Marko Laboratory Publications

2006-present (NU)

Heterochromatin flexibility contributes to chromosome segregation in the cell nucleus
M. Girard, M. O. de la Cruz, J. F. Marko, A. Erbas
bioRXiv preprint (2021)

High-resolution, genome-wide mapping of positive supercoiling in chromosomes
M.S. Guo, R. Kawamura, M. Littlehale, J.F. Marko, M.T. Taub
bioRXiv preprint (2021)

DNA tension-modulated translocation and loop extrusion by SMC complexes revealed by molecular dynamics simulations
S. Nomidis, S. Gruber, E. Carlon, J. F. Marko
bioRXiv preprint (2021)

HP1α is a chromatin crosslinker that controls nuclear and mitotic chromosome mechanics
A.R. Strom, R.J. Biggs, E. J. Banigan, X. Wang, K. Chiu, C. Herman, J. Collado, F. Yue, J.C. Ritland Politz, L.J. Tait, D. Scalzo, A. Telling, M. Groudine, C.P. Brangwynne, J.F. Marko, A.D. Stephens
bioRXiv preprint (2021)

Single-molecule micromanipulation studies of methylated DNA
T. Zaichuk, J. F. Marko
Biophys. J. 120, 2148-2155 (2021) [8 pages].

Compartment-dependent chromatin interaction dynamics revealed by liquid chromatin Hi-C
H. Belaghzal, T. Borrman, A.D. Stephens, D.L. Lafontaine, S.V. Venev, Z. Weng, J.F. Marko, J. Dekker
Nat. Genetics 53, 367-378 (2021) [12 pages]

The Smc5/6 Core Complex Is a Structure-Specific DNA Binding and Compacting Machine
D. Serrano, G. Cordero, R. Kawamura, A. Sverzhinsky, M. Sarker, S. Roy, C. Malo, J.M. Pascal, J.F. Marko, D. D'Amours
Mol. Cell 80, 1025-1038 (2020) [14 pages]

Coarse-grained modelling of DNA plectoneme pinning in the presence of base-pair mismatches
P.R. Desai, S. Brahmachari, J.F. Marko, S. Das, K.C. Neuman
Nucl. Acids Res. 48, 10713-25 (2020) [13 pages]

Micromanipulation of prophase I chromosomes from mouse spermatocytes reveals high stiffness and gel-like chromatin organization
R.J. Biggs, N. Liu, Y. Peng, J.F. Marko, H. Qiao
Commun. Biol. 3, 542 (2020) [7 pages].

Chromosome organization by one-sided and two-sided loop extrusion
E.J. Banigan, A.A. van den Berg, H.B. Brandao, J.F. Marko, L.A. Mirny
eLife 9, e53558 (2020) [46 pages].

Physics and biology (of chromosomes)
J.F. Marko
J. Mol. Biol. 432, 621-31 (2020) [10 pages].

Chromosome disentanglement driven via optimal compaction of loop-extruded brush structures
S. Brahmachari, J.F. Marko
Proc. Natl. Acad. Sci. USA 116, 24956-65 (2019) [10 pages].

How do DNA-bound proteins leave their binding sites? The role of facilitated dissociation
A. Erbas, J.F. Marko
Curr. Opin. Struct. Biol. 53, 118-124 (2019) [7 pages].

Mechanical unfolding of spectrin reveals a super-exponential dependence of unfolding rate on force
J.P. Renn, S. Bhattacharyya, H. Bai, C. He, H. Li, A.F. Oberhauser, J.F. Marko, D.E. Makarov, A. Matouschek
Sci. Rep. 9, 11101 (2019) [13 pages].

Physicochemical mechanotransduction alters nuclear shape and mechanics via heterochromatin formation
A.D. Stephens, P.Z. Liu, V. Kandula, H. Chen, L.M. Almassalha, C. Herman, V. Backman, T. O'Halloran, S.A. Adam, R.D. Goldman, E.J. Banigan, J.F. Marko
Mol. Biol. Cell 30, 2320-2330 (2019) [11 pages].

DNA-segment-capture model for loop extrusion by structural maintenance of chromosome (SMC) protein complexes
J.F. Marko, P. De Los Rios, A. Barducci, S. Gruber
Nucl. Acids. Res. 47, 6956-6972 (2019) [17 pages].

