Revisiting the central dogma one molecule at a time
Open accessAbstract
The faithful relay and timely expression of genetic information depend on specialized molecular machines, many of which function as nucleic acid translocases. The emergence over the last decade of single-molecule fluorescence detection and manipulation techniques with nm and Å resolution and their application to the study of nucleic acid translocases are painting an increasingly sharp picture of the inner workings of these machines, the dynamics and coordination of their moving parts, their thermodynamic efficiency, and the nature of their transient intermediates. Here we present an overview of the main results arrived at by the application of single-molecule methods to the study of the main machines of the central dogma.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The central dogma of molecular biology outlines the process of genetic information being transferred from DNA to mRNA to protein, representing a fundamental mechanism for biological information processing.
“The central dogma of molecular biology outlines the process of genetic information being transferred from DNA to mRNA to protein, representing a fundamental mechanism for biological information processing [109].”
From Challenges in AI-driven Biomedical Multimodal Data Fusion and Analysis (2025) · cites this paper as [109]
Cites
DNA helicases: Enzymes with essential roles in all aspects of DNA metabolism
Matson, S. W., Bean, D. W., & George, J. W. (1994) · BioEssays · doi:10.1002/bies.950160103 · Cited by 293 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
Photophysics of Fluorescent Probes for Single-Molecule Biophysics and Super-Resolution Imaging
Ha, T., & Tinnefeld, P. (2012) · Annual Review of Physical Chemistry · doi:10.1146/annurev-physchem-032210-103340 · Cited by 668 · see citing works
“FRET reports on distances between 3 nm and 8 nm, (4).”
Dynamic regulation of transcriptional states by chromatin and transcription factors
Voss, T. C., & Hager, G. L. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3623 · Cited by 504 · see citing works
Looping Back to Leap Forward: Transcription Enters a New Era
Levine, M., Cattoglio, C., & Tjian, R. (2014) · Cell · doi:10.1016/j.cell.2014.02.009 · Cited by 481 · see citing works
“Cell 1 tions in living cells, a parallel but equally enabling set of advances in single-molecule in vitro biochemistry is revolutionizing our ability to dissect themechanistic steps involved in cell-free single-molecule transcription assays (Figure 5B) (Bustamante et al., 2011; Deniz et al., 2008; Friedman and Gelles,…”
Mechanism of Transcriptional Bursting in Bacteria
Chong, S., Chen, C., Ge, H., & Xie, X. S. (2014) · Cell · doi:10.1016/j.cell.2014.05.038 · Cited by 428 · see citing works
“We note our assay is different from other existing in vitro transcription assays using single-molecule manipulation (Abbondanzieri et al., 2005; Bai et al., 2006; Billingsley et al., 2012; Bustamante et al., 2011; Herbert et al., 2008) or singlemolecule fluorescence imaging (Chakraborty et al.”
Principles of maximum entropy and maximum caliber in statistical physics
Pressé, S., Ghosh, K., Lee, J., & Dill, K. A. (2013) · Reviews of Modern Physics · doi:10.1103/revmodphys.85.1115 · Cited by 399 · see citing works
“…Vergassola, Villermaux, and Shraiman, 2007; Sanchez and Kondev, 2008; Shahrezaei and Swain, 2008; Southworth and Agard, 2008; Moffitt et al., 2009; Tkacik, Walczak, and Bialek, 2009; Eldar and Elowitz, 2010; Walczak, Tkacik, and Bialek, 2010; Yu et al., 2010; Bustamante, Cheng, and Mejia, 2011).”
Real-Time Imaging of Translation on Single mRNA Transcripts in Live Cells
Wang, C., Han, B., Zhou, R., & Zhuang, X. (2016) · Cell · doi:10.1016/j.cell.2016.04.040 · Cited by 353 · see citing works
ClpX(P) Generates Mechanical Force to Unfold and Translocate Its Protein Substrates
Maillard, R. A., Chistol, G., Sen, M., Righini, M., Tan, J., Kaiser, C., Hodges, H. C., Martin, A., & Bustamante, C. (2011) · Cell · doi:10.1016/j.cell.2011.04.010 · Cited by 280 · see citing works
“The characteristics of the translocation process of ClpX are fundamentally distinct from those of other molecular motors that have been studied under external force (Bustamante et al., 2011; Yildiz and Selvin, 2005).”
