1
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Fijen C, Drogalis Beckham L, Terino D, Li Y, Ramsden DA, Wood RD, Doublié S, Rothenberg E. Sequential requirements for distinct Polθ domains during theta-mediated end joining. Mol Cell 2024; 84:1460-1474.e6. [PMID: 38640894 PMCID: PMC11031631 DOI: 10.1016/j.molcel.2024.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 01/10/2024] [Accepted: 03/12/2024] [Indexed: 04/21/2024]
Abstract
DNA polymerase θ (Polθ) plays a central role in a DNA double-strand break repair pathway termed theta-mediated end joining (TMEJ). TMEJ functions by pairing short-sequence "microhomologies" (MHs) in single-stranded DNA at each end of a break and subsequently initiating DNA synthesis. It is not known how the Polθ helicase domain (HD) and polymerase domain (PD) operate to bring together MHs and facilitate repair. To resolve these transient processes in real time, we utilized in vitro single-molecule FRET approaches and biochemical analyses. We find that the Polθ-HD mediates the initial capture of two ssDNA strands, bringing them in close proximity. The Polθ-PD binds and stabilizes pre-annealed MHs to form a synaptic complex (SC) and initiate repair synthesis. Individual synthesis reactions show that Polθ is inherently non-processive, accounting for complex mutational patterns during TMEJ. Binding of Polθ-PD to stem-loop-forming sequences can substantially limit synapsis, depending on the available dNTPs and sequence context.
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Affiliation(s)
- Carel Fijen
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA.
| | - Lea Drogalis Beckham
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT 05405, USA
| | - Dante Terino
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Yuzhen Li
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77230, USA
| | - Dale A Ramsden
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Richard D Wood
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77230, USA
| | - Sylvie Doublié
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT 05405, USA
| | - Eli Rothenberg
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA.
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2
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Vermeer B, van Ossenbruggen J, Schmid S. Single-Molecule FRET-Resolved Protein Dynamics - from Plasmid to Data in Six Steps. Methods Mol Biol 2024; 2694:267-291. [PMID: 37824009 DOI: 10.1007/978-1-0716-3377-9_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
Single-molecule Förster resonance energy transfer (smFRET) is a powerful technique for the detection of conformational dynamics of biomolecules. While many smFRET experiments are performed using dye-labeled DNA, here we describe a comprehensive protocol to resolve the conformational dynamics of a protein system - notably from plasmid to data. Using the example of the heat-shock protein Hsp90, we describe the protein production and threefold site-specific bioconjugation, the smFRET measurement using total internal reflection fluorescence microscopy (TIRFM), and raw data processing to reveal time-resolved protein dynamics. The described smFRET approach is readily transferrable to the study of many more all-protein systems and their conformational energy landscape.
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Affiliation(s)
- Benjamin Vermeer
- Laboratory of Biophysics, Wageningen University & Research, Wageningen, The Netherlands
| | | | - Sonja Schmid
- Laboratory of Biophysics, Wageningen University & Research, Wageningen, The Netherlands.
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3
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Ray KK, Kinz-Thompson CD, Fei J, Wang B, Lin Q, Gonzalez RL. Entropic control of the free-energy landscape of an archetypal biomolecular machine. Proc Natl Acad Sci U S A 2023; 120:e2220591120. [PMID: 37186858 PMCID: PMC10214133 DOI: 10.1073/pnas.2220591120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 04/17/2023] [Indexed: 05/17/2023] Open
Abstract
Biomolecular machines are complex macromolecular assemblies that utilize thermal and chemical energy to perform essential, multistep, cellular processes. Despite possessing different architectures and functions, an essential feature of the mechanisms of action of all such machines is that they require dynamic rearrangements of structural components. Surprisingly, biomolecular machines generally possess only a limited set of such motions, suggesting that these dynamics must be repurposed to drive different mechanistic steps. Although ligands that interact with these machines are known to drive such repurposing, the physical and structural mechanisms through which ligands achieve this remain unknown. Using temperature-dependent, single-molecule measurements analyzed with a time-resolution-enhancing algorithm, here, we dissect the free-energy landscape of an archetypal biomolecular machine, the bacterial ribosome, to reveal how its dynamics are repurposed to drive distinct steps during ribosome-catalyzed protein synthesis. Specifically, we show that the free-energy landscape of the ribosome encompasses a network of allosterically coupled structural elements that coordinates the motions of these elements. Moreover, we reveal that ribosomal ligands which participate in disparate steps of the protein synthesis pathway repurpose this network by differentially modulating the structural flexibility of the ribosomal complex (i.e., the entropic component of the free-energy landscape). We propose that such ligand-dependent entropic control of free-energy landscapes has evolved as a general strategy through which ligands may regulate the functions of all biomolecular machines. Such entropic control is therefore an important driver in the evolution of naturally occurring biomolecular machines and a critical consideration for the design of synthetic molecular machines.
