Publications

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Jin Qian, Bing Wang, Irina Artsimovitch, David Dunlap, Laura Finzi
“Force and the α-C-terminal domains bias RNA polymerase recycling.” Preprint on BIORXIV, DOI:10.1101/2023.11.02.565415.

Jin Qian, Allison Cartee, Wenxuan Xu, Yan Yan, Bing Wang, Irina Artsimovitch, David Dunlap, Laura Finzi
“Reciprocating RNA Polymerase batters through roadblocks.” Accepted for publication in Nat. Comm. Preprint on BIORXIV. DOI:10.1101/2023.01.04.522798.

Jin Qian, Dylan Collette, Irina Artsimovitch, David Dunlap, Laura Finzi
“Detecting DNA Loops Using Tethered Particle Motion.” In: Heller, I., Dulin, D., Peterman, E.J. (eds) Single Molecule Analysis . Methods in Molecular Biology, vol 2694. Humana, New York, NY. DOI:10.1007/978-1-0716-3377-9_21.

Dylan Collette, David Dunlap and Laura Finzi
“Macromolecular Crowding and DNA: Bridging the Gap between In Vitro and In Vivo”, International Journal of Molecular Sciences, Review, in Special Issue “Recent Advances in Genome Maintenance Studies.” 2023, Volume 24, Issue 24, 17502. DOI:10.3390/ijms242417502

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J. Qian, D. Dunlap, & L. Finzi
"Thermodynamic Model of Bacterial Transcription" Phys. Rev. E, 2022. DOI:10.1103/PhysRevE.106.044406

W. Xu, Y. Yan, I.Artsimovitch, D. Dunlap, & L. Finzi
"Positive supercoiling favors transcription elongation through lac repressor-mediated DNA loops", Nucleic Acids Research, 2022. DOI: 10.1063/10.0006622

Y. Lu, G. Borjas, C. Hendrickson, Z.Vörö, D. Dunlap, K. Shearwin & L. Finzi
"RNA polymerase efficiently transcribes through DNA-scaffolded, cooperative bacteriophage repressor complexes", FEBS Letters, 2022. Editor Choice DOI: 10.1002/1873-3468.14447

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J. Qian, W. Xu, D. Dunlap, & L. Finzi
"Single-molecule insights into torsion and roadblocks in bacterial transcript elongation", Transcription, 2021. DOI: 10.1080/21541264.2021.1997315

A. Zhang, Y .Yan, F .Leng, D. Dunlap, & L. Finzi
"Ionic strength modulates HU protein-induced DNA supercoiling", Posted on BioRxiv, 2021. DOI: 10.1101/2021.10.14.464438

Y. Yan, W. Xu, S. Kumar, A. Zhang, F. Leng, D. Dunlap, & L. Finzi
"Negative DNA supercoiling makes protein-mediated looping deterministic and ergodic within the bacterial doubling time", Nucleic Acids Research, 2021. DOI: 10.1093/nar/gkab946

J. Piccolo, J.M. Harper, D. McCalla, W. Xu, S. Miller, J. Doan, D.T. Kovari, D. Dunlap, & L. Finzi
"Force spectroscopy with electromagnetic tweezers", Journal of Applied Physics, 2021. DOI: 10.1063/5.0060276

W.Xu, D. Dunlap, & L. Finzi
"Energetics of twisted DNA topologies", Biophysical Journal, 2021. DOI: 10.1016/j.bpj.2021.05.002

W.Xu, D. Dunlap, & L. Finzi
"Tethered Particle Microscopy", Encyclopedia of Biophysics, 2021. DOI: 10.1007/978-3-642-35943-9_489-1

D. Salerno, F. Mantegazza, V. Cassina, M. Cristofalo, Q. Shao, L. Finzi, & D. Dunlap
"Nanomechanics of negatively supercoiled diaminopurine-substituted DNA", Nucleic Acids Research, 2021. DOI: 10.1093/nar/gkab982

J. Qian, D. Dunlap, & L. Finzi
"Basic mechanisms and kinetics of pause-interspersed transcript elongation", Nucleic Acids Research, 2021. DOI: 10.1093/nar/gkaa1182

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DT Kovari, D. Dunlap, ER Weeks, & L. Finzi
"Model-free 3D localization with precision estimates for brightfield imaged particles", Optics Express, Optics Express: Vol. 27, Issue 21, pp. 29875-29895 (2019)

Cristofalo, M., Kovari, D., Corti, R., Salerno, D., Cassina, V., Dunlap, D., & Mantegazza, F.
"Nanomechanics of diaminopurine-substituted DNA", Biophysical journal, 2019. DOI: 10.1016/j.bpj.2019.01.027

