Publications

Human Topoisomerase IIα Promotes Chromatin Condensation Via a Phase Transition.
Wu M., Beck C., Lee J.H., Fulbright R.M., Jeong J., Inman J.T., Woodhouse M.V., Berger J.M., and Wang M.D.
BioRxiv. (2024). (PDF).

Chromatin Buffers Torsional Stress During Transcription.
Qian J., Lubkowska L., Zhang S., Tan C., Hong Y., Fulbright R.M., Inman J.T., Kay T.M., Jeong J., Gotte D., Berger J.M., Kashlev M., and Wang M.D.
BioRxiv. (2024). (PDF).

Torsion is a Dynamic Regulator of DNA Replication Stalling and Reactivation.
Jia X., Gao X., Zhang S., Inman J.T., Hong Y., Singh A., Patel S.S., and Wang M.D.
BioRxiv. (2024). (PDF).

RNA Polymerase II is a Polar Roadblock to a Progressing DNA Fork.
Kay T.M., Inman J.T., Lubkowska L., Le T.T., Qian J., Hall P.M., Wang D., Kashlev M., and Wang M.D.
BioRxiv. (2024). (PDF).

High-Resolution Genome-Wide Mapping of Chromatin Accessibility and Torsional Stress.
Hall P.H., Mayse L.A., Bai L., Smolka M.B., Pugh B.F., and Wang M.D.
BioRxiv. (2024). (PDF).

Geometry of Braided DNA Dictates Supercoiling Partition.
Hong Y., Park S., Wang H., and Wang M.D.
BioRxiv. (2024). (PDF).

Torsional Mechanics of Circular DNA.
Singh G., Hong Y., Inman J.T., Sethna J.P., and Wang M.D.
BioRxiv. (2024). (PDF).

DNA Polymerase Locks Replication Fork Under Stress.
Jia X., Inman J.T., Singh A., Patel S.S., and Wang M.D.
BioRxiv. (2024). (PDF).

Tunable Elliptical Cylinders for Rotational Mechanical Studies of Single DNA Molecules.
Hong Y., Ye F., Gao X., Inman J.T., and Wang M.D.
BioRxiv. (2024). (PDF).

An Effective Surface Passivation Assay for Single-Molecule Studies of Chromatin and Topoisomerase II.
Le T., Gao X., Park S., Lee J., Inman J.T., and Wang M.D.
BioRxiv. (2024). (PDF).

Optical torque calculations and measurements for DNA torsional studies.
Hong Y., Ye F., Qian J., Gao X., Inman J.T., and Wang M.D.
Biophysical Journal 123, 3080-3089. (2024). (PDF).

Joint Efforts of Replicative Helicase and SSB Ensure Inherent Replicative Tolerance of G-Quadruplex.
Guo L., Bao Y., Zhao Y., Ren Z., Bi L., Zhang X., Liu C., Hou X., Wang M.D., Sun B.
Advanced Science. (2023). (PDF).

Chromatinization modulates topoisomerase II processivity.
Lee J., Wu M., Inman J.T., Singh G., Park S., Lee J.H., Fulbright R.M., Hong Y., Jeong J., Berger J.M., and Wang M.D.
Nature Communications. 14, 6844. (2023). (PDF).

Etoposide Promotes DNA Loop Trapping and Barrier Formation by Topoisomerase II.
Le T., Wu M., Lee J.H., Bhatt N., Inman J.T., Berger J.M., and Wang M.D..
Nature Chemical Biology, published online (2023). (PDF).

• Research Briefing: “Topoisomerase II and etoposide — a tangled tale”. Nature Chemical Biology, published online (2023).
• Featured by Cornell Chronicle: Tweezers untangle chemotherapeutic’s impact on DNA.

Polarity of the CRISPR Roadblock to Transcription.
Hall P., Inman J.T., Fulbright R.M., Le T.T., Brewer J., Lambert G., Darst S., and Wang M.D.
Nature Structural & Molecular Biology, 29(12):1217-1227 (2022). (PDF).

• Featured by Cornell Chronicle: CRISPR insight: How to fine-tune the Cas protein’s grip on DNA.

Angular Optical Trapping to Directly Measure DNA Torsional Mechanics.
Gao, X., Inman, J.T., and Wang, M.D.
Methods in Molecular Biology 2478, 37-73. (2022). (PDF).

