing Address:

400 Dowman Drive
MSC - RM N211

Atlanta, GA 30322-2430

Education

  • Ph.D., University of Oregon, 1993

Research

Research Interests

DNA structure, topology and protein-DNA interactions, with a focus on single molecule manipulation and microscopy.

Publications

[1] Fernández-Sierra, M., Shao, Q., Fountain, C., Finzi, L., and Dunlap, D. (2015) E. coli Gyrase Fails to Negatively Supercoil Diaminopurine-Substituted DNA, Journal of Molecular Biology 427, 2305-2318.

[2] Priest, D. G., Kumar, S., Yan, Y., Dunlap, D. D., Dodd, I. B., and Shearwin, K. E. (2014) Quantitation of interactions between two DNA loops demonstrates loop domain insulation in E. coli cells, Proc Natl Acad Sci U S A 111, E4449-4457.

[3] Priest, D. G., Cui, L., Kumar, S., Dunlap, D. D., Dodd, I. B., and Shearwin, K. E. (2014) Quantitation of the DNA tethering effect in long-range DNA looping in vivo and in vitro using the Lac and λ repressors, Proceedings of the National Academy of Sciences 111, 349-354.

[4] Kumar, S., Manzo, C., Zurla, C., Ucuncuoglu, S., Finzi, L., and Dunlap, D. (2014) Enhanced Tethered-Particle Motion Analysis Reveals Viscous Effects, Biophysical Journal 106, 399-409.

[5] Ding, Y., Manzo, C., Fulcrand, G., Leng, F., Dunlap, D., and Finzi, L. (2014) DNA supercoiling: A regulatory signal for the λ repressor, Proceedings of the National Academy of Sciences 111, 15402-15407.

[6] Biton, Y. Y., Kumar, S., Dunlap, D., and Swigon, D. (2014) Lac repressor mediated DNA looping: monte carlo simulation of constrained DNA molecules complemented with current experimental results, PLoS One 9, e92475.

[7] Wang, H., Dodd, I. B., Dunlap, D. D., Shearwin, K. E., and Finzi, L. (2013) Single molecule analysis of DNA wrapping and looping by a circular 14mer wheel of the bacteriophage 186 CI repressor, Nucleic Acids Res 41, 5746-5756.

[8] Gao, N., Shearwin, K., Mack, J., Finzi, L., and Dunlap, D. (2013) Purification of bacteriophage lambda repressor, Protein Expression and Purification 91, 30-36.

[9] Shao, Q., Goyal, S., Finzi, L., and Dunlap, D. (2012) Physiological Levels of Salt and Polyamines Favor Writhe and Limit Twist in DNA, Macromolecules 45, 3188-3196.

[10] Manzo, C., Zurla, C., Dunlap, D. D., and Finzi, L. (2012) The effect of nonspecific binding of lambda repressor on DNA looping dynamics, Biophys J 103, 1753-1761.

[11] Goyal, S., Fountain, C., Dunlap, D., Family, F., and Finzi, L. (2012) Stretching DNA to quantify nonspecific protein binding, Physical Review E 86.

[12] Dunlap, D., Yokoyama, R., Ling, H., Sun, H.-Y., McGill, K., Cugusi, S., and Lucchesi, J. C. (2012) Distinct contributions of MSL complex subunits to the transcriptional enhancement responsible for dosage compensation in Drosophila, Nucleic Acids Research 40, 11281-11291.

[13] Leng, F., Chen, B., and Dunlap, D. D. (2011) Dividing a supercoiled DNA molecule into two independent topological domains, Proceedings of the National Academy of Sciences 108, 19973-19978.

[14] Finzi, L., Manzo, C., Zurla, C., Wang, H. W., Lewis, D., Adhya, S., and Dunlap, D. (2011) DNA Looping in Prophage Lambda: New Insight from Single-Molecule Microscopy, In Biophysics of DNA- Protein Interactions: From Single Molecules to Biological Systems (Williams, M. C., and Maher, L. J., Eds.), pp 193-212, Springer, New York.

[15] Dunlap, D., Zurla, C., Manzo, C., and Finzi, L. (2011) Probing DNA topology using tethered particle motion, Methods Mol Biol 783, 295-313.

[16] Dunlap, D., Zurla, C., Manzo, C., and Finzi, L. (2011) Probing DNA Topology Using Tethered Particle Motion, In Single Molecule Analysis (Peterman, E. J. G., and Wuite, G. J. L., Eds.), pp 295-313, Humana Press, New York, NY USA.

[17] Liebesny, P., Goyal, S., Dunlap, D., Family, F., and Finzi, L. (2010) Determination of the number of proteins bound non-specifically to DNA, Journal of Physics: Condensed Matter 22, 414104.

