Linking topology of large DNA molecules
J. F. Marko
doi:10.1016/j.physa.2010.01.003 (2010, accepted)

Barrier-to-autointegration factor (BAF) condenses DNA by looping
D. Skoko, M. Lia, Y. Huang, M. Mizuuchi, M. Cai, C.M. Bradley, P.J. Pease, B. Xiao, J.F. Marko, R. Craige, K. Mizuuchi,
Proc Natl Acad Sci USA 106, 16610-15 (2009) [6 pages]

Linking topology of tethered polymer rings with applications to chromosome segregation and estimation of the knotting length
J.F. Marko
Phys. Rev. E 79, 051905 (2009) [16 pages]

Micromechanics of single supercoiled DNA molecules
J.F. Marko
Mathematics of DNA Structure, Function and Interactions Series: The IMA Volumes in Mathematics and its Applications , Vol. 150 Benham, C.J.; Harvey, S.; Olson, W.K.; Sumners, D.W.L.; Swigon, D. (Eds.) 2009, XII, 368 p., Hardcover ISBN: 978-1-4419-0669-4, pp. 225-249. (click here for reprint)

Micromechanical studies of mitotic chromosomes
J.F. Marko
Chromosome Res. 16, 469-97 (2008) (29 pages)

Maxwell relations for single-DNA experiments: Monitoring protein binding and double-helix torque with force-extension measurements
H. Zhang and J.F. Marko
Phys. Rev. E 77, 031916 (2008) (9 pages)

Torque and dynamics of linking number relaxation in stretched supercoiled DNA
J.F. Marko
Phys. Rev. E 76, 021926 (2007) (13 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 U S A. 2007 Sep 11;104(37):14670-5

Nucleosome hopping and sliding kinetics determined from dynamics of single chromatin fibers in Xenopus egg extracts
P. Ranjith, J. Yan, J.F. Marko
Proc Natl Acad Sci U S A. 2007 Aug 21;104(34):13649-54

Pulling Apart Catalytically Active Tn5 Synaptic Complexes Using Magnetic Tweezers
C.D. Adams, B. Schnurr, J.F. Marko, W.S. Reznikoff
J. Mol. Biol. 367, 319-327 (2007)

Micromanipulation studies of chromatin fibers in Xenopus egg extracts reveal ATP-dependent chromatin assembly dynamics.
J. Yan, T.J. Maresca, D. Skoko, C.D. Adams, B. Xiao, M.O. Christensen, R. Heald, J.F. Marko
Mol. Biol. Cell 18, 464-474 (2007)

Tn5 transposase loops DNA in the absence of Tn5 transposon end sequences
C.D. Adams, B. Schnurr, D. Skoko, J.F. Marko, W.S. Reznikoff,
Mol. Micro. 62, 1558-1568 (2006)

Mechanism of chromosome compaction and looping by the E. coli nucleoid protein Fis
D. Skoko, D. Yoo, H. Bai, B. Schnurr, J. Yan, S. M. McLeod, J. F. Marko, and R. C. Johnson
J. Mol. Biol. 364, 777-798 (2006)

Filling of the one- dimensional lattice by k-mers proceeds via fast power-law-like kinetics
P. Ranjith, J.F. Marko
Phys. Rev. E 74, 041602 (2006) (4 pages)

1996-2006 (UIC)

Defining characteristics of Tn5 Transposase non-specific DNA binding
M. Steiniger, C.D. Adams, J.F. Marko, W.S. Reznikoff, Nucleic Acids Res. 34, 2820-32 (2006) (13 pages).

Proteolysis of Mitotic Chromosomes Induces Gradual and Anisotropic Decondensation Correlated with a Reduction of Elastic Modulus and Structural Sensitivity to Rarely Cutting Restriction Enzymes
L.H. Pope, C. Xiong, J.F. Marko, Mol. Biol. Cell 17, 104-13 (2006) (10 pages)

Low-Force DNA Condensation and Discontinuous High-Force Decondensation Reveal a Loop-Stabilizing Function of the Protein Fis
D. Skoko, J. Yan, R.C. Johnson, J.F. Marko, Phys. Rev. Lett. 95, 208101 (2005) (4 pages)

Introduction to single-DNA micromechanics in Multiple aspects of DNA and RNA from biophysics to bioinformatics Les Houches Session LXXXII, 211-270 (Elsevier, 2005)
Note that the last terms of Eqs. 4.8 and 4.9 should be each a factor of two smaller than what was printed.
Thanks to B. Duplantier for noticing this typo.