Resonator nanophotonic standing-wave array trap for single-molecule manipulation and measurement.
Ye, F., Inman, J.T., Hong, Y., Hall, P.M., and Wang, M.D.
Nature Communications 13, 77. (2022). (PDF).

• Featured by Cornell Chronicle: ‘Lab on a chip’ can measure protein-DNA interactions.

RNA Polymerase as a Torsional Motor.
J.L. Killian, J. Ma, and M.D. Wang.
RNA Polymerases as Molecular Motors: On the Road. (2022). (RSC).

Physics meets biology: The joining of two forces to further our understanding of cellular function.
Wang, M.D., Nicodemi, M., Dekker, N.H., Gregor, T., Holcman, D., van Oijen, A.M., and Manley, S.
Molecular Cell 81, 3033-3037. (2021). (ScienceDirect).

Ruler of life.
Wang, M.D.
Nature Physics 17, 986 (2021). (Nature).

Torsional Stiffness of Extended and Plectonemic DNA.
Gao, X., Hong, Y., Ye, F., Inman, J.T., and Wang, M.D.
Physical Review Letters 127, 028101. (2021). (PDF).

• Highlighted as Editor’s Suggestion.
• Featured by Physics of the American Physical Society: A Gentle Twist on DNA.
• Featured by Cornell Chronicle: New technique illuminates DNA helix.

Optical Tweezers in Single Molecule Biophysics.
Bustamante, C.J., Chemla, Y.R., Liu, S., and Wang, M.D.
Nature Reviews Methods Primer 1, 25. (2021). (Nature).

Dextran-coated iron oxide nanoparticle-induced nanotoxicity in neuron cultures.
Badman, R.P., Moore, S.L., Killian, J.L., Feng, T., Cleland, T.A., Hu, F., and Wang, M.D.
Scientific Reports 10, 11239. (2020). (PDF).

Towards Biological Applications of Nanophotonic Tweezers.
Badman, R.P., Ye, F., and Wang, M.D.
Current Opinion in Chemical Biology 53, 158-166. (2019). (ScienceDirect).

Synergistic Coordination of Chromatin Torsional Mechanics and Topoisomerase Activity.
Le, T.T., Gao, X., Park, S., Lee, J., Inman, J.T., Lee, J.H., Killian, J.L., Badman, R.P., Berger, J.M., and Wang, M.D.
Cell 179, 619-631. (2019). (PDF).

• Featured by Cell Press YouTube Channel: Untangling DNA during replication.
• Preview by F. Kouzine and D. Levens: “The texture of chromatin.” Cell 179, 579-581 (2019). (Cell).
• Featured by Cornell Chronicle: Scientists underwind mystery behind DNA replication.

High Trap Stiffness Microcylinders for Nanophotonic Trapping.
Badman, R.P., Ye, F., Caravan, W., and Wang, M.D.
ACS Applied Materials & Interfaces 11, 25074-25080 (2019). (ACS).

Transcription factor regulation of RNA polymerase’s torque generation capacity.
Ma, J., Tan, C., Gao, X., Fulbright, R.M., Roberts, J.W., and Wang, M.D.
Proceedings of the National Academy of Sciences 116, 2583-2588. (2019).
Preprint available under bioRxiv (bioRxiv).

Optical tweezers: a force to be reckoned with.
Killian, J.L., Ye, F., and Wang, M.D.
Cell 175, 1445-1448. (2018). (ScienceDirect).

High-performance image-based measurements of biological forces and interactions in a dual optical trap.
Killian, J.L., Inman, J.T., and Wang, M.D.
ACS Nano. 12, 11963–11974. (2018).
Preprint available under bioRxiv (bioRxiv).

Molecular highways-navigating collisions of DNA motor proteins.
Le, T.T., and Wang, M.D.
Journal of Molecular Biology 430, 4513-4524. (2018). (ScienceDirect).

Single-molecule angular optical trapping for studying transcription under torsion.
Ma, J., Tan, C., and Wang, M.D.
Methods in Molecular Biology 1805, 301-332. (2018). (Springer).

Helicase promotes replication re-initiation from an RNA transcript.
Sun, B., Singh, A., Sultana, S., Inman, J.T., Patel, S.S., and Wang, M.D.
Nature Communications 9, 2306. (2018).
Preprint available under bioRxiv (bioRxiv).