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Affiliation(s)
- Korak Kumar Ray
- Department of Chemistry, Columbia University, New York, NY10027
| | | | - Jingyi Fei
- Department of Chemistry, Columbia University, New York, NY10027
| | - Bin Wang
- Department of Mechanical Engineering, Columbia University, New York, NY10027
| | - Qiao Lin
- Department of Mechanical Engineering, Columbia University, New York, NY10027
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4
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Yeou S, Hwang J, Yi J, Kim C, Kim SK, Lee NK. Cytosine methylation regulates DNA bendability depending on the curvature. Chem Sci 2022; 13:7516-7525. [PMID: 35872822 PMCID: PMC9242020 DOI: 10.1039/d1sc07115g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 06/01/2022] [Indexed: 11/21/2022] Open
Abstract
Cytosine methylation plays an essential role in many biological processes, such as nucleosome inactivation and regulation of gene expression. The modulation of DNA mechanics may be one of the regulatory mechanisms influenced by cytosine methylation. However, it remains unclear how methylation influences DNA mechanics. Here, we show that methylation has contrasting effects on the bending property of dsDNA depending on DNA curvature. We directly applied bending force on 30 base pairs of dsDNA using a D-shaped DNA nanostructure and measured the degree of bending using single-molecule fluorescence resonance energy transfer without surface immobilization. When dsDNA is weakly bent, methylation increases the stiffness of dsDNA. The stiffness of dsDNA increased by approximately 8% with a single methylation site for 30 bp dsDNA. When dsDNA is highly bent by a strong force, it forms a kink, i.e., a sharp bending of dsDNA. Under strong bending, methylation destabilizes the non-kink form compared with the kink form, which makes dsDNA near the kink region apparently more bendable. However, if the kink region is methylated, the kink form is destabilized, and dsDNA becomes stiffer. As a result, methylation increases the stiffness of weakly bent dsDNA and concurrently can promote kink formation, which may stabilize the nucleosome structure. Our results provide new insight into the effect of methylation, showing that cytosine methylation has opposite effects on DNA mechanics depending on its curvature and methylation location.
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Affiliation(s)
- Sanghun Yeou
- Department of Chemistry, Seoul National University 08832 Seoul Republic of Korea
| | - Jihee Hwang
- Department of Chemistry, Seoul National University 08832 Seoul Republic of Korea
| | - Jaehun Yi
- Department of Chemistry, Seoul National University 08832 Seoul Republic of Korea
| | - Cheolhee Kim
- National Science Museum Daejeon 34143 Republic of Korea
| | - Seong Keun Kim
- Department of Chemistry, Seoul National University 08832 Seoul Republic of Korea
| | - Nam Ki Lee
- Department of Chemistry, Seoul National University 08832 Seoul Republic of Korea
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5
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Zhou Y, Jia E, Sheng Y, Qiao Y, Wang Y, Shi H, Liu Z, Pan M, Tu J, Bai Y, Zhao X, Ge Q, Lu Z. Sensitive and Low-Bias Transcriptome Sequencing Using Agarose PCR. ACS APPLIED MATERIALS & INTERFACES 2022; 14:19154-19167. [PMID: 35446027 DOI: 10.1021/acsami.2c02133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Transcriptome sequencing has emerged as an important research tool for exploring the mysteries of life at the single-cell level. However, its wide application is limited by the bias associated with the amplification reactions which is essential for library building of trace RNA. In this study, low-melting-point agarose was added to the amplification reactions to take advantage of its molecular crowding effect and polymer cross-linked structure to improve the sensitivity of the reactions and reduce bias. To further evaluate the performance of the method, it was applied to transcriptome sequencing of microregion samples from brain tissue sections of mice with Parkinson's disease at the single cell level. The results showed that agarose PCR had better performance than in-tube PCR. Further application of agarose PCR to transcriptome library sequencing could obtain data closer to that of unamplified. With the addition of low melting point agarose, the sensitivity of the amplification reaction was significantly increased, while homogeneity was increased by approximately 2-fold. Not only that, but this work also provides 11% sensitivity improvement for spatial transcriptomic study on Parkinson's disease-associated gene detection. The agarose PCR provides a new tool for efficient and homogeneous amplification of trace samples and can be widely used for spatial transcriptome library sequencing and studies.
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Affiliation(s)
- Ying Zhou
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
| | - Erteng Jia
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
| | - Yuqi Sheng
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
| | - Yi Qiao
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
| | - Ying Wang
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
| | - Huajuan Shi
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
| | - Zhiyu Liu
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
| | - Min Pan
- School of Medicine, Southeast University, Nanjing 210097, China
| | - Jing Tu
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
| | - Yunfei Bai
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
| | - Xiangwei Zhao
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
| | - Qinyu Ge
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
| | - Zuhong Lu
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
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6
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Turvey MW, Gabriel KN, Lee W, Taulbee JJ, Kim JK, Chen S, Lau CJ, Kattan RE, Pham JT, Majumdar S, Garcia D, Weiss GA, Collins PG. Single-molecule Taq DNA polymerase dynamics. SCIENCE ADVANCES 2022; 8:eabl3522. [PMID: 35275726 PMCID: PMC8916733 DOI: 10.1126/sciadv.abl3522] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 01/21/2022] [Indexed: 06/14/2023]
Abstract
Taq DNA polymerase functions at elevated temperatures with fast conformational dynamics-regimes previously inaccessible to mechanistic, single-molecule studies. Here, single-walled carbon nanotube transistors recorded the motions of Taq molecules processing matched or mismatched template-deoxynucleotide triphosphate pairs from 22° to 85°C. By using four enzyme orientations, the whole-enzyme closures of nucleotide incorporations were distinguished from more rapid, 20-μs closures of Taq's fingers domain testing complementarity and orientation. On average, one transient closure was observed for every nucleotide binding event; even complementary substrate pairs averaged five transient closures between each catalytic incorporation at 72°C. The rate and duration of the transient closures and the catalytic events had almost no temperature dependence, leaving all of Taq's temperature sensitivity to its rate-determining open state.