Entropic Compression of Interacting DNA Loops
S. Sankararaman, J.F. Marko, Phys. Rev. Lett. 95, 078104 (2005) (4 pages)

Statistics of loop formation along double helix DNAs
J. Yan, R. Kawamura, J.F. Marko, Phys. Rev. E 71, 061905 (2005) (17 pages)

Single chromatin fiber stretching reveals physically distinct populations of disassembly events
L.H. Pope, M.L. Bennink, K.A. van Leijenhorst-Groener, D. Nikova, J. Greve, J.F. Marko Biophys. J. 88, 3572-83 (2005)

Formation of loops in DNA under tension
S. Sankararaman, J.F. Marko, Phys. Rev. E 71, 021911 (2005) (13 pages)

Defining a Centromere-like Element in Bacillus subtilis by Identifying the Binding Sites for the Chromosome-Anchoring Protein RacA
S. Ben-Yehuda, M. Fujita, X.S. Liu, B. Gorbatyuk, D. Skoko, J. Yan, J.F. Marko, J.S. Liu, P. Eichenberger, D.Z. Rudner, R. Losick, Molecular Cell 17, 773-82 (2005).

Micromechanical Analysis of the Binding of DNA-Bending Proteins HMGB1, NHP6A, and HU Reveals Their Ability To Form Highly Stable DNA-Protein Complexes
D. Skoko, B. Wong, R.C. Johnson, J.F. Marko, Biochemistry 43, 13867-74 (2004) (8 pages).

Localized single-stranded bubble mechanism for cyclization of short double helix DNA
J. Yan, J.F. Marko, Phys. Rev. Lett. 93, 108108 (2004) (4 pages).

Overstretching and force-driven strand-separation of double-helix DNA,
J. Yan, J.-F. Leger, S. Cocco, D. Chatenay, J.F. Marko, Phys. Rev. E 70, 011910 (2004) (18 pages).

Near-field-magnetic-tweezer manipulation of single DNA molecules
J. Yan, D. Skoko, J.F. Marko Phys. Rev. E 70, 011905 (2004) (5 pages)

How do site-specific DNA-binding proteins find their targets? (Survey and Summary),
S.E. Halford, J.F. Marko, Nucl. Acids. Res. 32, 3040-52 (2004).

Micromechanics of chromatin and chromosomes M.G. Poirier and J.F. Marko, Curr. Top. Dev. Biol. 55, 75-141 (2003)

Micromechanics of chromatin and chromosomes
J.F. Marko and M.G. Poirier, Biochem. Cell. Biol. 81, 209-20 (2003)

Effect of DNA-distorting proteins on DNA elastic response
J. Yan and J.F. Marko, Phys. Rev. E 68, 011905 (2003)

Force-extension behavior of folding polymers
S. Cocco, J.F. Marko, R. Monasson, A. Sarkar, J. Yan, Eur. Phys. J. E 10, 249-263 (2003)

Slow nucleic acid unzipping from sequence-defined barriers
S. Cocco, J.F. Marko, R. Monasson, Eur. Phys. J. E 10, 153-161 (2003)

The micromechanics of DNA
J.F. Marko, S. Cocco, Physics World 16, No.3, 37-41 (2003)

Unzipping dynamics of long DNAs
S. Cocco, R. Monasson, J.F. Marko, Phys. Rev. E 66, 051914 (2002)

Mitotic chromosomes are chromatin networks without an internal protein scaffold
M.G. Poirier, J.F. Marko, Proc. Natl. Acad. Sci USA 99, 15393-15397 (2002)

Commentary by A.S. Belmont
Mitotic chromosome scaffold structure: New approaches to an old controversy
Proc. Natl. Acad. Sci. USA 99, 15855-7 (2002)

Dynamics of chromosome compaction during mitosis
A. Sarkar, S. Eroglu, M.G. Poirier, P. Gupta, A. Nemani, J.F. Marko
Exp. Cell Res. 277, 48-56 (2002)

Theoretical micromechanics of DNA and DNA-protein complexes
A. Sarkar
Ph.D. Thesis, University of Illinois at Chicago (2002)
(Note that sections of this thesis have been separately published as research papers)

The bending rigidity of mitotic chromosomes
M.G. Poirier, S. Eroglu, J.F. Marko
Mol. Biol. Cell 13, 2170-9 (2002)