Receptor-ligand rebinding kinetics in confinement
A. Erbas, M. Olvera de la Cruz, J.F. Marko
Biophys. J. 116, 1609-1624 (2019) [16 pages].

Multimodal interference-based imaging of nanoscale structure and macromolecular motion uncovers UV induced cellular paroxysm
S. Gladstein, L.M. Almassalha, L. Cherkezyan, J.E. Chandler, A. Eshein, A. Eid, D. Zhang, W. Wu, G.M. Bauer, A.D. Stephens, S. Morochnik, H. Subramanian, J.F. Marko, G.A. Ameer, I. Szleifer, V. Backman
Nature. Comm. 10, 1652 (2019) [15 pages].

Chromatin's physical properties shape the nucleus and its functions
A.D. Stephens, E. Banigan, J.F. Marko,
Curr. Opin. Cell Biol. 58, 76-84 (2019) [9 pages].

Twist-bend coupling and the statistical mechanics of the twistable wormlike-chain model of DNA: Perturbation theory and beyond
S.K. Nomidis, E. Skoruppa, E. Carlon, J.F. Marko,
Phys. Rev. E, 99, 032414 (2019) [16 pages].

Effects of altering histone post-translational modifications on mitotic chromosome structure and mechanics
R. Biggs, P.Z. Liu, A.D. Stephens, J.F. Marko,
Mol. Biol. Cell 30, 820-827 (2019) [8 pages].

DNA Mechanics and Topology
S. Brahmachari, J.F. Marko,
Adv. Exp. Med. Biol. 1092, 11-39 (2018) [29 pages].

Condensin controls mitotic chromosome stiffness and stability without forming a structurally contiguous scaffold
M. Sun, R. Biggs, J. Hornick, J.F. Marko,
Chrom. Res. 26, 277-295 (2018) [19 pages].

Bend-Induced Twist Waves and the Structure of Nucleosomal DNA.
E. Skruppa, S.K. Nomidis, J.F. Marko, E. Carlon,
Phys. Rev. Lett. 121, 088101 (2018) [5 pages].

Defect-facilitated buckling in supercoiled double-helix DNA.
S. Brahmachari, A. Dittmore, Y. Takagi, K.C. Neuman, J.F. Marko
Phys. Rev. E 97, 022416 (2018) [12 pages].

Effects of electrostatic interactions on ligand dissociation kinetics.
A. Erbas, M. Olvera de la Cruz, J.F. Marko
Phys. Rev. E 97, 022405 (2018) [12 pages].

DNA Mechanics
J.F. Marko
Nuclear Architecture and Dynamics, Ch. 1, pp. 3-39, Elsevier (2018) [37 pages].

Single-molecule magnetic tweezer analysis of topoisomerases
K.H. Gunn, J.F. Marko, A. Mondragon
Methods Mol. Biol. 1703, 139-152 (2018) [14 pages]

Separate roles for chromatin and lamins in nuclear mechanics
A.D. Stephens, E.J. Banigan, J.F. Marko
Nucleus 9, 119-124 (2017) [6 pages].

Chromatin histone modifications and rigidity affect nuclear morphology independent of lamins
A.D. Stephens, P.Z. Liu, E.J. Banigan, L.M. Almassalha, V. Backman, S.A. Adam, R.D. Goldman, J.F. Marko
Mol. Biol. Cell 29, 220-233 (2018) [14 pages].

Oligomerization and ATP stimulate condensin-mediated DNA compaction
R.A. Keenholtz, T. Dhanaraman, R. Palou, J. Yu, D. D'Amours, J.F. Marko
Sci. Rep. 7, 14279 (2017) [13 pages].

Nucleation of multiple buckled structures in intertwined DNA double helices
S. Brahmachari, K.H. Gunn, R.D. Giuntoli, A. Mondragon, J.F. Marko
Phys. Rev. Lett. 119, 188103 (2017) [5 pages].

Supercoiling DNA locates mismatches
A. Dittmore, S. Brahmachari, Y. Takagi, J.F. Marko, K.C. Neuman
Phys. Rev. Lett. 119, 147801 (2017) [5 pages].

Mechanics and buckling of biopolymeric shells and cell nuclei
E.J. Banigan, A.D. Stephens, J.F. Marko
Biophys. J. 113, 1654-1663 (2017) [10 pages].