Self-citationSitters, G., Kamsma, D., Thalhammer, G., Ritsch-Marte, M., Peterman, E., & Wuite, G. (2014) · Nature Methods · doi:10.1038/nmeth.3183 · Cited by 294
Type I restriction enzymes and their relatives
Loenen, W. A., Dryden, D., Raleigh, E., & Wilson, G. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt847 · Cited by 250 · see citing works
“The motor domain belongs to the RecA-like ATP-dependent family, a clade of the Additional Strand Conserved E family (107), of which the well-known AAA+ motor proteins are another clade (108).”
Chowdhury, D. (2013) · Physics Reports · doi:10.1016/j.physrep.2013.03.005 · Cited by 218 · see citing works
Schmidt, B., Osheroff, N., & Berger, J. (2012) · Nature Structural &Molecular Biology · doi:10.1038/nsmb.2388 · Cited by 155 · see citing works
“(1) Homodimer at the beginning of cycle.”
Combined versatile high-resolution optical tweezers and single-molecule fluorescence microscopy.
Sirinakis, G., Ren, Y.-Y., Gao, Y., Xi, Z., & Zhang, Y.-L. (2012) · Review of Scientific Instruments · doi:10.1063/1.4752190 · Cited by 155 · see citing works
Microscopic reversibility as the organizing principle of molecular machines
Astumian, R. D. (2012) · Nature Nanotechnology · doi:10.1038/nnano.2012.188 · Cited by 168 · see citing works
The Physics and Physical Chemistry of Molecular Machines
Astumian, R. D., Mukherjee, S., & Warshel, A. (2016) · ChemPhysChem · doi:10.1002/cphc.201600184 · Cited by 153 · see citing works
Nascent RNA structure modulates the transcriptional dynamics of RNA polymerases
Zamft, B., Bintu, L., Ishibashi, T., & Bustamante, C. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1205063109 · Cited by 117 · see citing works
Self-citationRemotely Activated Protein-Producing Nanoparticles
Schroeder, A., Goldberg, M. S., Kastrup, C. J., Wang, Y., Jiang, S., Joseph, B. J., Levins, C. G., Kannan, S. T., Langer, R., & Anderson, D. G. (2012) · Nano Letters · doi:10.1021/nl2036047 · Cited by 114 · see citing works
Optical Tweezers: A Force to Be Reckoned With
Killian, J. L., Ye, F., & Wang, M. D. (2018) · Cell · doi:10.1016/j.cell.2018.11.019 · Cited by 105 · see citing works
“In the time since the pioneering work of optical tweezers was established, the application of optical tweezers to the study of cellular structures, motor proteins, nucleic acids, and other biomolecules has flourished, providing impactful and often surprising discoveries and cementing the importance of optical trapping…”
Robinson, A., & van Oijen, A. V. (2013) · Nature Reviews Microbiology · doi:10.1038/nrmicro2994 · Cited by 93 · see citing works
Multiplexed single-molecule force spectroscopy using a centrifuge
Yang, D., Ward, A., Halvorsen, K., & Wong, W. P. (2016) · Nature Communications · doi:10.1038/ncomms11026 · Cited by 92 · see citing works
Mechanics and Single-Molecule Interrogation of DNA Recombination
Bell, J. C., & Kowalczykowski, S. C. (2016) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-060614-034352 · Cited by 78 · see citing works
Introduction: Molecular Motors
Iino, R., Kinbara, K., & Bryant, Z. D. (2020) · Chemical Reviews · doi:10.1021/acs.chemrev.9b00819 · Cited by 96 · see citing works
Nanopore detection of single molecule RNAP-DNA transcription complex.
Raillon, C., Cousin, P., Traversi, F., Garcia-Cordero, E., Hernandez, N., & Radenovic, A. (2012) · Nano letters (Print) · doi:10.1021/nl3002827 · Cited by 80
Astumian, R. D. (2015) · Biophysical Journal · doi:10.1016/j.bpj.2014.11.3459 · Cited by 88 · see citing works
“The effect of the disequilibrium between substrate and product in the bulk is based solely on mass action—there is no, nor can there be, a mechanical (58) smoking gun such as a power-stroke to which we can point as the essential step in free-energy transduction (59).”
