John F. Marko Professor of Molecular Biosciences, Physics & Astronomy

Research Interests

Protein-DNA interactions, and chromosome structure and dynamics

A good deal of the lab's work uses biophysical methods, with particular emphasis on micromanipulation of single DNA molecules and single chromosomes. Recent projects in the lab have included studies of the internal structure of eukaryote mitotic chromosomes, single-DNA studies of DNA-folding proteins from bacteria, studies of DNA topoisomerases, and studies of the dynamics of self-organization of chromatin using Xenopus egg extracts. The lab also carries out theoretical modeling work related to these experimental studies. Future directions for the lab include combining fluorescence microscopy and force microscopy in experiments on DNA-protein complexes and whole chromosomes, and in-vivo studies of coupling of chromosome dynamics to gene expression.

Selected Publications

An orthogonal single-molecule experiment reveals multiple-attempt dynamics of type IA topoisomerasesGunn KH, Marko JF, and Mondragón A. Nature Structural & Molecular Biology. 2017 May;24(5):484-490.

Facilitated dissociation of transcription factors from single DNA binding sites. Kamar RI, Banigan EJ, Erbas A, Giuntoli RD, Olvera de la Cruz M, Johnson RC, and Marko JF. PNAS. 2017 April 18;114(16):E3251-E3257.

Crossover-site sequence and DNA torsional stress control strand interchanges by the Bxb1 site-specific serine recombinase. Keenholtz RA, Grindley NDF, Hatfull GF, and Marko JF. Nucleic Acids Research. 2016 October 14;44(18):8921-8932.

An assay for 26S proteasome activity based on fluorescence anisotropy measurements of dye-labeled protein substratesBhattacharyya S, Renn JP, Yu H, Marko JF, and Matouschek A. Analytical Biochemistry. 2016 September 15;509:50-59.

Dependence of the structure and mechanics of metaphase chromosomes on oxidized cysteinesEastland A, Hornick J, Kawamura R, Nanavati D, and Marko JF. Chromosome Research. 2016 September;24(3):339-353.

Cell division: A sticky problem for chromosomes. Brangwynne CP and Marko JF. Nature. 2016 July 14;535(7611):234-235.

Facilitated Dissociation of a Nucleoid Protein from the Bacterial Chromosome. Hadizadeh N, Johnson RC, and Marko JF. Journal of Bacteriology. 2016 June;198(12):1735-1742.

Chromosome Compaction by Active Loop Extrusion. Goloborodko A, Marko JF, and Mirny LA. Biophysical Journal. 2016 May 24;110(10):2162-2168.

Compaction and segregation of sister chromatids via active loop extrusion. Goloborodko A, Imakaev MV, Marko JF, and Mirny LA. eLife. 2016 May 18;5:e14864.

Controlled rotation mechanism of DNA strand exchange by the Hin serine recombinase. Xiao B, McLean MM, Lei X, Marko JF, and Johnson RC. Scientific Reports. 2016 April 1;6:23697.

Role of transcription factor-mediated nucleosome disassembly in PHO5 gene expression. Kharerin H, Bhat PJ, Marko JF, and Padinhateeri R. Scientific Reports. 2016 February 4;6:20319.

Self-propulsion and interactions of catalytic particles in a chemically active medium. Banigan EJ and Marko JF. Physical Review E. 2016 January;93(1):012611.

DNA-Segment-Facilitated Dissociation of Fis and NHP6A from DNA Detected via Single-Molecule Mechanical Response. Giuntoli RD, Linzer NB, Banigan EJ, Sing CE, Olvera de la Cruz M, Graham JS, Johnson RC, and Marko JF. Journal of Molecular Biology. 2015 September 25;427(19):3123-3136.

Age-associated alterations in the micromechanical properties of chromosomes in the mammalian egg. Hornick JE, Duncan FE, Sun M, Kawamura R, Marko JF, and Woodruff TK. Journal of Assisted Reproduction and Genetics. 2015 May;32(5):765-769.

Single-molecule analysis uncovers the difference between the kinetics of DNA decatenation by bacterial topoisomerases I and III.  Terekhova K, Marko JF, and Mondragón A. Nucleic Acids Research. 2014 October 13;42(18):11657-11667.

View all publications by John F. Marko listed in the National Library of Medicine (PubMed). Current and former IBiS students in blue.