A comparison of nucleosome organization in Drosophila cell lines
R.L. Martin, J. Maiorano, G.J. Beitel, J.F. Marko, G. McVicker, Y.N. Fondufe-Mittendorf,
PLOSOne 12, e0178590 (2017) [23 pages].

Torque and buckling of stretched intertwined double-helix DNAs
S. Brahmachari, J.F. Marko
Phys. Rev. E 95, 052401 (2017) [16 pages].

An orthogonal single-molecule experiment reveals multiple-attempt dynamics of type IA topoisomerases
K.H. Gunn, J.F. Marko, A. Mondragon
Nat. Struct. Mol. Biol. 24, 484-490 (2017) [7 pages].

Facilitated dissociation of transcription factors from single DNA binding sites
R.I. Kamar, E.J. Banigan, A. Erbas, R.D. Giuntoli, M. Olvera de la Cruz, R.C. Johnson, J.F. Marko
Proc. Natl. Acad. Sci. USA 114, E3251-7 (2017) [7 pages].

Chromatin and lamin A determine two different mechanical response regimes of the cell nucleus.
A.D. Stephens, E.J. Banigan, S.A. Adam, R.D. Goldman, J.F. Marko
Mol. Biol. Cell 28, 1984-1996 (2017) [13 pages].

Crossover-site sequence and DNA torsional stress control strand interchanges by the Bxb1 site-specific serine recombinase
R.A. Keenholtz, N.D.F. Grindley, G.F. Hatfull, J.F. Marko
Nucl. Acids Res. 44, 8921-8932 (2016) [12 pages].

Cell division: A sticky problem for chromosomes
C. Brangwynne, J.F. Marko
Nature (News and Views) 535, 234-235 (2016) [2 pages].

An assay for 26S proteasome activity based on fluorescence anisotropy measurements of dye-labeled protein substrates
S. Bhattacharyya, J.P. Renn, H. Yu, J.F. Marko, A. Matouschek
Anal. Biochem. 509, 50-59 (2016) [10 pages].

Dependence of the structure and mechanics of metaphase chromosomes on oxidized cysteines
A. Eastland, R. Kawamura, J. Hornick, J.F. Marko
Chrom. Res. 24, 339-353 (2016) [15 pages].

Chromosome Compaction by Active Loop Extrusion
A. Goloborodko, J.F. Marko, L. Mirny
Biophys. J. 110, 2162-8 (2016) [7 pages].

Compaction and segregation of sister chromatids via active loop extrusion
A. Goloborodko, M.V. Imakaev, J.F. Marko, L. Mirny
eLife 5, e14864 (2016) [16 pages].

Facilitated dissociation of a nucleoid protein from the bacterial chromosome
N. Hadizadeh, R.C. Johnson, J.F. Marko
J. Bact. 198, 1735-1742 (2016) [8 pages].
J Bact. cover story and image

Controlled rotation mechanism of DNA strand exchange by the Hin serine recombinase
B. Xiao, M.M. McLean, X. Lei, J.F. Marko, R.C. Johnson
Sci. Rep. 6, 23697 (2016) [13 pages].

Role of transcription factor-mediated nucleosome disassembly in PHO5 gene expression
H. Kharerin, P.J. Bhat, J.F. Marko, R. Padinhateeri
Sci. Rep. 6, 20319 (2016) [7 pages].

Self-propulsion and interactions of catalytic particles in a chemically active medium
E.J. Banigan, J.F. Marko
Phys. Rev. E. 93, 012611 (2016) [10 pages].

Forces, fluctuations, and self-organization in the nucleus.
T. Pederson, M.C. King, J.F. Marko
Mol. Biol. Cel 26, 3915-9 (2015) [5 pages].

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 (2014) [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]

There is a factor of 2 error in some of the equations; if you are interested please consult the erratum.

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].

A physical sciences network characterization of non-tumorigenic and metastatic cells
Physical Sciences - Oncology Centers Network
Sci Rep. 3, 1449 (2013) [12 pages].

Studies of bacterial topoisomerases I and III at the single-molecule level
K. Terekhova, J.F. Marko, A. Mondragon
Biochem. Soc. Trans. 41, 571-5 (2013) [5 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].

Range of interaction between DNA-bending proteins is controlled by the second-longest correlation length for bending fluctuations
H. Zhang, J.F. Marko
Phys. Rev. Lett. 109, 248301 (2012) [5 pages].

