John F. Marko
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.
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.
Torque correlation length and stochastic twist dynamics of DNA. Banigan EJ and Marko JF. Physical Review E. 2014 June 13;89(6):062706.
Stochastic Ratchet Mechanisms for Replacement of Proteins Bound to DNA. Cocco S, Marko JF, and Monasson R. Physical Review Letters. 2014 June 13;112(23):238101.
Multiple-binding-site mechanism explains concentration-dependent unbinding rates of DNA-binding proteins. Sing CE, Olvera de la Cruz M, and Marko JF. Nucleic Acids Research. 2014 April;42(6):3783-3791.
Nucleosome positioning and kinetics near transcription-start-site barriers are controlled by interplay between active remodeling and DNA sequence. Parmar JJ, Marko JF, and Padinhateeri R. Nucleic Acids Research. 2014 January 7;42(1):128-136.
Global force-torque phase diagram for the DNA double helix: Structural transitions, triple points, and collapsed plectonemes. Marko JF and Neukirch S. Physical Review E. 2013 December 27;88(6):062722.
The SMC1-SMC3 cohesin heterodimer structures DNA through supercoiling-dependent loop formation. Sun M, Nishino T, and Marko JF. Nucleic Acids Research. 2013 July 8;41(12):6149-6160.
ATP Hydrolysis Enhances RNA Recognition and Antiviral Signal Transduction by the Innate Immune Sensor, Laboratory of Genetics and Physiology 2 (LGP2). Bruns AM, Pollpeter D, Hadizadeh N, Myong S, Marko JF, and Horvath CM. Journal of Biological Chemistry. 2013 January 11;288(2):938-946.
Histone H1 compacts DNA under force and during chromatin assembly. Xiao B, Freedman BS, Miller KE, Heald R, and Marko JF. Molecular Biology of the Cell. 2012 December 15;23(24):4864-4871.
Range of Interaction between DNA-Bending Proteins is Controlled by the Second-Longest Correlation Length for Bending Fluctuations. Zhang H and Marko JF. Physical Review Letters. 2012 December 14;109(24):248301.
Self-organization of domain structures by DNA-loop-extruding enzymes. Alipour E and Marko JF. Nucleic Acids Research. 2012 December;40(22):11202-11212.
Variation of the folding and dynamics of the Escherichia coli chromosome with growth conditions. Hadizadeh Yazdi N, Guet CC, Johnson RC, and Marko JF. Molecular Microbiology. 2012 December;86(6):1318-1333.
Bacterial topoisomerase I and topoisomerase III relax supercoiled DNA via distinct pathways. Terekhova K, Gunn KH, Marko JF, and Mondragón A. Nucleic Acids Research. 2012 November;40(20):10432-10440.
Remote control of DNA-acting enzymes by varying the Brownian dynamics of a distant DNA end. Bai H, Kath JE, Zörgiebel FM, Sun M, Ghosh P, Hatfull GF, Grindley NDF, and Marko JF. PNAS. 2012 October 9;109(41):16546-16551.
View all publications by John F. Marko listed in the National Library of Medicine (PubMed). Current and former IBiS students in blue.