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S. Sarkar, S. Goyal, N. Gao, J. Mack, B. Thompson, D. Dunlap, K. Chattopadhyay, L. Finzi
"Specifically bound Lambda repressor dimers promote adjacent non-specific binding", PLOS One, 2018. PLoS ONE 13(4): e0194930

Y. Yan, Y. Ding, F. Leng, D. Dunlap, L. Finzi
"Protein-mediated loops in supercoiled DNA create large topological domains", Nucleic Acids Research, 2018. DOI: 10.1093/nar/gky153

Y. Yan, F. Leng, L. Finzi, D. Dunlap
"Protein-mediated looping of DNA under tension requires supercoiling", Nucleic Acids Research, 2018. DOI:10.1093/nar/gky021

D.T. Kovari, Y. Yan, L. Finzi, D. Dunlap
"Tethered Particle Motion: An Easy Technique for Probing DNA Topology and Interactions with Transcription Factors" in "Methods in Molecular biology: Single-Molecule Analysis: Methods and Protocols", ed. E.J.G. Peterman, series editor John Walker, vol 1665, Humana Press, New York, NY, p317-340 (2018). DOI: 10.1007/978-1-4939-7271-5_17

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Z. Vörös, Y. Yan, D. Kovari, L. Finzi, D. Dunlap
"Proteins mediating DNA loops effectively block transcription", Protein Science, 2017. DOI: 10.1002/pro.3156

S. Ucuncuoglu, D.A. Schneider, E.R. Weeks, D. Dunlap, L. Finzi "Chapter Sixteen - Multiplexed, Tethered Particle Microscopy for Studies of DNA-Enzyme Dynamics", Methods in Enzymology, 2017. DOI: 10.1016/bs.mie.2016.08.008

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S. Ucuncuoglu, K. L. Engel, P. K. Purohit, D. D. Dunlap, D. A. Schneider, L. Finzi
"Direct characterization of transcription elongation by RNA polymerase I" Plos One, 2016. DOI:10.1371/journal.pone.0159527. eCollection 2016

Laura Finzi and Wilma K. Olson
"The emerging role of DNA supercoiling as a dynamic player in genomic structure and function" Biophysics Reviews, 2016. DOI:10.1007/s12551-016-0214-x

Laura Finzi and David D. Dunlap
"upercoiling biases the formation of loops involved in gene regulation" Biophysics Reviews, 2016. DOI:10.1007/s12551-016-0211-0

Suleyman Ucuncuoglu, David A. Schneider, Eric Weeks, David Dunlap, and Laura Finzi
"Multiplexed, tethered particle microscopy for studies of DNA-enzyme dynamics" Methods in Enzymology, 2016. DOI:10.1016/bs.mie.2016.08.008

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M.Fernandez, Q. Shao, C.Fountain, L. Finzi, and D. Dunlap
"E. coli gyrase fails to negatively supercoil diaminopurine-substituted DNA" Journal of Molecular Biology, 2015. DOI:10.1016/j.jmb.2015.04.006

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Y.Ding, C. Manzo, G.Flucrand, F.leng, D. Dunlap, and L. Finzi
"DNA supercoiling: A regulatory signal for the Lambda repressor" PNAS, 2014. DOI: 10.1073/pnas.1320644111

D.Priest, S.Kumar, Y.Yan, D.Dunlap, I.Dodd, K.Shearwin
"Quantitation of interactions between two DNA loops demonstrates loop domain insulation in E.coli cells" PNAS, 2014. DOI: 10.1073/pnas.1410764111

S.Kumar, C. Manzo, C.Zurla, S.Ucuncuoglu, L. Finzi, and D. Dunlap
"Enhanced tethered-particle motion analysis reveals viscous effects" Biophys J, 2014. DOI: 10.1016/j.bpj.2013.11.4501

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M.A. Mendes, R.F. Guerra, M.C. Berns, C. Manzo, S. Masiero, L. Finzi, M. M. Kater, and L. Colombo
"MADS Domain Transcription Factors Mediate Short-Range DNA Looping That Is Essential for Target Gene Expression in Arabidopsis" The Plant Cell, 2013. DOI:10.1105/tpc.112.108688

N. Gao, K.E. Shearwin, J. Mack, L. Finzi, and D. Dunlap
"Purification of Bacteriophage Lambda Repressor" Protein Expression and Purification, 2013. DOI:10.1016/j.pep.2013.06.013

H. Wang, I.B. Dodd, D.D. Dunlap, K.E. Shearwin, and L. Finzi
"Single molecule analysis of DNA wrapping and looping by a circular 14mer wheel of the bacteriophage 186 CI repressor" NAR, 2013. DOI: 10.1093/nar/gkt298.