Patel, S. S., Pandey, M., & Nandakumar, D. (2011) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2011.08.003 · Cited by 75 · see citing works
Challenges in AI-driven Biomedical Multimodal Data Fusion and Analysis
Liu, J., Cen, X., Yi, C., Wang, F.-A., Ding, J., Cheng, J., Wu, Q., Gai, B., Zhou, Y., He, R., et al. (2025) · Genomics, Proteomics & Bioinformatics · doi:10.1093/gpbjnl/qzaf011 · Cited by 75 · see citing works
“The central dogma of molecular biology outlines the process of genetic information being transferred from DNA to mRNA to protein, representing a fundamental mechanism for biological information processing [109].”
Bueren-Calabuig, J. A., Giraudon, C., Galmarini, C., Egly, J., & Gago, F. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr512 · Cited by 67
“In fact, local melting leading to strand separation is necessary for such vital processes as replication, transcription, recombination or repair (3) and can be affected by the presence of non-covalently bound [e.”
Theoretical perspectives on biological machines
Mugnai, M. L., Hyeon, C., Hinczewski, M., & Thirumalai, D. (2020) · Reviews of Modern Physics · doi:10.1103/revmodphys.92.025001 · Cited by 84 · see citing works
“A Final remark 39 Acknowledgments 40 References 40 I. INTRODUCTION The opening sentence of a perspective by Bustamante (Bustamante et al., 2011) on the workings of nucleic acid translocases begins with the quote, “The operative industry of Nature is so prolific that machines will be eventually…”
Nguyen, H., Jiang, Y., Mohapatra, S., Wang, W., Barnes, J. C., Oldenhuis, N. J., Chen, K. K., Axelrod, S., Huang, Z., Chen, Q., et al. (2021) · Nature Chemistry · doi:10.1038/s41557-021-00826-8 · Cited by 64 · see citing works
Transcription reinitiation by RNA polymerase III.
Dieci, G., Bosio, M. C., Fermi, B., & Ferrari, R. (2013) · Biochimica et Biophysica Acta · doi:10.1016/j.bbagrm.2012.10.009 · Cited by 61 · see citing works
“Learning more about chromatin influence on Pol III facilitated recycling, together with approaches allowing to monitor transcription at the single molecule level in living cells [111], could also help to understand the molecular bases for the extremely high rates of Pol III transcript synthesis in vivo.”
Kemmerich, F. E., Swoboda, M., Kauert, D. J., Grieb, M. S., Hahn, S., Schwarz, F. W., Seidel, R., & Schlierf, M. (2016) · Nano letters (Print) · doi:10.1021/acs.nanolett.5b03956 · Cited by 60
Topics on Cervical Cancer With an Advocacy for Prevention
Rajkumar, R. (2012) · InTech eBooks · doi:10.5772/1458 · Cited by 29 · see citing works
High-throughput single-molecule analysis of DNA–protein interactions by tethered particle motion
Plénat, T., Tardin, C., Rousseau, P., & Salomé, L. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks250 · Cited by 58
Measuring Cation Dependent DNA Polymerase Fidelity Landscapes by Deep Sequencing
Zamft, B. M., Marblestone, A. H., Kording, K. P., Schmidt, D., Martin-Alarcon, D. A., Tyo, K. E. J., Boyden, E. S., & Church, G. M. (2012) · PLoS ONE · doi:10.1371/journal.pone.0043876 · Cited by 58 · see citing works
“DNA polymerases are complex biochemical machines [5].”
Tuning the Music: Acoustic Force Spectroscopy (AFS) 2.0.
Kamsma, D., Creyghton, R., Sitters, G., Wuite, G., & Peterman, E. (2016) · Methods · doi:10.1016/j.ymeth.2016.05.002 · Cited by 51
Byrd, A. K., Matlock, D. L., Bagchi, D., Aarattuthodiyil, S., Harrison, D., Croquette, V., & Raney, K. (2012) · Journal of Molecular Biology · doi:10.1016/j.jmb.2012.04.007 · Cited by 50
Desai, V. P., Frank, F., Lee, A., Righini, M., Lancaster, L., Noller, H. F., Tinoco, I., & Bustamante, C. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.07.024 · Cited by 63 · see citing works
“Such questions are also broadly applicable to many molecular motors that couple the activity of protein or chemical factors to their movement along a substrate (Bustamante et al., 2011).”