[18] Finzi, L., and Dunlap, D. D. (2010) Single-molecule approaches to probe the structure, kinetics, and thermodynamics of nucleoprotein complexes that regulate transcription, J Biol Chem 285, 18973-18978.

[19] Zurla, C., Manzo, C., Dunlap, D., Lewis, D. E. A., Adhya, S., and Finzi, L. (2009) Direct demonstration and quantification of long-range DNA looping by the λ bacteriophage repressor, Nucleic Acids Research 37, 2789-2795.

[20] Wang, H., Finzi, L., Lewis, D. E., and Dunlap, D. (2009) AFM studies of lambda repressor oligomers securing DNA loops, Curr Pharm Biotechnol 10, 494-501.

[21] Lia, G., Indrieri, M., Owen-Hughes, T., Finzi, L., Podesta, A., Milani, P., and Dunlap, D. (2008) ATP-dependent looping of DNA by ISWI, Journal of Biophotonics 1, 280-286.

[22] Zurla, C., Samuely, T., Bertoni, G., Valle, F., Dietler, G., Finzi, L., and Dunlap, D. D. (2007) Integration host factor alters LacI-induced DNA looping, Biophysical Chemistry 128, 245-252.

[23] Guerra, R. F., Imperadori, L., Mantovani, R., Dunlap, D. D., and Finzi, L. (2007) DNA compaction by the nuclear factor-Y, Biophysical Journal 93, 176-182.

[24] Nelson, P. C., Zurla, C., Brogioli, D., Beausang, J. F., Finzi, L., and Dunlap, D. (2006) Tethered particle motion as a diagnostic of DNA tether length, J Phys Chem B 110, 17260-17267.

[25] Lia, G., Praly, E., Ferreira, H., Stockdale, C., Tse-Dinh, Y. C., Dunlap, D., Croquette, V., Bensimon, D., and Owen-Hughes, T. (2006) Direct observation of DNA distortion by the RSC complex, Mol Cell 21, 417-425.

[26] Podesta, A., Indrieri, M., Brogioli, D., Manning, G. S., Milani, P., Guerra, R., Finzi, L., and Dunlap, D. (2005) Positively charged surfaces increase the flexibility of DNA, Biophys J 89, 2558-2563.

[27] Podesta, A., Imperadori, L., Colnaghi, W., Finzi, L., Milani, P., and Dunlap, D. (2004) Atomic force microscopy study of DNA deposited on poly L-ornithine-coated mica, J Microsc 215, 236-240.

[28] Lia, G., Bensimon, D., Croquette, V., Allemand, J. F., Dunlap, D., Lewis, D. E. A., Adhya, S. C., and Finzi, L. (2003) Supercoiling and denaturation in Gal repressor/heat unstable nucleoid protein (HU)-mediated DNA looping, Proceedings Of The National Academy Of Sciences Of The United States Of America 100, 11373-11377.

[29] Finzi, L., and Dunlap, D. (2003) Single-molecule studies of DNA architectural changes induced by regulatory proteins, Methods Enzymol 370, 369-378.

[30] Pennuto, M., Dunlap, D., Contestabile, A., Benfenati, F., and Valtorta, F. (2002) Fluorescence Resonance Energy Transfer Detection of Synaptophysin I and Vesicle-associated Membrane Protein 2 Interactions during Exocytosis from Single Live Synapses, Molecular Biology of the Cell 13, 2706-2717.

[31] Menegon, A., Dunlap, D. D., Castano, F., Benfenati, F., Czernik, A. J., Greengard, P., and Valtorta, F. (2000) Use of phosphosynapsin I-specific antibodies for image analysis of signal transduction in single nerve terminals, J Cell Sci 113 ( Pt 20), 3573-3582.

[32] Dunlap, D. D., Maggi, A., Soria, M. R., and Monaco, L. (1997) Nanoscopic structure of DNA condensed for gene delivery, Nucleic Acids Res 25, 3095-3101.

[33] Dunlap, D., Cattelino, A., de Curtis, I., and Valtorta, F. (1996) Cytoplasmic topography of focal contacts, Febs Letters 382, 65-72.

[34] Dunlap, D., Smith, S., Bustamante, C., Tamayo, J., and Garcia, R. (1995) A very low current scanning tunneling microscope, Review of Scientific Instruments 66, 4876.

[35] Dunlap, D. D., Garcia, R., Schabtach, E., and Bustamante, C. (1993) Masking generates contiguous segments of metal-coated and bare DNA for scanning tunneling microscope imaging, Proc Natl Acad Sci U S A 90, 7652-7655.

[36] Dunlap, D. D., and Bustamante, C. (1989) Images of single-stranded nucleic acids by scanning tunnelling microscopy, Nature 342, 204-206.