L. Finzi and D. Dunlap
"Tethered particle Microscopy (TPM)" in "Encyclopedia of Biophysics", Springer (Berlin Heidelberg), 2579-2582 (2013). Tethered particle Microscopy (TPM)

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C. Manzo, C. Zurla, D. Dunlap, and L. Finzi
"The effect of non-specific binding of lambda repressor on DNA looping dynamics" Biophys. J.,103(8),1753,2012. DOI: 10.1016/j.bpj.2012.09.006.

S. Goyal, C. Foutain, D. Dunlap, F. Family, and L. Finzi
"Stretching DNA to quantify nonspecific protein binding" Phys. Rev. E, 2012. DOI: 10.1103/PhysRevE.86.011905.

Q. Shao, S. Goyal, L. Finzi, and D. Dunlap
"Physiological Levels of Salt and Polyamines Favor Writhe and Limit Twist in DNA" Macromolecules, 2012. DOI: 10.1021/ma300211t.

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D. Lewis, P. Le, C. Zurla, L. Finzi, and S. Adhya
"Multilevel autoregulation of lambda repressor protein CI by DNA looping in vitro" PNAS, 2011. DOI: 10.1073/pnas.1111221108.

D. Dunlap, C. Zurla, C. Manzo and L. Finzi
"Probing DNA Topology Using Tethered Particle Motion" in "methods in Molecular Biology: Single-Molecule Analysis: Methods and Protocols"
eds. E.J.G. Peterman and G Wuite, series editor John Walker, Springer vol. 783, pp. 295-313, 2011. DOI 10.1007/978-1-61779-282-3_16.

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L. Finzi, C. Manzo, C. Zurla, H. Wang, D. Lewis, S. Adhya and D. Dunlap
"DNA Looping in Prophage Lambda: New Insight from Single-Molecule Microscopy" in "Biophysics of DNA-protein interactions: From single molecules to biological systems"
Eds. M. Williams and L. J Maher, Springer pp. 193-212, 2010. DOI 10.1007/978-0-387-92808-1.

Paul Liebesny, Sachin Goyal, David Dunlap, Fereydoon Family and Laura Finzi
"Determination of the Number of Protein Bound non-specifically to DNA" JPCM, DOI:10.1088/0953-8984/22/41/414104 (2010)

L. Finzi and D. Dunlap
"Single-molecule approaches to structure, kinetics and thermodynamics of transcriptional regulatory nucleoprotein complexes" minireview, JBC, DOI:10.1074/jbc.R109.062612 (2010)

C. Manzo and L. Finzi
"Quantitative analysis of DNA looping kinetics from tethered particle motion experiments" Methods in Enzymology, Ed. Nils G. Walter, 2010

D. E. A. Lewis, S. J. Lee, S. Semsey, K. Virnik, L. Finzi and S. Adhya
"Role of HU in regulation of gal promoters" in " Bacterial Chromatin"
Eds: C. Dorman and R. T. Dame, 2010 Springer DOI: 10.1007/978-90-481-3473-1_17

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H. Wang, L. Finzi, D. E. A. Lewis, D. D. Dunlap
"AFM Studies of Lambda Repressor Oligomers Securing DNA Loops" Current Pharmaceutical Biotechnology, 10, 494-501 (2009)

C. Zurla, C. Manzo, D. D. Dunlap, D. E. A. Lewis, S. Adhya, L. Finzi
"Direct demonstration and quantification of long-range DNA looping by the lambda bacteriophage repressor" NAR, DOI:10.1093/nar/gkp134 (2009)

L. Finzi
"Perspectives on DNA looping", in IMA Volume on "Mathematics of DNA structure, Function, and Interactions" Eds
C. J. Benham, S. Harvey, W. K. Olson, D. L. Sumners, and D. Swigon Spring Science-Business Media, LLC,DOI 10.1007/978-1-4419-0670-0

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G. Lia, M. Indrieri, T. Owen-Hughes, L. Finzi, A. Podesta', P. Milani, D.Dunlap
"ATP-dependent looping of DNA by ISWI", Special issue:" From single molecules and single cells to tissue imaging" Journal of Biophotonics 4,280-286 (2008)

G. Lia, S. Semsey, D. e. lewis, S. Adhya, D. Besinmon, D. Dunlap, L. Finzi
"The Antiparallel loops in Gal DNA" NAR, 36, 4204-4210 (2008)