Self-citationCrenarchaeal chromatin proteins Cren7 and Sul7 compact DNA by inducing rigid bends
Driessen, R. P. C., Meng, H., Suresh, G., Shahapure, R., Lanzani, G., Priyakumar, U., White, M., Schiessel, H., van Noort, J., & Dame, R. T. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1053 · Cited by 45
“However, cellular machineries involved in replication and transcription, such as helicases and polymerases, may directly drive the proteins to dissociate (54), allowing access to the DNA track.”
Recent Developments in Solid-Phase Strategies towards Synthetic, Sequence-Defined Macromolecules.
Hill, S. A., Gerke, C., & Hartmann, L. (2018) · Chemistry - An Asian Journal · doi:10.1002/asia.201801171 · Cited by 43
Single Molecule Data Analysis: An Introduction
Tavakoli, M., Taylor, J. N., Li, C.-B., Komatsuzaki, T., & Pressé, S. (2016) · Advances in chemical physics · doi:10.1002/9781119324560.ch4 · Cited by 39 · see citing works
“Statistical approaches have been invaluable in generating detailed mechanistic insight into realms previously inaccessible at every step along biology’s central dogma [42, 43].”
High Spatiotemporal-Resolution Magnetic Tweezers: Calibration and Applications for DNA Dynamics
Dulin, D., Cui, T. J., Cnossen, J. P., Docter, M. W., Lipfert, J., & Dekker, N. H. (2015) · Biophysical Journal · doi:10.1016/j.bpj.2015.10.018 · Cited by 92 · see citing works
Whitley, K. D., Comstock, M. J., & Chemla, Y. (2017) · Methods in molecular biology · doi:10.1007/978-1-4939-6421-5_8 · Cited by 38
Simple mechanics of protein machines
Flechsig, H., & Mikhailov, A. S. (2019) · Journal of The Royal Society Interface · doi:10.1098/rsif.2019.0244 · Cited by 30 · see citing works
D'Heygère, F., Schwartz, A., Coste, F., Castaing, B., & Boudvillain, M. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv505 · Cited by 33
“The latter depends on multiple factors governing the mechanochemical transduction mechanism and yield (42), some of which may vary between the MtbRho and EcRho motors.”
Omnipresent Maxwell's demons orchestrate information management in living cells
Boël, G., Danot, O., de Lorenzo, V., & Danchin, A. (2019) · Microbial Biotechnology · doi:10.1111/1751-7915.13378 · Cited by 52 · see citing works
Dynamics and stoichiometry of a regulated enhancer-binding protein in live Escherichia coli cells
Mehta, P. D., Jovanović, G., Lenn, T., Bruckbauer, A., Engl, C., Ying, L., & Buck, M. (2013) · Nature Communications · doi:10.1038/ncomms2997 · Cited by 29 · see citing works
Modeling stochastic kinetics of molecular machines at multiple levels: from molecules to modules.
Chowdhury, D. (2013) · Biophysical Journal · doi:10.1016/j.bpj.2013.04.042 · Cited by 31 · see citing works
“Single-molecule studies (51,52) have provided deep insights into the mechanochemical kinetics of almost all types of molecular machines (59), including cytoskeletal motors (19), as well as machines for genomic processes (22,60), such as helicase motors (45) and machines for templatedirected polymerization (e.”
Molecular motors for DNA translocation in prokaryotes
Allemand, J., Maier, B., & Smith, D. E. (2012) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2011.12.023 · Cited by 30
An optical trap combined with three-color FRET.
Lee, S., & Hohng, S. (2013) · Journal of the American Chemical Society · doi:10.1021/ja408767p · Cited by 29
High-Resolution Optical Tweezers Combined With Single-Molecule Confocal Microscopy
Whitley, K. D., Comstock, M. J., & Chemla, Y. (2016) · Methods in Enzymology · doi:10.1016/bs.mie.2016.10.036 · Cited by 28
High-throughput, high-force probing of DNA-protein interactions with magnetic tweezers.