Micromechanical properties of mitotic chromosomes (review)
M.G. Poirier, J.F. Marko
J. Muscle Res. Cell. Motil. 23, 409-431 (2002)

Theoretical models for single-molecule DNA and RNA experiments: from elasticity to unzipping (review)
S. Cocco, J.F. Marko, R. Monasson
C. R. Physique (Paris) 3, 569-584 (2002)

Force and kinetic barriers to initiation of DNA unzipping
S. Cocco, R. Monasson, J.F. Marko
Phys. Rev. E 65, 041907 (2002)

Effect of internal friction on biofilament dynamics
M.G. Poirier and J.F. Marko
Phys. Rev. Lett. 88, 228103-6 (2002)

Reversible hypercondensation and decondensation of mitotic chromosomes
studied using combined chemical-micromechanical techniques
M.G. Poirier, T. Monhait, J.F. Marko
J. Cell. Biochem. 85, 422-34 (2002)

Micromechanical-Biochemical Studies of Mitotic Chromosome Structure
M.G. Poirier
Ph.D. Thesis, University of Illinois at Chicago (2001)
(Note that sections of this thesis have been separately published as research papers)

Removal of DNA-bound proteins by DNA twisting
A. Sarkar and J.F. Marko
Phys. Rev. E 64, 061909-061918 (2001)

Force and kinetic barriers to unzipping of the DNA double helix
S. Cocco, R. Monasson and J.F. Marko
Proc. Natl. Acad. Sci. USA 98, 8603-13 (2001)

Short note on the scaling behavior of communication by 'slithering' on a supercoiled DNA
J.F. Marko
Physica A 296, 289-292 (2001)

Structural transitions in DNA driven by external force and torque
A. Sarkar, J.-F. Leger, D. Chatenay and J.F. Marko
Phys. Rev. E 63, 051903-051912 (2001)

Chromosome elasticity and mitotic polar ejection force
measured in living Drosophila embyros by four-dimensional microscopy-based motion analysis
W.F. Marshall, J.F. Marko, D.A. Agard and J.W. Sedat
Curr. Biol. 11, 569-78 (2001)

Probing chromosome structure using dynamic force relaxation
M.G. Poirier, S. Eroglu, A. Nemani, P. Gupta and J.F. Marko
Phys. Rev. Lett. 86 360-3 (2001)

Kinetic proofreading can explain the supression of supercoiling
of circular DNA molecules by type-II topoisomerases
J. Yan, M.O. Magnasco and J.F. Marko
Phys. Rev. E 63, 031909-031919;(2001)

One- and three-dimensional pathways for proteins to reach specific DNA sites
N.P. Stanford, M.D. Szczelkun, J.F. Marko, S.E. Halford
EMBO J. 19, 6546-57 (2000)

Reversible and irreversible unfolding of mitotic newt chromosomes by applied force
M. Poirier, S. Eroglu, D. Chatenay and J.F. Marko, Mol. Biol. Cell. 11, 269-276 (2000)

Kinetic proofreading mechanism for DNA disentanglement by topoisomerases
J. Yan, M.O. Magnasco and J.F. Marko, Nature 401, 932-935 (1999)

Structural transformations of a twisted and stretched DNA
J.F. Leger, J. Robert, L. Bordieu, A. Sarkar, D. Chatenay and J.F. Marko,
Phys. Rev. Lett. 83, 1066-1069 (1999)

Coupling of intra- and intermolecular linkage complexity of two DNAs
J. F. Marko, Phys. Rev. E 59, 900-912 (1999)

RecA binding to a single double-stranded DNA molecule: a possible role of DNA conformational fluctuations
J.F. Leger, J. Robert, L. Bordieu, D. Chatenay and J.F. Marko,
Proc. Natl. Acad. Sci. USA,  95, 12295 (1998)

Architecture of a bacterial chromosome (review)
N. J. Trun and J. F. Marko, American Society for Microbiology News 64, 276 (1998)

Polymer models of meiotic and mitotic chromosomes
J. F. Marko and E. D. Siggia, Mol. Biol. Cell  8, 2217 (1997)

Interphase chromosomes undergo constrained diffusional motion in living cells
W.F. Marshall, A. Straight, J.F. Marko, J. Swedlow, A. Dernburg, A. Belmont, A.W. Murray, D.A. Agard DA, J.W. Sedat
Current Biology 7, 930-9 9 (1997)