Mfd dynamically regulates transcription via a release and catch-up mechanism.
Le, T.T., Yang, Y., Tan, C., Suhanovsky, M.M., Fulbright, R.M., Jr., Inman, J.T., Li, M., Lee, J., Perelman, S., Roberts, J.W., Deaconescu, A.M., and Wang, M.D.
Cell 173, 1823. (2018). (PDF).

• Featured by Cornell Chronicle: Newly developed techniques shed light on key protein’s regulatory ability.

Nanophotonic trapping: precise manipulation and measurement of biomolecular arrays.
Baker, J.E., Badman, R.P., and Wang, M.D.
Wiley Interdisciplinary Reviews Nanomedicine and Nanobiotechnology 10, e1477. (2017). (WIREs).

Tunable nanophotonic array traps with enhanced force and stability.
Ye, F., Soltani, M., Inman, J.T., and Wang, M.D.
Optics Express 25, 7907-7918. (2017). (OSA Publishing).

Single-molecule optical-trapping techniques to study molecular mechanisms of a replisome.
Sun, B., and Wang, M.D.
Methods in Enzymology 582, 55-84. (2017). (PDF).

DNA looping mediates nucleosome transfer.
Brennan, L.D., Forties, R.A., Patel, S.S., and Wang, M.D.
Nature Communications 7, 13337. (2016). (PDF).

Biocompatible and high stiffness nanophotonic trap array for precise and versatile manipulation.
Ye, F., Badman, R.P., Inman, J.T., Soltani, M., Killian, J.L., and Wang, M.D.
Nano Letters 16, 6661-6667. (2016). (PDF).

DNA supercoiling during transcription.
Ma, J., and Wang, M.D.
Biophysical Reviews 8, 75-87. (2016). (PDF).

The Chd1 chromatin remodeler can sense both entry and exit sides of the nucleosome.
Nodelman, I.M., Horvath, K.C., Levendosky, R.F., Winger, J., Ren, R., Patel, A., Li, M., Wang, M.D., Roberts, E., and Bowman, G.D.
Nucleic Acids Research 44, 7580-7591. (2016). (PDF).

Single-molecule perspectives on helicase mechanisms and functions.
Sun, B., and Wang, M.D.
Critical Reviews in Biochemistry and Molecular Biology 51, 15-25. (2016). (PDF).

T7 replisome directly overcomes DNA damage.
Sun, B., Pandey, M., Inman, J.T., Yang, Y., Kashlev, M., Patel, S.S., and Wang, M.D.
Nature Communications 6, 10260. (2015). (PDF).

Dynamic regulation of transcription factors by nucleosome remodeling.
Li, M., Hada, A., Sen, P., Olufemi, L., Hall, M.A., Smith, B.Y., Forth, S., McKnight, J.N., Patel, A., Bowman, G.D., Bartholomew, B., and Wang, M.D.
Elife 4, e06249. (2015). (PDF).

DNA Y structure: A versatile, multidimensional single molecule assay.
Inman, J.T., Smith, B.Y., Hall, M.A., Forties, R.A., Jin, J., Sethna, J.P., and Wang, M.D.
Nano Letters 14, 6475-6480. (2014). (PDF).

Nanophotonic trapping for precise manipulation of biomolecular arrays.
Soltani, M., Lin, J., Forties, R.A., Inman, J.T., Saraf, S.N., Fulbright, R.M., Lipson, M., and Wang, M.D.
Nature Nanotechnology 9, 448-452. (2014). (PDF).

• Featured by Cornell Chronicle: Optical traps on chip manipulate many molecules at once.
• Featured by Physics Today: Precision trapping on a microfluidic chip.
• Featured by Nanotechweb: Multiple optical traps economize on laser power.

Interplay between DNA supercoiling and transcription elongation.
Ma, J., and Wang, M.
Transcription 5, e28636. (2014). (PDF).

Discovering the power of single molecules.
Forties, R.A., and Wang, M.D.
Cell 157, 4-7. (2014). (PDF).

Super-resolution microscopy reveals decondensed chromatin structure at transcription sites.
Wang, Y.J., Maharana, S., Wang, M.D., and Shivashankar, G.V.
Scientific Reports 4, 4477. (2014). (PDF).