Berghuis, B. A., Köber, M., van Laar, T., & Dekker, N. (2016) · Methods · doi:10.1016/j.ymeth.2016.03.025 · Cited by 28 · see citing works
Inside single cells: quantitative analysis with advanced optics and nanomaterials
Cui, Y., & Irudayaraj, J. (2014) · Wiley Interdisciplinary Reviews Nanomedicine and Nanobiotechnology · doi:10.1002/wnan.1321 · Cited by 28 · see citing works
Chodera, J., Keller, B., Elms, P. J., Noé, F., Kaiser, C. M., Ewall-Wice, A., Marqusee, S., Bustamante, C. J., & Hinrichs, N. (2011) · doi:10.48550/arxiv.1108.1430 · Cited by 25
Self-citationNanoengineering of biohybrid micro/nanobots for programmed biomedical applications.
Shivalkar, S., Chowdhary, P., Afshan, T., Chaudhary, S., Roy, A., Samanta, S., & Sahoo, A. (2022) · Colloids and Surfaces B: Biointerfaces · doi:10.1016/j.colsurfb.2022.113054 · Cited by 24 · see citing works
Reuther, C., Catalano, R., Salhotra, A., Vemula, V., Korten, T., Diez, S., & Månsson, A. (2021) · New Journal of Physics · doi:10.1088/1367-2630/ac10ce · Cited by 25 · see citing works
Elwakil, M. M. A., Suzuki, R., Khalifa, A. M., Elshami, R. M., Isono, T., Elewa, Y. H. A., Sato, Y., Nakamura, T., Satoh, T., & Harashima, H. (2023) · Advanced Functional Materials · doi:10.1002/adfm.202303795 · Cited by 28 · see citing works
Chemla, Y. (2016) · Biopolymers · doi:10.1002/bip.22880 · Cited by 21 · see citing works
DNA motion capture reveals the mechanical properties of DNA at the mesoscale.
Price, A., Pilkiewicz, K., Graham, T. G. W., Song, D., Eaves, J., & Loparo, J. (2015) · Biophysical Journal · doi:10.1016/j.bpj.2015.04.022 · Cited by 21
“ViðRiÞzV Ri þ fidZi þ 1 2 kt;i ðdXiÞ(2) þ ðdYiÞ(2) þ 1 2 kk;iðdZiÞ(2); (3)”
Buskila, A.-A. A., Kannaiah, S., & Amster‐Choder, O. (2014) · RNA Biology · doi:10.4161/rna.36135 · Cited by 39 · see citing works
Note: Direct force and ionic-current measurements on DNA in a nanocapillary.
Otto, O., Steinbock, L., Wong, D. W., Gornall, J., & Keyser, U. F. (2011) · Review of Scientific Instruments · doi:10.1063/1.3623502 · Cited by 21
Helicase processivity and not the unwinding velocity exhibits universal increase with force.
Pincus, D. L., Chakrabarti, S., & Thirumalai, D. (2015) · Biophysical Journal · doi:10.1016/j.bpj.2015.05.020 · Cited by 18 · see citing works
“Single molecule experiments have demonstrated that the unwinding velocities of some he- licases increase dramatically with increase in the external force, while others show little response.”
Astumian, R. D. (2014) · ACS Nano · doi:10.1021/nn507039b · Cited by 19 · see citing works
Optimizing Scoring Function of Protein-Nucleic Acid Interactions with Both Affinity and Specificity
Yan, Z., & Wang, J. (2013) · PLoS ONE · doi:10.1371/journal.pone.0074443 · Cited by 18 · see citing works
“The protein-nucleic acid (protein-DNA and protein-RNA) recognition is essential to the regulation of gene expression at every level of the central dogma of molecular biology, including replication, transcription and translation of genetic information [1].”
Cell Signaling Experiments Driven by Optical Manipulation
Difato, F., Pinato, G., & Cojoc, D. (2013) · International Journal of Molecular Sciences · doi:10.3390/ijms14058963 · Cited by 18 · see citing works
“A comprehensive outlook on the development of OT technology and its applications in different fields can be found in several very good reviews [8–13].”