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Affiliation(s)
- Mackenzie W. Turvey
- Department of Physics and Astronomy, University of California, Irvine, Irvine, CA 92697-4575, USA
| | - Kristin N. Gabriel
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697-3900, USA
| | - Wonbae Lee
- Department of Physics and Astronomy, University of California, Irvine, Irvine, CA 92697-4575, USA
| | - Jeffrey J. Taulbee
- Department of Physics and Astronomy, University of California, Irvine, Irvine, CA 92697-4575, USA
| | - Joshua K. Kim
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025, USA
| | - Silu Chen
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025, USA
| | - Calvin J. Lau
- Department of Physics and Astronomy, University of California, Irvine, Irvine, CA 92697-4575, USA
| | - Rebecca E. Kattan
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697-3900, USA
| | - Jenifer T. Pham
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025, USA
| | - Sudipta Majumdar
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025, USA
| | | | - Gregory A. Weiss
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697-3900, USA
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025, USA
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697-3958, USA
| | - Philip G. Collins
- Department of Physics and Astronomy, University of California, Irvine, Irvine, CA 92697-4575, USA
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7
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Millar DP. Conformational Dynamics of DNA Polymerases Revealed at the Single-Molecule Level. Front Mol Biosci 2022; 9:826593. [PMID: 35281261 PMCID: PMC8913937 DOI: 10.3389/fmolb.2022.826593] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 01/20/2022] [Indexed: 12/25/2022] Open
Abstract
DNA polymerases are intrinsically dynamic macromolecular machines. The purpose of this review is to describe the single-molecule Förster resonance energy transfer (smFRET) methods that are used to probe the conformational dynamics of DNA polymerases, focusing on E. coli DNA polymerase I. The studies reviewed here reveal the conformational dynamics underpinning the nucleotide selection, proofreading and 5′ nuclease activities of Pol I. Moreover, the mechanisms revealed for Pol I are likely employed across the DNA polymerase family. smFRET methods have also been used to examine other aspects of DNA polymerase activity.
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8
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Evans GW, Craggs T, Kapanidis AN. The Rate-limiting Step of DNA Synthesis by DNA Polymerase Occurs in the Fingers-closed Conformation. J Mol Biol 2022; 434:167410. [PMID: 34929202 PMCID: PMC8783057 DOI: 10.1016/j.jmb.2021.167410] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/22/2021] [Accepted: 12/12/2021] [Indexed: 12/03/2022]
Abstract
DNA polymerases maintain genomic integrity by copying DNA with high fidelity, part of which relies on the polymerase fingers opening-closing transition, a series of conformational changes during the DNA synthesis reaction cycle. Fingers opening and closing has been challenging to study, mainly due to the need to synchronise molecular ensembles. We previously studied fingers opening-closing on single polymerase-DNA complexes using single-molecule FRET; however, our work was limited to pre-chemistry reaction steps. Here, we advance our analysis to extensible substrates, and observe DNA polymerase (Pol) conformational changes across the entire DNA polymerisation reaction in real-time, gaining direct access to an elusive post-chemistry step rate-limiting for DNA synthesis. Our results showed that Pol adopts the fingers-closed conformation during polymerisation, and that the post-chemistry rate-limiting step occurs in the fingers-closed conformation. We found that fingers-opening in the Pol-DNA binary complex in the absence of polymerisation is slow (∼5.3 s-1), and comparable to the rate of fingers-opening after polymerisation (3.4 s-1); this indicates that the fingers-opening step itself could be largely responsible for the slow post-chemistry step, with the residual rate potentially accounted for by pyrophosphase release. We also observed that DNA chain-termination of the 3' end of the primer increases substantially the rate of fingers-opening in the Pol-DNA binary complex (5.3 → 29 s-1), demonstrating that the 3'-OH residue is important for the kinetics of fingers conformational changes. Our observations offer mechanistic insight and tools to offer mechanistic insight for all nucleic acid polymerases.
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Affiliation(s)
- Geraint W Evans
- Department of Physics and Biological Physics Research Group, Clarendon Laboratory, University of Oxford, Parks Road, Oxford OX1 3PU, United Kingdom. https://twitter.com/geraintwe
| | - Timothy Craggs
- Department of Physics and Biological Physics Research Group, Clarendon Laboratory, University of Oxford, Parks Road, Oxford OX1 3PU, United Kingdom; Sheffield Institute for Nucleic Acids, Department of Chemistry, University of Sheffield, Brook Hill, Sheffield S3 7HF, United Kingdom. https://twitter.com/Craggs_Lab
| | - Achillefs N Kapanidis
- Department of Physics and Biological Physics Research Group, Clarendon Laboratory, University of Oxford, Parks Road, Oxford OX1 3PU, United Kingdom.