RNA polymerase is a powerful torsional motor.
Ma, J., and Wang, M.D.
Cell Cycle 13, 337-338. (2014). (PDF).

Torque modulates nucleosome stability and facilitates H2A/H2B dimer loss.
Sheinin, M.Y., Li, M., Soltani, M., Luger, K., and Wang, M.D.
Nature Communications 4, 2579. (2013). (PDF).

Small molecule injection into single-cell C. elegans embryos via carbon-reinforced nanopipettes.
Brennan, L.D., Roland, T., Morton, D.G., Fellman, S.M., Chung, S., Soltani, M., Kevek, J.W., McEuen, P.M., Kemphues, K.J., and Wang, M.D.
PLoS One 8, e75712. (2013). (PDF).

On the move.
Forties, R.A., Ma, J., and Wang, M.D.
Elife 2, e01414. (2013). (PDF).

Single-molecule unzipping force analysis of HU-DNA complexes.
Dame, R.T., Hall, M.A., and Wang, M.D.
ChemBioChem 14, 1954-1957. (2013). (PDF).

Transcription under torsion.
Ma, J., Bai, L., and Wang, M.D.
Science 340, 1580-1583. (2013). (PDF).

• Featured by Cornell Chronicle: Physicists tease out twisted torques of DNA.

Torque measurement at the single-molecule level.
Forth, S., Sheinin, M.Y., Inman, J., and Wang, M.D.
Annual Review of Biophysics 42, 583-604. (2013). (PDF).

A DNA twist diffuses and hops.
Sheinin, M.Y., and Wang, M.D.
Science 338, 56-57. (2012). (PDF).

Electro-optofluidics: achieving dynamic control on-chip.
Soltani, M., Inman, J.T., Lipson, M., and Wang, M.D.
Optics Express 20, 22314-22326. (2012). (PDF).

Unzipping single DNA molecules to study nucleosome structure and dynamics.
Li, M., and Wang, M.D.
Methods in Enzymology 513, 29-58. (2012). (PDF).

Recent advances in single molecule studies of nucleosomes.
Killian, J.L., Li, M., Sheinin, M.Y., and Wang, M.D.
Current Opinion in Structural Biology 22, 80-87. (2012). (PDF).

Angular optical trapping.
Forth, S., and Wang, M.D.
In Encyclopedia of Biophysics, N.G. Walter, ed. (2012).

ATP-induced helicase slippage reveals highly coordinated subunits.
Sun, B., Johnson, D.S., Patel, G., Smith, B.Y., Pandey, M., Patel, S.S., and Wang, M.D.
Nature 478, 132-135. (2011). (PDF).

• Featured by Cornell ChronicleScientists learn how enzyme parts coordinate to unzip DNA

Underwound DNA under tension: structure, elasticity, and sequence-dependent behaviors.
Sheinin, M.Y., Forth, S., Marko, J.F., and Wang, M.D.
Physical Review Letters 107, 108102. (2011). (PDF).

Direct measurements of torque during Holliday junction migration.
Forth, S., Deufel, C., Patel, S.S., and Wang, M.D.
Biophysical Journal 101, L5-7. (2011). (PDF).

Structure and Scm3-mediated assembly of budding yeast centromeric nucleosomes.
Dechassa, M.L., Wyns, K., Li, M., Hall, M.A., Wang, M.D., and Luger, K.
Nature Communications 2, 313. (2011). (PDF).

A257T linker region mutant of T7 helicase-primase protein is defective in DNA loading and rescued by T7 DNA polymerase.
Patel, G., Johnson, D.S., Sun, B., Pandey, M., Yu, X., Egelman, E.H., Wang, M.D., and Patel, S.S.
Journal of Biological Chemistry 286, 20490-20499. (2011). (PDF).

Comparison of pause predictions of two sequence-dependent transcription models.
Bai, L., and Wang, M.D.
Journal of Statistical Mechanics 2010, P12007. (2010). (PDF).

Passive torque wrench and angular position detection using a single-beam optical trap.
Inman, J., Forth, S., and Wang, M.D.
Optics Letters 35, 2949-2951. (2010). (PDF).

