Publications


Broadwater, D.W.B., R.B. Altman, S.C. Blanchard, and H.D. Kim. 2018. ERASE: a novel surface reconditioning strategy for single-molecule experimentsNucleic Acids Research doi.org/10.1093/nar/gky1168

Wadsworth, G. M., Parikh, R. Y., Choy, J. S., and Kim, H. D. mRNA detection in budding yeast with single fluorophores. 2017. Nucleic Acids Research doi:10.1093/nar/gkx568 

Waters, J.T., H.D. Kim, J.C. Gumbart, X.-J. Lu, and S.C. Harvey. 2016. DNA Scrunching in the Packaging of Viral Genomes. J. Phys. Chem. B. DOI: 10.1021/acs.jpcb.6b02149

Waters, J.T., X.-J. Lu, R. Galindo-Murillo, J.C. Gumbart, H.D. Kim, T.E. Cheatham, and S.C. Harvey. 2016. Transitions of Double-Stranded DNA Between the A- and B-Forms. J. Phys. Chem. B. doi:10.1021/acs.jpcb.6b021551. 

Waters, JT, Kim, HD. Force distribution in a semiflexible loop. Physical Review E (2016). http://dx.doi.org/10.1103/PhysRevE.93.043315
Read a feature article: The Contrarian Dance of DNA.

Broadwater DWB Jr, Kim HD. The effect of base pair mismatch on DNA strand displacement. Biophysical Journal (2016). doi:10.1016/j.bpj.2016.02.027

Jeong J, Le TT, Kim HD. Single-molecule fluorescence studies on DNA looping. Methods (2016). doi:10.1016/j.ymeth.2016.04.005 

Waters, JT, Kim, HD. Calculation of a fluctuating entropic force by phase space sampling. Phys. Rev. E 92, 013308 (2015). doi:10.1103/PhysRevE.92.013308
One can calculate an entropic force by brute force from classical mechanics. Although the mean of the broad force distribution is equal to the entropic force, the most probable force is not.

Chang YW, Fragkopoulos AA, Marquez SM, Kim HD, Angelini TE, Fernandez-Nieves A. Biofilm formation in geometries with different surface curvature and oxygen availability. New Journal of Physics 2015;17(3):033017. doi:10.1088/1367-2630/17/3/033017
Cells can grow everywhere, above or below a surface of either positive or negative Gaussian curvature as long as oxygen is around.

Le TT, Kim HD. Probing the elastic limit of DNA bendingNucleic Acids Research 2014;42(16):10786–94. PMID: 25122748 
We experimentally determined the angular limit of the famous worm-like chain model of DNA: DNA bends like an elastic rod only up to about 7 degrees per base pair. 

Le TT, Kim HD. Studying DNA looping by single-molecule FRETJournal of Visualized Experiments 2014;88. doi:10.3791/51667
A step-by-step video protocol on how to implement single-molecule FRET with one of the easiest systems around. 

Lee TJ, Parikh RY, Weitz JS, Kim HD. Suppression of expression between adjacent genes within heterologous modules in yeast. G3 (Bethesda). 2014;4(1):109–16. PMID: 24281423
Modification of genomic DNA can bring about subtle effects because nucleosome positioning can be affected. 

Waters JT, Kim HD. Equilibrium statistics of a surface-pinned semiflexible polymer. Macromolecules 2013;46(16):6659–6666.
A few things to consider when experimenting with surface-attached polymers: looping dynamics of a polymer may become faster or slower depending on how it is confined.

Parikh RY, Kim HD. The effect of an intervening promoter nucleosome on gene expression. PLoS ONE 2013;8(5):e63072. PMID: 23700413
Because nucleosomes compact DNA inside the cell, they are thought to hinder reading of the genetic code. Here, we propose an intriguing mechanism of how nucleosomes may help decode the genetic code.

Le TT, Kim HD. Measuring shape-dependent looping probability of DNA. Biophysical Journal 2013;104(9):2068–2076. PMID: 23663850
Which DNA loops faster, a C-shape or an S-shape? We measured looping probabilities of DNA molecules of different curvatures.





Publications Before Kim Lab 

[1] H.D. Kim*, T. Shay*, E.K. O'Shea, and A. Regev, “Transcriptional Regulatory Circuits: Predicting Numbers from Alphabets,” Science, vol. 325, 2009, p. 429.  
[2]

H.D. Kim and E.K. O’Shea, “A quantitative model of transcription factor–activated gene expression,” Nature Structural & Molecular Biology, vol. 15, 2008, p. 1192.  
[3] S. Uemura, M. Dorywalska, T.H. Lee, H.D. Kim, J.D. Puglisi, and S. Chu, “Peptide bond formation destabilizes Shine–Dalgarno interaction on the ribosome,” Nature, vol. 446, 2007, p. 454.  
[4] T.H. Lee, S.C. Blanchard, H.D. Kim, J.D. Puglisi, and S. Chu, “The role of fluctuations in tRNA selection by the ribosome,” Proceedings of the National Academy of Sciences, vol. 104, 2007, p. 13661.  
[5] H.D. Kim, J.D. Puglisi, and S. Chu, “Fluctuations of transfer RNAs between classical and hybrid states,” Biophysical Journal, vol. 93, 2007, pp. 3575–3582.  
[6] U. Mohanty, A. Spasic, H.D. Kim, and S. Chu, “Ion Atmosphere of Three-Way Junction Nucleic Acid” J. Phys. Chem. B, vol. 109, 2005, pp. 21369–21374.  
[7] M. Dorywalska, S.C. Blanchard, R.L. Gonzalez, H.D. Kim, S. Chu, and J.D. Puglisi, “Site-specific labeling of the ribosome for single-molecule spectroscopy,” Nucleic Acids Research, vol. 33, 2005, p. 182.  
[8] S.C. Blanchard*, H.D. Kim*, R.L. Gonzalez*, J.D. Puglisi, and S. Chu, “tRNA dynamics on the ribosome during translation,” Proceedings of the National Academy of Sciences, vol. 101, 2004, p. 12893.  
[9] S.C. Blanchard, R.L. Gonzalez*, H.D. Kim*, S. Chu, and J.D. Puglisi, “tRNA selection and kinetic proofreading in translation,” Nature structural & molecular biology, vol. 11, 2004, pp. 1008–1014.  
[10] X. Zhuang, H. Kim, M.J. Pereira, H.P. Babcock, N.G. Walter, and S. Chu, “Correlating structural dynamics and function in single ribozyme molecules,” Science, vol. 296, 2002, p. 1473.  
[11] H.D. Kim, G.U. Nienhaus, T. Ha, J.W. Orr, J.R. Williamson, and S. Chu, “Mg2+-dependent conformational change of RNA studied by fluorescence correlation and FRET on immobilized single molecules,” Proceedings of the National Academy of Sciences, vol. 99, 2002, p. 4284.  
[12] X. Zhuang, T. Ha, H.D. Kim, T. Centner, S. Labeit, and S. Chu, “Fluorescence quenching: A tool for single-molecule protein-folding study,” Proceedings of the National Academy of Sciences, vol. 97, 2000, p. 14241.  
[13] T. Ha, X. Zhuang, H.D. Kim, J.W. Orr, J.R. Williamson, and S. Chu, “Ligand-induced conformational changes observed in single RNA molecules,” Proceedings of the National Academy of Sciences of the United States, vol. 96, 1999, p. 9077.