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9
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DNA Polymerase-Parental DNA Interaction Is Essential for Helicase-Polymerase Coupling during Bacteriophage T7 DNA Replication. Int J Mol Sci 2022; 23:ijms23031342. [PMID: 35163266 PMCID: PMC8835902 DOI: 10.3390/ijms23031342] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/19/2022] [Accepted: 01/22/2022] [Indexed: 11/17/2022] Open
Abstract
DNA helicase and polymerase work cooperatively at the replication fork to perform leading-strand DNA synthesis. It was believed that the helicase migrates to the forefront of the replication fork where it unwinds the duplex to provide templates for DNA polymerases. However, the molecular basis of the helicase-polymerase coupling is not fully understood. The recently elucidated T7 replisome structure suggests that the helicase and polymerase sandwich parental DNA and each enzyme pulls a daughter strand in opposite directions. Interestingly, the T7 polymerase, but not the helicase, carries the parental DNA with a positively charged cleft and stacks at the fork opening using a β-hairpin loop. Here, we created and characterized T7 polymerases each with a perturbed β-hairpin loop and positively charged cleft. Mutations on both structural elements significantly reduced the strand-displacement synthesis by T7 polymerase but had only a minor effect on DNA synthesis performed against a linear DNA substrate. Moreover, the aforementioned mutations eliminated synergistic helicase-polymerase binding and unwinding at the DNA fork and processive fork progressions. Thus, our data suggested that T7 polymerase plays a dominant role in helicase-polymerase coupling and replisome progression.
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10
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Vermeer B, Schmid S. Can DyeCycling break the photobleaching limit in single-molecule FRET? NANO RESEARCH 2022; 15:9818-9830. [PMID: 35582137 PMCID: PMC9101981 DOI: 10.1007/s12274-022-4420-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 04/05/2022] [Accepted: 04/06/2022] [Indexed: 05/03/2023]
Abstract
UNLABELLED Biomolecular systems, such as proteins, crucially rely on dynamic processes at the nanoscale. Detecting biomolecular nanodynamics is therefore key to obtaining a mechanistic understanding of the energies and molecular driving forces that control biomolecular systems. Single-molecule fluorescence resonance energy transfer (smFRET) is a powerful technique to observe in real-time how a single biomolecule proceeds through its functional cycle involving a sequence of distinct structural states. Currently, this technique is fundamentally limited by irreversible photobleaching, causing the untimely end of the experiment and thus, a narrow temporal bandwidth of ≤ 3 orders of magnitude. Here, we introduce "DyeCycling", a measurement scheme with which we aim to break the photobleaching limit in smFRET. We introduce the concept of spontaneous dye replacement by simulations, and as an experimental proof-of-concept, we demonstrate the intermittent observation of a single biomolecule for one hour with a time resolution of milliseconds. Theoretically, DyeCycling can provide > 100-fold more information per single molecule than conventional smFRET. We discuss the experimental implementation of DyeCycling, its current and fundamental limitations, and specific biological use cases. Given its general simplicity and versatility, DyeCycling has the potential to revolutionize the field of time-resolved smFRET, where it may serve to unravel a wealth of biomolecular dynamics by bridging from milliseconds to the hour range. ELECTRONIC SUPPLEMENTARY MATERIAL Supplementary material is available for this article at 10.1007/s12274-022-4420-5 and is accessible for authorized users.
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Affiliation(s)
- Benjamin Vermeer
- NanoDynamicsLab, Laboratory of Biophysics, Wageningen University, Stippeneng 4, 6708WE Wageningen, The Netherlands
| | - Sonja Schmid
- NanoDynamicsLab, Laboratory of Biophysics, Wageningen University, Stippeneng 4, 6708WE Wageningen, The Netherlands
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11
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Bocanegra R, Ismael Plaza GA, Pulido CR, Ibarra B. DNA replication machinery: Insights from in vitro single-molecule approaches. Comput Struct Biotechnol J 2021; 19:2057-2069. [PMID: 33995902 PMCID: PMC8085672 DOI: 10.1016/j.csbj.2021.04.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 04/03/2021] [Accepted: 04/03/2021] [Indexed: 11/16/2022] Open
Abstract
The replisome is the multiprotein molecular machinery that replicates DNA. The replisome components work in precise coordination to unwind the double helix of the DNA and replicate the two strands simultaneously. The study of DNA replication using in vitro single-molecule approaches provides a novel quantitative understanding of the dynamics and mechanical principles that govern the operation of the replisome and its components. ‘Classical’ ensemble-averaging methods cannot obtain this information. Here we describe the main findings obtained with in vitro single-molecule methods on the performance of individual replisome components and reconstituted prokaryotic and eukaryotic replisomes. The emerging picture from these studies is that of stochastic, versatile and highly dynamic replisome machinery in which transient protein-protein and protein-DNA associations are responsible for robust DNA replication.
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Affiliation(s)
- Rebeca Bocanegra
- IMDEA Nanociencia, Faraday 9, Campus Cantoblanco, 28049 Madrid, Spain
| | - G A Ismael Plaza
- IMDEA Nanociencia, Faraday 9, Campus Cantoblanco, 28049 Madrid, Spain
| | - Carlos R Pulido
- IMDEA Nanociencia, Faraday 9, Campus Cantoblanco, 28049 Madrid, Spain
| | - Borja Ibarra
- IMDEA Nanociencia, Faraday 9, Campus Cantoblanco, 28049 Madrid, Spain
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12
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Abstract
Classical enzyme kinetic theories are summarized and linked with modern discoveries here. The sequential catalytic events along time axis by enzyme are analyzed at the molecular level, and by using master equations, this writing tries to connect the microscopic molecular behavior of enzyme to kinetic data (like velocity and catalytic coefficient k) obtained in experiment: 1/k = t equals to the sum of the times taken by the constituent individual steps. The relationships between catalytic coefficient k, catalytic rate or velocity, the amount of time taken by each step and physical or biochemical conditions of the system are discussed, and the perspective and hypothetic equations proposed here regarding diffusion, conformational change, chemical conversion, product release steps and the whole catalytic cycle provide an interpretation of previous experimental observations and can be testified by future experiments.