Synergistic action of RNA polymerases in overcoming the nucleosomal barrier.
Jin, J., Bai, L., Johnson, D.S., Fulbright, R.M., Kireeva, M.L., Kashlev, M., and Wang, M.D.
Nature Structural & Molecular Biology 17, 745-752. (2010). (PDF).

• Featured by Cornell Chronicle: Physics of gene transcription observed by Cornell University researchers

Discontinuities at the DNA supercoiling transition.
Daniels, B.C., Forth, S., Sheinin, M.Y., Wang, M.D., and Sethna, J.P.
Physical review E, Statistical, nonlinear, and soft matter physics 80, 040901. (2009). (PDF).

Twist-stretch coupling and phase transition during DNA supercoiling.
Sheinin, M.Y., and Wang, M.D.
Physical Chemistry Chemical Physics 11, 4800-4803. (2009). (PDF).

High-resolution dynamic mapping of histone-DNA interactions in a nucleosome.
Hall, M.A., Shundrovsky, A., Bai, L., Fulbright, R.M., Lis, J.T., and Wang, M.D.
Nature Structural & Molecular Biology 16, 124-129. (2009). (PDF).

• Featured by Cornell Chronicle: Researchers ‘unzip’ molecules to measure interactions keeping DNA packed in cells

Kinetic modeling of transcription elongation.
Bai, L., Shundrovsky, A., and Wang, M.D.
In RNA Polymerases as Molecular Motors (The Royal Society of Chemistry), pp. 263-280. (2009). (PDF).

A biophysicist marvels at the idea of grabbing microscopic particles with light by tweaking its phase.
Wang, M.D.
Nature 454, 921. (2008).

Abrupt buckling transition observed during the plectoneme formation of individual DNA molecules.
Forth, S., Deufel, C., Sheinin, M.Y., Daniels, B., Sethna, J.P., and Wang, M.D.
Physical Review Letters 100, 148301. (2008). (PDF).

Single molecule studies of RNA polymerase transcription.
Shundrovsky, A., Bai, L., Santangelo, T.J., and Wang, M.D.
In Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology, I. Artsitmovitch, ed. (2008).

Single-molecule studies reveal dynamics of DNA unwinding by the ring-shaped T7 helicase.
Johnson, D.S., Bai, L., Smith, B.Y., Patel, S.S., and Wang, M.D.
Cell 129, 1299-1309. (2007). (PDF).

• Previews by T. Ha. “Need for Speed: Mechanical Regulation of a Replicative Helicase.” Cell 129:1249-50 (2007) (Full Text PDF).
• Featured by Cornell Chronicle: Cornell researchers determine how an enzyme plays a key role in gene copying

Nanofabricated quartz cylinders for angular trapping: DNA supercoiling torque detection.
Deufel, C., Forth, S., Simmons, C.R., Dejgosha, S., and Wang, M.D.
Nature Methods 4, 223-225. (2007). (PDF).

Mechanochemical kinetics of transcription elongation.
Bai, L., Fulbright, R.M., and Wang, M.D.
Physical Review Letters 98, 068103. (2007). (PDF).

Probing SWI/SNF remodeling of the nucleosome by unzipping single DNA molecules.
Shundrovsky, A., Smith, C.L., Lis, J.T., Peterson, C.L., and Wang, M.D.
Nature Structural & Molecular Biology 13, 549-554. (2006). (PDF).

Single-molecule analysis of RNA polymerase transcription.
Bai, L., Santangelo, T.J., and Wang, M.D.
Annual Review of Biophysics and Biomolecular Structure 35, 343-360. (2006). (PDF).

Detection of forces and displacements along the axial direction in an optical trap.
Deufel, C., and Wang, M.D.
Biophysical Journal 90, 657-667. (2006). (PDF).

Detection of high-affinity and sliding clamp modes for MSH2-MSH6 by single-molecule unzipping force analysis.
Jiang, J., Bai, L., Surtees, J.A., Gemici, Z., Wang, M.D., and Alani, E.
Molecular Cell 20, 771-781. (2005). (PDF).

Functional hydrogel surfaces: Binding kinesin-based molecular motor proteins to selected patterned sites.
Yu, T.Y., Wang, Q., Johnson, D.S., Wang, M.D., and Ober, C.K.
Advanced Functional Materials 15, 1303-1309. (2005). (PDF).