Parallel multispot smFRET analysis using an 8-pixel SPAD array
Ingargiola, A., Colyer, R., Kim, D., Panzeri, F., Lin, R., Gulinatti, A., Rech, I., Ghioni, M., Weiss, S., & Michalet, X. (2012) · BiOS · doi:10.1117/12.909470 · Cited by 18
Single-molecule imaging and manipulation of biomolecular machines and systems
Iino, R., Iida, T., Nakamura, A., Saita, E., You, H., & Sako, Y. (2017) · Biochimica et Biophysica Acta (BBA) - General Subjects · doi:10.1016/j.bbagen.2017.08.008 · Cited by 14 · see citing works
Mechanisms of diffusional search for specific targets by DNA-dependent proteins
Mechetin, G. V., & Zharkov, D. (2014) · Biochemistry (Moscow) · doi:10.1134/s0006297914060029 · Cited by 17
The azimuthal path of myosin V and its dependence on lever-arm length
Lewis, J. H., Beausang, J. F., Sweeney, H. L., & Goldman, Y. E. (2012) · The Journal of General Physiology · doi:10.1085/jgp.201110715 · Cited by 13 · see citing works
Singh, D., Robin, T., Urbakh, M., & Reuveni, S. (2024) · bioRxiv · doi:10.1038/s41467-025-57327-2 · Cited by 16 · see citing works
Resolving Molecular Heterogeneity with Single-Molecule Centrifugation
Luo, Y., Chang, J. T., Yang, D., Bryan, J. S., MacIsaac, M., Pressé, S., & Wong, W. P. (2023) · Journal of the American Chemical Society · doi:10.1021/jacs.2c11450 · Cited by 16
The development of single molecule force spectroscopy: from polymer biophysics to molecular machines
Bustamante, C., & Yan, S. (2022) · Quarterly Reviews of Biophysics · doi:10.1017/s0033583522000087 · Cited by 31 · see citing works
“…into the methionine-encoding mRNA translation start codon, AUG, whose placing at the P site of the small subunit is directed by an upstream Shine–Dalgarno (SD) sequence complementary to a segment of the 16S ribosomal RNA (Kaminishi et al., 2007; Korostelev et al., 2007; Bustamante et al., 2011).”
Self-citationOptical tweezers studies of transcription by eukaryotic RNA polymerases
Lisica, A., & Grill, S. (2017) · Biomolecular Concepts · doi:10.1515/bmc-2016-0028 · Cited by 15 · see citing works
“First, these techniques provide the ability to simplify the complex in vivo transcription machinery and to track and manipulate individual RNA polymerase mole cules, one at a time, without the myriad of additional interactions that take place inside a cell (4, 5).”
Step Detection in Single-Molecule Real Time Trajectories Embedded in Correlated Noise
Arunajadai, S. G., & Cheng, W. (2013) · PLoS ONE · doi:10.1371/journal.pone.0059279 · Cited by 14 · see citing works
“These molecular motors move in steps [8,9,10,11,12].”
Self-citationSirbuly, D., Friddle, R., Villanueva, J., & Huang, Q. (2015) · Reports on progress in physics. Physical Society · doi:10.1088/0034-4885/78/2/024101 · Cited by 14 · see citing works
Nucleosome‐remodelling machines and other molecular motors observed at the single‐molecule level
Lavelle, C., Praly, É., Bensimon, D., Cam, É. L., & Croquette, V. (2011) · The FEBS Journal · doi:10.1111/j.1742-4658.2011.08280.x · Cited by 14 · see citing works
RNA research for drug discovery: Recent advances and critical insight
Aja, P. M., Agu, P. C., Ogbu, C. O., Alum, E. U., Fasogbon, I. V., Musyoka, A. M., Ngwueche, W., Egwu, C. O., Tusubira, D., & Ross, K. (2025) · Gene · doi:10.1016/j.gene.2025.149342 · Cited by 16 · see citing works
Kim, J., Lee, S., Suh, J., Park, J., & Shin, H.-J. (2013) · doi:10.1063/1.4791599 · Cited by 13
Zhang, Y.-L., Sirinakis, G., Gundersen, G., Xi, Z., & Gao, Y. (2012) · Methods in Enzymology · doi:10.1016/b978-0-12-391938-0.00001-x · Cited by 13
Theory of optical tweezing of dielectric microspheres in chiral host media and its applications
Ali, R., Dutra, R. S., Pinheiro, F. A., Rosa, F. S., & Maia, P. A. (2020) · Scientific Reports · doi:10.1038/s41598-020-73530-1 · Cited by 12 · see citing works
A tour de force on the double helix: Exploiting DNA mechanics to study DNA-based molecular machines
Wasserman, M., & Liu, S.-X. (2019) · Biochemistry · doi:10.1021/acs.biochem.9b00346 · Cited by 12
Ruer, M., Krainer, G., Gröger, P., & Schlierf, M. (2018) · bioRxiv · doi:10.1101/323055 · Cited by 12
Zhong, Z.-S., Soh, L. H., Lim, M., & Chen, G. (2015) · ChemPlusChem · doi:10.1002/cplu.201500144 · Cited by 12
Processivity, velocity and universal characteristics of nucleic acid unwinding by helicases
Chakrabarti, S., Jarzynski, C., & Thirumalai, D. (2018) · bioRxiv · doi:10.1101/366914 · Cited by 11
“However, this may not be an accurate description of other helicases like the NS3 in which the domains surround both the strands of the nucleic acid, and the junction may be protected to some extent from external forces (5).”