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13
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Fijen C, Mahmoud MM, Kronenberg M, Kaup R, Fontana M, Towle-Weicksel JB, Sweasy JB, Hohlbein J. Using single-molecule FRET to probe the nucleotide-dependent conformational landscape of polymerase β-DNA complexes. J Biol Chem 2020; 295:9012-9020. [PMID: 32385112 PMCID: PMC7335799 DOI: 10.1074/jbc.ra120.013049] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 05/07/2020] [Indexed: 11/06/2022] Open
Abstract
Eukaryotic DNA polymerase β (Pol β) plays an important role in cellular DNA repair, as it fills short gaps in dsDNA that result from removal of damaged bases. Since defects in DNA repair may lead to cancer and genetic instabilities, Pol β has been extensively studied, especially its mechanisms for substrate binding and a fidelity-related conformational change referred to as "fingers closing." Here, we applied single-molecule FRET to measure distance changes associated with DNA binding and prechemistry fingers movement of human Pol β. First, using a doubly labeled DNA construct, we show that Pol β bends the gapped DNA substrate less than indicated by previously reported crystal structures. Second, using acceptor-labeled Pol β and donor-labeled DNA, we visualized dynamic fingers closing in single Pol β-DNA complexes upon addition of complementary nucleotides and derived rates of conformational changes. We further found that, while incorrect nucleotides are quickly rejected, they nonetheless stabilize the polymerase-DNA complex, suggesting that Pol β, when bound to a lesion, has a strong commitment to nucleotide incorporation and thus repair. In summary, the observation and quantification of fingers movement in human Pol β reported here provide new insights into the delicate mechanisms of prechemistry nucleotide selection.
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Affiliation(s)
- Carel Fijen
- Laboratory of Biophysics, Wageningen University & Research, Wageningen, The Netherlands; Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, Connecticut, USA.
| | - Mariam M Mahmoud
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Meike Kronenberg
- Laboratory of Biophysics, Wageningen University & Research, Wageningen, The Netherlands
| | - Rebecca Kaup
- Laboratory of Biophysics, Wageningen University & Research, Wageningen, The Netherlands
| | - Mattia Fontana
- Laboratory of Biophysics, Wageningen University & Research, Wageningen, The Netherlands
| | - Jamie B Towle-Weicksel
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Joann B Sweasy
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Johannes Hohlbein
- Laboratory of Biophysics, Wageningen University & Research, Wageningen, The Netherlands; Microspectroscopy Research Facility, Wageningen University & Research, Wageningen, The Netherlands.
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14
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Craggs TD, Sustarsic M, Plochowietz A, Mosayebi M, Kaju H, Cuthbert A, Hohlbein J, Domicevica L, Biggin PC, Doye JPK, Kapanidis AN. Substrate conformational dynamics facilitate structure-specific recognition of gapped DNA by DNA polymerase. Nucleic Acids Res 2020; 47:10788-10800. [PMID: 31544938 PMCID: PMC6846080 DOI: 10.1093/nar/gkz797] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 09/02/2019] [Accepted: 09/18/2019] [Indexed: 01/23/2023] Open
Abstract
DNA-binding proteins utilise different recognition mechanisms to locate their DNA targets; some proteins recognise specific DNA sequences, while others interact with specific DNA structures. While sequence-specific DNA binding has been studied extensively, structure-specific recognition mechanisms remain unclear. Here, we study structure-specific DNA recognition by examining the structure and dynamics of DNA polymerase I Klenow Fragment (Pol) substrates both alone and in DNA–Pol complexes. Using a docking approach based on a network of 73 distances collected using single-molecule FRET, we determined a novel solution structure of the single-nucleotide-gapped DNA–Pol binary complex. The structure resembled existing crystal structures with regards to the downstream primer-template DNA substrate, and revealed a previously unobserved sharp bend (∼120°) in the DNA substrate; this pronounced bend was present in living cells. MD simulations and single-molecule assays also revealed that 4–5 nt of downstream gap-proximal DNA are unwound in the binary complex. Further, experiments and coarse-grained modelling showed the substrate alone frequently adopts bent conformations with 1–2 nt fraying around the gap, suggesting a mechanism wherein Pol recognises a pre-bent, partially-melted conformation of gapped DNA. We propose a general mechanism for substrate recognition by structure-specific enzymes driven by protein sensing of the conformational dynamics of their DNA substrates.
