John Marko


PhD, Massachusetts Institute of Technology

Interdisciplinary Biological Sciences Program
Department of Molecular Biosciences
Department of Physics and Astronomy

Office Phone: 847.467.1276
Lab Phone: 847.467.1187
Email
Marko Lab

Research

Our group uses biophysical methods to study mechanisms of biomolecule function, as well as problems in cell biology. We use "magnetic tweezers" micromanipulation and fluorescence visualization to study biomolecule interactions - mainly protein-DNA interactions, and we use micropipette manipulation and force measurement to study large-scale chromosome and nucleus structure.

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. Our group 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 chromosome organization through the cell cycle.

Selected Publications

DNA-segment-facilitated dissociation of Fis and NHP6A from DNA detected
via single-molecule mechanical response
R.D. Giuntoli, N.B. Linzer, E.J. Banigan, C.E. Sing, M. Olvera de la Cruz,
J.S. Graham, R.C. Johnson, J.F. Marko
J. Mol. Biol. 427, 3123-36 (2015) [14 pages].

Age-associated alterations in the micromechanical properties of
chromosomes in the mammalian egg
J.E. Hornick, F.E. Duncan, M. Sun, R. Kawamura, J.F. Marko, T.K. Woodruff
J. Assist. Reprod. Genet. 32, 765-769 (2015) [5 pages].

Biophysics of protein-DNA interactions and chromosome organization
J.F. Marko
Physica A 418, 126-153 (2015) [28 pages].

Single-molecule analysis uncovers the difference between the kinetics of
DNA decatenation by bacterial topoisomerases I and III.
K. Terekhova, J.F. Marko, A. Mondragon
Nucl. Acids. Res. 42, 11657-67 (2015) [11 pages].

Nuclear physics (of the cell, not the atom)
T. Pederson, J.F. Marko
Mol. Biol. Cell. 25, 3466-69 (2014) [4 pages].

Torque correlation length and stochastic twist dynamics of DNA
E.J. Banigan, J.F. Marko
Phys. Rev. E 89, 062706 (2014) [7 pages]

Stochastic ratchet mechanisms for replacement of proteins bound to DNA
S. Cocco, J.F. Marko, R. Monasson
Phys. Rev. Lett. 112, 238101 (2014) [4 pages]

Multiple-binding-site mechanism explains concentration-dependent unbinding
rates of DNA-binding proteins
C.E. Sing, M.O. de la Cruz, J.F. Marko
Nucl. Acids Res. 42 3783-91 (2014) [9 pages].

Nucleosome positioning and kinetics near transcription-start-site barriers
are controlled by interplay between active remodeling and DNA sequence
J.J. Parmar, J.F. Marko, R. Padinhateeri
Nucleic Acids Res. 42 128-36 (2014) [9 pages].

Global force-torque phase diagram for the DNA double helix: Structural
transitions, triple points, and collapsed plectonemes
J.F. Marko, S. Neukirch
Phys. Rev. E 88, 062722 (2013) [18 pages].

Binding-rebinding dynamics of proteins interacting nonspecifically with a
long DNA molecule
A. Parsaeian, M.O. de la Cruz, J.F. Marko
Phys. Rev. E 88, 040703(R) (2013) [4 pages].

The SMC1-SMC3 cohesin heterodimer structures DNA through
supercoiling-dependent loop formation
M. Sun, T. Nishino, J.F. Marko
Nucleic Acids Res. 41, 6149-60 (2013) [12 pages].

ATP hydrolysis enhances RNA recognition and antiviral signal transduction
by the innate immune sensor LGP2
A.M. Bruns, D. Pollpeter, N. Hadizadeh, S. Myong, J.F. Marko, C.M. Horvath
J. Biol. Chem. 288, 938-946 (2013) [9 pages].

Self-organization of domain structures by DNA-loop-extruding enzymes
E. Alipour, J.F. Marko
Nucl. Acids Res. 40, 11202-12 (2012) [11 pages].

Remote control of DNA-acting enzymes by varying the Brownian dynamics of a
distant DNA end
H. Bai, J.E. Kath, F.M. Zorgiebel, M. Sun, P. Ghosh, G.F. Hatfull, N.D.F.
Grindley, J.F. Marko
Proc. Natl. Acad. Sci. USA 109, 16546-51 (2012) [6 pages].

Variation of the folding and dynamics of the Escherichia coli chromosome
with growth conditions.
N. Hadizadeh Yazdi, C.C. Guet, R.C Johnson, J.F. Marko
Mol. Micro. 86, 1318-33 (2012) [16 pages].

Single-molecule analysis reveals the molecular bearing mechanism of DNA
strand exchange by a serine recombinase
H. Bai, M. Sun, P. Ghosh, G.F. Hatfull, N.D.F. Grindley, J.F. Marko
Proc. Natl. Acad. Sci. USA, 108, 7419-24 (2011) [6 pages].

Micromechanics of human mitotic chromosomes
M. Sun, R. Kawamura, J.F. Marko
Phys. Biol. 8, 015003 (2011) [10 pages].

Concentration-dependent exchange accelerates turnover of proteins bound to
double-stranded DNA
J.S. Graham, R.C. Johnson, J.F. Marko
Nucl. Acids Res. 39, 2249-59 (2010) [11 pages].

Mitotic chromosomes are constrained by topoisomerase II-sensitive DNA
entanglements
R. Kawamura, L.H. Pope, M.O. Christensen, M. Sun, K. Terekhova, F. Boege,
Ch. Mielke, A.H. Andersen, J.F. Marko
J. Cell Biol. 188, 653-63 (2010) [11 pages]

Topoisomerase V relaxes supercoiled DNA by a constrained swiveling
mechanism
B. Taneja, B. Schnurr, A. Slesarev, J.F. Marko, A. Mondragon
Proc Natl Acad Sci USA. 2007 Sep 11;104(37):14670-5.

 

Links

PubMed listing of Marko publications

Recent Photos

October 27, 2015