Collepardo-Guevara, R., & Schlick, T. (2013) · Biochemical Society Transactions · doi:10.1042/bst20120349 · Cited by 11
Huxley’s Model for Muscle Contraction Revisited: The Importance of Microscopic Reversibility
Astumian, R. D. (2015) · Topics in current chemistry · doi:10.1007/128_2015_644 · Cited by 14 · see citing works
“The Brownian information ratchet mechanism by which all chemically driven molecular machines work can be much better described in terms of a chemical paradigm involving specificity gating, as discussed for ion pumps [45], than in terms of a mechanical paradigm anticipated by Bustamante, Cheng, and Mejia [46].”
Coumarins as Fluorescent Labels of Biomolecules
Pereira, A., Martins, S., & Caldeira, A. T. (2019) · Phytochemicals in Human Health · doi:10.5772/intechopen.85973 · Cited by 10
“With specific and efficient fluorescent labelling, the proteins can be visualized in real time for the elucidation of their functions in a complex biological network, which also allows the detection of the protein-protein interactions, fundamental to understand intra- and intercellular communications [26].”
The effect of linker histone's nucleosome binding affinity on chromatin unfolding mechanisms.
Collepardo-Guevara, R., & Schlick, T. (2011) · Biophysical Journal · doi:10.1016/j.bpj.2011.07.044 · Cited by 10
Single-Molecule Measurements Using Acoustic Force Spectroscopy (AFS).
Kamsma, D., & Wuite, G. (2018) · Methods in molecular biology · doi:10.1007/978-1-4939-7271-5_18 · Cited by 10
Effect of fluoride ion on the stability of DNA hairpin
Liu, C., Zhai, W., Gong, H., Liu, Y.-H., & Chen, H. (2017) · doi:10.1016/j.cplett.2017.04.028 · Cited by 9
Fabrication of birefringent nanocylinders for single-molecule force and torque measurement
Li, P.-C., Chang, J.-C., Porta, A. L., & Yu, E. T. (2014) · Nanotechnology · doi:10.1088/0957-4484/25/23/235304 · Cited by 9
“S Online supplementary data available from stacks.iop.org/NANO/25/235304/mmedia Keywords: optical tweezer, nanosphere lithography, subwavelength optics (Some figures may appear in colour only in the online journal)”
Low cost and massively parallel force spectroscopy with fluid loading on a chip
Akbari, E., Shahhosseini, M., Robbins, A., Poirier, M., Song, J. W., & Castro, C. (2022) · Nature Communications · doi:10.1038/s41467-022-34212-w · Cited by 8
Naranjo, T., Cerrón, F., Nieto-Ortega, B., Latorre, A., Somoza, Á., Ibarra, B., & Pérez, E. (2017) · Chemical Science · doi:10.1039/c7sc03044d · Cited by 8
Theoretical and computational tools to model multistable gene regulatory networks
Bocci, F., Jia, D., Nie, Q. H., Jolly, M. K., & Onuchic, J. N. (2023) · Reports on Progress in Physics · doi:10.1088/1361-6633/acec88 · Cited by 14 · see citing works
Residence Time Analysis of RNA Polymerase Transcription Dynamics: A Bayesian Sticky HMM Approach
Kılıç, Z., Sgouralis, I., & Pressé, S. (2020) · bioRxiv · doi:10.1101/2020.07.28.132373 · Cited by 7
“Although it is believed that the long residence times are providing enough time for the transcription activities to be regulated (24, 25, 30), backtracking plays a role in helping elongation factor (GreB) to enforce RNAP for controlling its accuracy in transcription and translocation (50).”