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Affiliation(s)
- Timothy D Craggs
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
| | - Marko Sustarsic
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
| | - Anne Plochowietz
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
| | - Majid Mosayebi
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK.,School of Physics, Institute for Research in Fundamental Sciences (IPM), Tehran 19538-33511, Iran
| | - Hendrik Kaju
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Andrew Cuthbert
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
| | - Johannes Hohlbein
- Laboratory of Biophysics, Wageningen University & Research, Wageningen 6708 WE, The Netherlands.,Microspectroscopy Research Facility Wageningen, Wageningen University & Research, Wageningen 6708 WE, The Netherlands
| | - Laura Domicevica
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Philip C Biggin
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Jonathan P K Doye
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Achillefs N Kapanidis
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
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15
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Kato H, Mutte SK, Suzuki H, Crespo I, Das S, Radoeva T, Fontana M, Yoshitake Y, Hainiwa E, van den Berg W, Lindhoud S, Ishizaki K, Hohlbein J, Borst JW, Boer DR, Nishihama R, Kohchi T, Weijers D. Design principles of a minimal auxin response system. NATURE PLANTS 2020; 6:473-482. [PMID: 32415296 DOI: 10.1038/s41477-020-0662-y] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 04/09/2020] [Indexed: 06/11/2023]
Abstract
Auxin controls numerous growth processes in land plants through a gene expression system that modulates ARF transcription factor activity1-3. Gene duplications in families encoding auxin response components have generated tremendous complexity in most land plants, and neofunctionalization enabled various unique response outputs during development1,3,4. However, it is unclear what fundamental biochemical principles underlie this complex response system. By studying the minimal system in Marchantia polymorpha, we derive an intuitive and simple model where a single auxin-dependent A-ARF activates gene expression. It is antagonized by an auxin-independent B-ARF that represses common target genes. The expression patterns of both ARF proteins define developmental zones where auxin response is permitted, quantitatively tuned or prevented. This fundamental design probably represents the ancestral system and formed the basis for inflated, complex systems.
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Affiliation(s)
- Hirotaka Kato
- Laboratory of Biochemistry, Wageningen University, Wageningen, The Netherlands
- Graduate School of Science, Kobe University, Kobe, Japan
| | - Sumanth K Mutte
- Laboratory of Biochemistry, Wageningen University, Wageningen, The Netherlands
| | - Hidemasa Suzuki
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Isidro Crespo
- Alba Synchrotron, Cerdanyola del Vallès, Barcelona, Spain
| | - Shubhajit Das
- Laboratory of Biochemistry, Wageningen University, Wageningen, The Netherlands
| | - Tatyana Radoeva
- Laboratory of Biochemistry, Wageningen University, Wageningen, The Netherlands
| | - Mattia Fontana
- Laboratory of Biochemistry, Wageningen University, Wageningen, The Netherlands
- Laboratory of Biophysics, Wageningen University, Wageningen, The Netherlands
| | | | - Emi Hainiwa
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Willy van den Berg
- Laboratory of Biochemistry, Wageningen University, Wageningen, The Netherlands
| | - Simon Lindhoud
- Laboratory of Biochemistry, Wageningen University, Wageningen, The Netherlands
| | | | - Johannes Hohlbein
- Laboratory of Biophysics, Wageningen University, Wageningen, The Netherlands
| | - Jan Willem Borst
- Laboratory of Biochemistry, Wageningen University, Wageningen, The Netherlands
| | - D Roeland Boer
- Alba Synchrotron, Cerdanyola del Vallès, Barcelona, Spain
| | | | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University, Wageningen, The Netherlands.
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16
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Liptak C, Mahmoud MM, Eckenroth BE, Moreno MV, East K, Alnajjar KS, Huang J, Towle-Weicksel JB, Doublié S, Loria J, Sweasy JB. I260Q DNA polymerase β highlights precatalytic conformational rearrangements critical for fidelity. Nucleic Acids Res 2019; 46:10740-10756. [PMID: 30239932 PMCID: PMC6237750 DOI: 10.1093/nar/gky825] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 09/05/2018] [Indexed: 11/14/2022] Open
Abstract
DNA polymerase β (pol β) fills single nucleotide gaps in DNA during base excision repair and non-homologous end-joining. Pol β must select the correct nucleotide from among a pool of four nucleotides with similar structures and properties in order to maintain genomic stability during DNA repair. Here, we use a combination of X-ray crystallography, fluorescence resonance energy transfer and nuclear magnetic resonance to show that pol β‘s ability to access the appropriate conformations both before and upon binding to nucleotide substrates is integral to its fidelity. Importantly, we also demonstrate that the inability of the I260Q mutator variant of pol β to properly navigate this conformational landscape results in error-prone DNA synthesis. Our work reveals that precatalytic conformational rearrangements themselves are an important underlying mechanism of substrate selection by DNA pol β.