Specific contributions of histone tails and their acetylation to the mechanical stability of nucleosomes.
Brower-Toland, B., Wacker, D.A., Fulbright, R.M., Lis, J.T., Kraus, W.L., and Wang, M.D.
Journal of Molecular Biology 346, 135-146. (2005). (PDF).

A single-molecule technique to study sequence-dependent transcription pausing.
Shundrovsky, A., Santangelo, T.J., Roberts, J.W., and Wang, M.D.
Biophysical Journal 87, 3945-3953. (2004). (PDF).

Sequence-dependent kinetic model for transcription elongation by RNA polymerase.
Bai, L., Shundrovsky, A., and Wang, M.D.
Journal of Molecular Biology 344, 335-349. (2004). (PDF).

Molecular mechanism of transcription inhibition by peptide antibiotic Microcin J25.
Adelman, K., Yuzenkova, J., La Porta, A., Zenkin, N., Lee, J., Lis, J.T., Borukhov, S., Wang, M.D., and Severinov, K.
Molecular Cell 14, 753-762. (2004). (PDF).

Optical torque wrench: angular trapping, rotation, and torque detection of quartz microparticles.
La Porta, A., and Wang, M.D.
Physical Review Letters 92, 190801. (2004). (PDF).

• Featured in Physical Review Focus by D. Monroe: Twisty Tweezers.

Use of optical trapping techniques to study single-nucleosome dynamics.
Brower-Toland, B., and Wang, M.D.
Methods in Enzymology 376, 62-72. (2004). (PDF).

Dynamic force spectroscopy of protein-DNA interactions by unzipping DNA.
Koch, S.J., and Wang, M.D.
Physical Review Letters 91, 028103. (2003). (PDF).

• Featured by Cornell Chronicle: Biophysicists ‘unzip’ DNA technique that could aid drug development

Single molecule analysis of RNA polymerase elongation reveals uniform kinetic behavior.
Adelman, K., La Porta, A., Santangelo, T.J., Lis, J.T., Roberts, J.W., and Wang, M.D.
Proceedings of the National Academy of Sciences of the United States of America 99, 13538-13543. (2002). (PDF).

Probing protein-DNA interactions by unzipping a single DNA double helix.
Koch, S.J., Shundrovsky, A., Jantzen, B.C., and Wang, M.D.
Biophysical Journal 83, 1098-1105. (2002). (PDF).

Mechanical disruption of individual nucleosomes reveals a reversible multistage release of DNA.
Brower-Toland, B.D., Smith, C.L., Yeh, R.C., Lis, J.T., Peterson, C.L., and Wang, M.D.
Proceedings of the National Academy of Sciences of the United States of America 99, 1960-1965. (2002). (PDF).

• New insights into unwrapping DNA from the nucleosome from a single-molecule optical tweezers method.
  Commentary by Jeffrey J. Hayes and Jeffrey C. Hansen. ibid 99:1752 (2002) (Full Text PDF).

Stretching of single collapsed DNA molecules.
Baumann, C.G., Bloomfield, V.A., Smith, S.B., Bustamante, C., Wang, M.D., and Block, S.M.
Biophysical Journal 78, 1965-1978. (2000). (PDF).

Manipulation of single molecules in biology.
Wang, M.D.
Current Opinion in Biotechnology 10, 81-86. (1999). (PDF).

Estimating the persistence length of a worm-like chain molecule from force-extension measurements.
Bouchiat, C., Wang, M.D., Allemand, J., Strick, T., Block, S.M., and Croquette, V.
Biophysical Journal 76, 409-413. (1999). (PDF).

Force and velocity measured for single molecules of RNA polymerase.
Wang, M.D., Schnitzer, M.J., Yin, H., Landick, R., Gelles, J., and Block, S.M.
Science 282, 902-907. (1998). (PDF).

Stretching DNA with optical tweezers.
Wang, M.D., Yin, H., Landick, R., Gelles, J., and Block, S.M.
Biophysical Journal 72, 1335-1346. (1997). (PDF).

Transcription against an applied force.
Yin, H., Wang, M.D., Svoboda, K., Landick, R., Block, S.M., and Gelles, J.
Science 270, 1653-1657. (1995). (PDF).

• RNA polymerase gets very pushy.
  News by C. O’Brein.
  ibid 270:1568 (1995) (Full Text PDF).