Histone H1 compacts DNA under force and during chromatin assembly.
B. Xiao, B.S. Freedman, K.E. Miller, R. Heald, J.F. Marko
Mol. Biol. Cell 23, 4864-71 (2012) [8 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].
Comment on this paper by L. Le Chat and O. Espeli.

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].

Bacterial topoisomerase I and topoisomerase III relax supercoiled DNA via distinct pathways.
K. Terekhova, K.H. Gunn, J.F. Marko, A. Mondragon,
Nucl. Acids Res. 40, 10432-40 (2012) [9 pages].

The mitotic chromosome: structure and mechanics (book chapter, click here for PDF)
J.F. Marko
in Genome Organization and Function in the Cell Nucleus, ed. K. Rippe, Wiley-VCH, Ch. 18, 449-485, (2012) [37 pages]

The liquid drop nature of nucleoli (Commentary)
J.F. Marko
Nucleus 3, 115-7 (2012) [3 pages].

Competition between curls and plectonemes near the buckling transition of stretched supercoiled DNA
J.F. Marko, S. Neukirch
Phys. Rev. E 85, 011908 (2012) [19 pages]

Counting proteins bound to a single DNA molecule
J.S. Graham, R.C. Johnson, J.F. Marko
Biochem. Biophys. Res. Commun. 415, 131-4 (2011) [4 pages].

Underwound DNA under Tension: Structure, Elasticity, and Sequence-Dependent Behaviors
M.Y. Sheinin, S. Forth, J.F. Marko, M.D. Wang
Phys. Rev. Lett. 107, 108102 (2011) [5 pages].

Nucleosome positioning in a model of active chromatin remodeling enzymes
R. Padinhateeri, J.F. Marko
Proc. Natl. Acad. Sci. USA 108, 7799-803 (2011) [5 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].

Force-driven unbinding of proteins HU and Fis from DNA quantified using a thermodynamic Maxwell relation
B. Xiao, H. Zhang, R.C. Johnson, J.F. Marko,
Nucl. Acids Res. 39, 5568-77 (2011) [10 pages].

Scaling of linking and writhing numbers for spherically confined and topologically equilibrated flexible polymers
J.F. Marko
J. Stat. Phys. 142, 1353-1370 (2011) [18 pages].

Analytical description of extension, torque and supercoiling radius of a stretched, twisted DNA
S. Neukirch, J.F. Marko,
Phys. Rev. Lett. 106, 138104 (2011) [4 pages]

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

Transition dynamics and selection of the distinct S-DNA and strand unpeeling modes of double helix overstretching
H. Fu, H. Chen, X. Zhang, Y. Qu, J.F. Marko, J. Yan,
Nucl. Acids Res. 39 3473-81 (2011) [9 pages].

Intrinsic and force-generated cooperativity in a theory of DNA-bending proteins
H. Zhang and J.F. Marko
Phys. Rev. E 82, 051906 (2010) [15 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].

Interdependence of behavioural variability and response to small stimuli in bacteria.
H. Park, W. Pontius, C.C. Guet, J.F. Marko, T. Emonet, P. Cluzel
Nature 468, 819-823 (2010) [7 pages].

Modulation of HU-DNA interactions by salt concentration and applied force
B. Xiao, R.C. Johnson, J.F. Marko
Nucl. Acids Res. 38, 6176-85 (2010) [9 pages].

Two distinct overstretched DNA states
H. Fu, H. Chen, J.F. Marko, J. Yan
Nucl. Acids Res. 38, 5594-600 (2010) [7 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]

Linking topology of large DNA molecules
J. F. Marko
Physica A 389, 2297-3001 (2010) [5 pages]

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. (Springer, New York), 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)

Microscopic DNA fluctuations are in accord with macroscopic DNA stretching elasticity without strong dependence on force-field choice
M. Feig, J.F. Marko, M. Pettitt, in Metal-Ligand Interactions. NATO Science Series (Series II: Mathematics, Physics and Chemistry), vol 116. pp. 193-204, Russo N., Salahub D.R., Witko M. (eds), Springer, Dordrecht (2003) (12 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) [pdf]

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

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) [pdf]

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) [pdf]

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) [pdf]

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) [pdf]

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) [pdf]

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) [pdf]

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)