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Affiliation(s)
- Cary Liptak
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Mariam M Mahmoud
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Brian E Eckenroth
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT 05405, USA
| | - Marcus V Moreno
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT 05405, USA
| | - Kyle East
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
| | - Khadijeh S Alnajjar
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Ji Huang
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Jamie B Towle-Weicksel
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Sylvie Doublié
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT 05405, USA
| | - J Patrick Loria
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
- To whom correspondence should be addressed. Tel: +203 436 2518; Fax: +203 436 6144; . Correspondence may also be addressed to Joann B. Sweasy. Tel: +203 737 2626; Fax: +203 785 6309;
| | - Joann B Sweasy
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06520, USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
- To whom correspondence should be addressed. Tel: +203 436 2518; Fax: +203 436 6144; . Correspondence may also be addressed to Joann B. Sweasy. Tel: +203 737 2626; Fax: +203 785 6309;
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17
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Gong W, Das P, Samanta S, Xiong J, Pan W, Gu Z, Zhang J, Qu J, Yang Z. Redefining the photo-stability of common fluorophores with triplet state quenchers: mechanistic insights and recent updates. Chem Commun (Camb) 2019; 55:8695-8704. [PMID: 31073568 DOI: 10.1039/c9cc02616a] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Light microscopy can offer certain advantages over electron microscopy in terms of acquiring detailed insights into the biological/intra-cellular milieu. In recent years, with the development of new fluorescence imaging technologies, it has become extremely important to assess the role of designing appropriate fluorophores in acquiring desired biological information without encountering any untoward hitches. Over the years, external fluorophores have been prevalently used in fluorescence microscopy and single-molecule fluorescence microscopy-based studies. Photostable fluorogenic probes with high extinction coefficients and quantum yields, exhibiting minimum autofluorescence and photobleaching properties, are preferred in single-molecule microscopy as they can tolerate long-term laser exposure. Therefore, the development of triplet state quenchers and/or any other suitable new strategy to ensure the photo-stability of the fluorophores during long-term live cell imaging exercises is highly anticipated. In this feature article, various strategies for stabilizing fluorophores, including the mechanisms of TSQ-induced stabilization, have been thoroughly reviewed considering contemporary literature reports and applications.
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Affiliation(s)
- Wanjun Gong
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China.
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18
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Fontana M, Fijen C, Lemay SG, Mathwig K, Hohlbein J. High-throughput, non-equilibrium studies of single biomolecules using glass-made nanofluidic devices. LAB ON A CHIP 2018; 19:79-86. [PMID: 30468446 DOI: 10.1039/c8lc01175c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Single-molecule detection schemes offer powerful means to overcome static and dynamic heterogeneity inherent to complex samples. However, probing biomolecular interactions and reactions with high throughput and time resolution remains challenging, often requiring surface-immobilized entities. Here, we introduce glass-made nanofluidic devices for the high-throughput detection of freely-diffusing single biomolecules by camera-based fluorescence microscopy. Nanochannels of 200 nm height and a width of several micrometers confine the movement of biomolecules. Using pressure-driven flow through an array of parallel nanochannels and by tracking the movement of fluorescently labelled DNA oligonucleotides, we observe conformational changes with high throughput. In a device geometry featuring a T-shaped junction of nanochannels, we drive steady-state non-equilibrium conditions by continuously mixing reactants and triggering chemical reactions. We use the device to probe the conformational equilibrium of a DNA hairpin as well as to continuously observe DNA synthesis in real time. Our platform offers a straightforward and robust method for studying reaction kinetics at the single-molecule level.
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Affiliation(s)
- Mattia Fontana
- Laboratory of Biophysics, Wageningen University and Research, Stippeneng 4, Wageningen, 6708 WE, The Netherlands
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19
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Schmid S, Hugel T. Efficient use of single molecule time traces to resolve kinetic rates, models and uncertainties. J Chem Phys 2018; 148:123312. [PMID: 29604821 DOI: 10.1063/1.5006604] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Single molecule time traces reveal the time evolution of unsynchronized kinetic systems. Especially single molecule Förster resonance energy transfer (smFRET) provides access to enzymatically important time scales, combined with molecular distance resolution and minimal interference with the sample. Yet the kinetic analysis of smFRET time traces is complicated by experimental shortcomings-such as photo-bleaching and noise. Here we recapitulate the fundamental limits of single molecule fluorescence that render the classic, dwell-time based kinetic analysis unsuitable. In contrast, our Single Molecule Analysis of Complex Kinetic Sequences (SMACKS) considers every data point and combines the information of many short traces in one global kinetic rate model. We demonstrate the potential of SMACKS by resolving the small kinetic effects caused by different ionic strengths in the chaperone protein Hsp90. These results show an unexpected interrelation between conformational dynamics and ATPase activity in Hsp90.
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Affiliation(s)
- Sonja Schmid
- Institute of Physical Chemistry II, University of Freiburg, Albertstr. 23 a, 79104 Freiburg, Germany
| | - Thorsten Hugel
- Institute of Physical Chemistry II, University of Freiburg, Albertstr. 23 a, 79104 Freiburg, Germany
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20
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Pusuluk O, Farrow T, Deliduman C, Burnett K, Vedral V. Proton tunnelling in hydrogen bonds and its implications in an induced-fit model of enzyme catalysis. Proc Math Phys Eng Sci 2018. [DOI: 10.1098/rspa.2018.0037] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The role of proton tunnelling in biological catalysis is investigated here within the frameworks of quantum information theory and thermodynamics. We consider the quantum correlations generated through two hydrogen bonds between a substrate and a prototypical enzyme that first catalyses the tautomerization of the substrate to move on to a subsequent catalysis, and discuss how the enzyme can derive its catalytic potency from these correlations. In particular, we show that classical changes induced in the binding site of the enzyme spreads the quantum correlations among all of the four hydrogen-bonded atoms thanks to the directionality of hydrogen bonds. If the enzyme rapidly returns to its initial state after the binding stage, the substrate ends in a new transition state corresponding to a quantum superposition. Open quantum system dynamics can then naturally drive the reaction in the forward direction from the major tautomeric form to the minor tautomeric form without needing any additional catalytic activity. We find that in this scenario the enzyme lowers the activation energy so much that there is no energy barrier left in the tautomerization, even if the quantum correlations quickly decay.