InfluentialWang, L., Wasserman, M. R., Feldman, M. B., Altman, R. B., & Blanchard, S. C. (2011) · Annals of the New York Academy of Sciences · doi:10.1111/j.1749-6632.2012.06839.x · Cited by 8 · see citing works
Active hydrodynamic theory of euchromatin and heterochromatin
Rautu, S., Zidovska, A., Saintillan, D., & Shelley, M. J. (2025) · Physical Review X · doi:10.1103/8n8h-7gx6 · Cited by 6 · see citing works
“Single-molecule assays provide measurements of stall forces for nuclear enzymes such as helicases, RNA polymerases (Pol II), and DNA polymerases [108 – 110], but the effective force f a relevant here depends on how much of this load projects along the chromatin chain direction and may be reduced by…”
Capera-Aragones, P., Tyson, R., & Foxall, E. (2023) · Theoretical Ecology · doi:10.1007/s12080-023-00552-6 · Cited by 6 · see citing works
“In addition, its role in explaining the results of new experiments in few-particles systems, which traditionally lie outside the strict purview of the classical theory, has grown exponentially in recent years (Hamill et al. 1981; Methfessel et al. 1986; Rhoades et al. 2004; Walczak et al. 2010; Tkačik et al. 2009; Bus…”
A Horizontal Magnetic Tweezers for Studying Single DNA Molecules and DNA-Binding Proteins
Fabian, R., Gaire, S., Tyson, C., Adhikari, R., Pegg, I., & Sarkar, A. (2021) · Molecules · doi:10.3390/molecules26164781 · Cited by 6
“Interestingly, several molecular machines such as RNA polymerase and DNA polymerase have been observed to apply [5]”
Optical manipulation of a single human virus for study of viral-cell interactions
Hou, X., DeSantis, M., Tian, C., & Cheng, W. (2016) · NanoScience + Engineering · doi:10.1117/12.2239051 · Cited by 6
“On the one hand, we can use optical tweezers for manipulation of single molecules [22], single viruses and single cells; on the other hand, we can use continuous-wave laser-excited TPF to image live cells without the need of additional laser source.”
Self-citationClark, D., & Pazdernik, N. (2015) · doi:10.1016/b978-0-12-385015-7.00002-8 · Cited by 6
Information management in DNA replication modeled by directional, stochastic chains with memory
Arias-Gonzalez, J. R. (2016) · The Journal of Chemical Physics · doi:10.1063/1.4967335 · Cited by 7 · see citing works
- Authors
- Bustamante, C., Cheng, W., & Mejia, Y. X.
- Affiliations
- Howard Hughes Medical Institute (US)
- University of Michigan (US)
- Max Planck Institute for Biophysical Chemistry (DE)
- Corresponding author
- Bustamante, Carlos
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2011-02
- Volume
- 144
- Issue
- 4
- Pages
- 480-497
- ISSN
- 0092-8674 (ISSN-L)
- PMC
- PMC3063003
- OpenAlex
- W2007349694
- Cited by
- 173
- References
- 0
- Citations by year
- 2026: 5 · 2025: 7 · 2024: 5 · 2023: 11 · 2022: 9 · 2021: 11 · 2020: 3 · 2019: 8 · 2018: 9 · 2017: 10 · 2016: 19 · 2015: 13 · 2014: 11 · 2013: 19 · 2012: 20
- FWCI
- 1.56
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Cell (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Max Planck Institute for Plasma Physics (submittedVersion)
- Funders
- Howard Hughes Medical Institute
- Topics
- Physical Sciences › Physics and Astronomy › Atomic and Molecular Physics, and Optics › Force Microscopy Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Biophysics › Advanced Fluorescence Microscopy Techniques
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Keywords
- central dogma, single-molecule fluorescence, molecular machines, DNA replication, transcription, RNA processing, thermodynamic efficiency, transient intermediates, molecular dynamics
- MeSH terms
- Chromosomes, DNA Replication, DNA Helicases, Enzymes, Nucleic Acids, Thermodynamics, Transcription, Genetic, Protein Biosynthesis, Virus Assembly
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