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C. Zurla, G. Bertoni, F. Valle, G. Dietler, L. Finzi, D. Dunlap
"Architectural role of IHF in the regulation of transcription at the single molecule level" Biophysical Chemistry 128, 245 - 252 (2007)

F. Guerra, L. Imperadori, D. Dunlap, R. Mantovani, L. Finzi
"DNA Compaction by the nuclear factor-Y" Biophy. J., 93(1):176-182 (2007)

J. F. Beausang, C. Zurla, C. Manzo, D. Dunlap, L. Finzi, and P. Nelson
"DNA Looping Kinetics Analyzed Using Diffusive Hidden Markov Model" Biophys. J. - 92:L64-L66 (2007)

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J. F. Beausang, C. Zurla, L. Sullivan, L. Finzi, P. C. Nelson
"Elementary simulation of tethered Brownian motion" AJP q-bio.BM/0610007

P. Nelson, C. Zurla, D. Brogioli, J. F. Beausang, L. Finzi, and D. Dunlap
"Tethered Particle Motion as a Diagnostic of DNA Tether Length" The Journal of Physical Chemistry B, 110 (34): 17260-17267 (2006)

C. Zurla, A Franzini, G. Galli, D.D. Dunlap, D.E.A. Lewis, S. Adhya and L. Finzi
"Novel tethered particle motion analysis of CI protein-mediated DNA looping in the regulation of bacteriophage lambda" Journal of Physics:Condensed Matter, 18, S225-S234 (2006)

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A. Podesta M. Indrieri, D. Brogioli, J. S. Manning, P. Milani, R. Guerra, L. Finzi, D. Dunlap
"Positively charged surfaces increase the flexibility of DNA" Biophys J., 89:2558-2563 (2005)

E. Consoli, R. Croce, D. Brogioli, D. Dunlap and L. Finzi
"Diffusion of phosphorylated and non-phosphorylated Light Harvesting Complex II in the thylakoid membranes" EMBO reports, 6(8):782-6 (2005)

G. Garab, P. Galaida, I. Pomozi, L. Finzi, T. Praznovszky, P. Ormos, H. Van Amerongen
"Alignment of biological microparticles by polarized laser beam" Eur. Biophys. J., 34(4):335-43 (2005)

M. Kooiker, C. Airoldi, A. Losa, P.S. Manzotti, L. Finzi, M. M. Kater and L. Colombo
"Basic pentacysteine1 a GA-Binding Protein that Induces Conformational Changes in the Regulatory Region of the Homeotic Arabidopsis Gene SEEDSTICK" The Plant Cell, 17:722-729 (2005)

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A. Podesta L. Imperadori, W. Colnaghi, L. Finzi, P. Milani and D. D. Dunlap
"Atomic Force Microscopy studies of DNA deposited on poly-L-ornithine coated mica" Journal of Microscopy 215:236-240 (2004)

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G. Lia, D. Bensimon, V. Croquette, J-F. Allemand, D. Dunlap, DAE. Lewis, S. Adhya, L. Finzi
"Supercoiling and denaturation in GalR/HU-mediated DNA looping as seen by single-molecule microscopy" PNAS, 100:11373-377 (2003)

L. Finzi and D. Dunlap
"Single molecule studies of DNA architectural changes induced by regulatory proteins" in Methods in Enzymology, invited article, Eds. Adhya & Garges, vol 370:369-378 (2003)

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M. Capitanio, G. Romano, R. Ballerini, D. Dunlap, L. Finzi, M. Giuntini and F.S. Pavone
"Calibration of an Optical Tweezer with DIC Signals" Reviews of Scientific Instruments, 73:1687-1696 (2002)

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L. Finzi, P. Galajda, and G. Garab
"Labeling phosphorylated LHCII with microspheres for tracking studies and force measurements" J. Photochem. Photobiol B:Biology, 65:1-4 (2001)

L. Sacconi, G. Romano, R. Ballerini, M. Capitanio, M. De Pas, D. Dunlap, M. Giuntini, L. Finzi and F.S. Pavone
"A 3D micro-TOP magneto-optical trap for micro-objects manipulation" Optics Letters, 26:1359-61, (2001)

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L. Finzi and J. Gelles
"Measurement of Lac Repressor-mediated loop formation and Breakdown in Single DNA molecules" Science 267, 378-380 (1995)

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S. Smith, L. Finzi and C. Bustamante
"Direct Mechanical Measurements of the Elasticity of single DNA molecules Using Magnetic Beads" Science 258:1122 (1992)