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Affiliation(s)
- Onur Pusuluk
- Department of Physics, İstanbul Technical University, Maslak, Istanbul 34469, Turkey
| | - Tristan Farrow
- Department of Physics, University of Oxford, Parks Road, Oxford OX1 3PU, UK
- Centre for Quantum Technologies, National University of Singapore, 3 Science Drive 2, Singapore 117543, Singapore
| | - Cemsinan Deliduman
- Department of Physics, Mimar Sinan Fine Arts University, Bomonti, Istanbul 34380, Turkey
| | - Keith Burnett
- University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Vlatko Vedral
- Department of Physics, University of Oxford, Parks Road, Oxford OX1 3PU, UK
- Centre for Quantum Technologies, National University of Singapore, 3 Science Drive 2, Singapore 117543, Singapore
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21
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Duchi D, Mazumder A, Malinen AM, Ebright RH, Kapanidis AN. The RNA polymerase clamp interconverts dynamically among three states and is stabilized in a partly closed state by ppGpp. Nucleic Acids Res 2018; 46:7284-7295. [PMID: 29878276 PMCID: PMC6101503 DOI: 10.1093/nar/gky482] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Revised: 05/09/2018] [Accepted: 05/16/2018] [Indexed: 02/06/2023] Open
Abstract
RNA polymerase (RNAP) contains a mobile structural module, the 'clamp,' that forms one wall of the RNAP active-center cleft and that has been linked to crucial aspects of the transcription cycle, including promoter melting, transcription elongation complex stability, transcription pausing, and transcription termination. Using single-molecule FRET on surface-immobilized RNAP molecules, we show that the clamp in RNAP holoenzyme populates three distinct conformational states and interconvert between these states on the 0.1-1 s time-scale. Similar studies confirm that the RNAP clamp is closed in open complex (RPO) and in initial transcribing complexes (RPITC), including paused initial transcribing complexes, and show that, in these complexes, the clamp does not exhibit dynamic behaviour. We also show that, the stringent-response alarmone ppGpp, which reprograms transcription during amino acid starvation stress, selectively stabilizes the partly-closed-clamp state and prevents clamp opening; these results raise the possibility that ppGpp controls promoter opening by modulating clamp dynamics.
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Affiliation(s)
- Diego Duchi
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
| | - Abhishek Mazumder
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
- Waksman Institute of Microbiology and Department of Chemistry, Rutgers University, Piscataway, NJ 08854, USA
| | - Anssi M Malinen
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
| | - Richard H Ebright
- Waksman Institute of Microbiology and Department of Chemistry, Rutgers University, Piscataway, NJ 08854, USA
| | - Achillefs N Kapanidis
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
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22
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Fijen C, Montón Silva A, Hochkoeppler A, Hohlbein J. A single-molecule FRET sensor for monitoring DNA synthesis in real time. Phys Chem Chem Phys 2018; 19:4222-4230. [PMID: 28116374 DOI: 10.1039/c6cp05919h] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We developed a versatile DNA assay and framework for monitoring polymerization of DNA in real time and at the single-molecule level. The assay consists of an acceptor labelled DNA primer annealed to a DNA template that is labelled on its single stranded, downstream overhang with a donor fluorophore. Upon extension of the primer using a DNA polymerase, the overhang of the template alters its conformation from a random coil to the canonical structure of double stranded DNA. This conformational change increases the distance between the donor and the acceptor fluorophore and can be detected as a decrease in the Förster resonance energy transfer (FRET) efficiency between both fluorophores. Remarkably, the DNA assay does not require any modification of the DNA polymerase and albeit the simple and robust spectroscopic readout facilitates measurements even with conventional fluorimeters or stopped-flow equipment, single-molecule FRET provides additional access to parameters such as the processivity of DNA synthesis and, for one of the three DNA polymerases tested, the detection of binding and dissociation of the DNA polymerase to DNA. We furthermore demonstrate that primer extensions by a single base can be resolved.
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Affiliation(s)
- Carel Fijen
- Laboratory of Biophysics, Wageningen University and Research, Stippeneng 4, Wageningen, 6708 WE, The Netherlands.
| | - Alejandro Montón Silva
- Laboratory of Biophysics, Wageningen University and Research, Stippeneng 4, Wageningen, 6708 WE, The Netherlands. and Department of Pharmacy and Biotechnology, University of Bologna, Viale Risorgimento 4, Bologna, 40136, Italy
| | - Alejandro Hochkoeppler
- Department of Pharmacy and Biotechnology, University of Bologna, Viale Risorgimento 4, Bologna, 40136, Italy
| | - Johannes Hohlbein
- Laboratory of Biophysics, Wageningen University and Research, Stippeneng 4, Wageningen, 6708 WE, The Netherlands. and Microspectroscopy Centre, Wageningen University and Research, Stippeneng 4, Wageningen, 6708 WE, The Netherlands
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23
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Recent progress in dissecting molecular recognition by DNA polymerases with non-native substrates. Curr Opin Chem Biol 2017; 41:43-49. [PMID: 29096323 DOI: 10.1016/j.cbpa.2017.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 10/05/2017] [Indexed: 11/22/2022]
Abstract
DNA polymerases must discriminate the correct Watson-Crick base pair-forming deoxynucleoside triphosphate (dNTP) substrate from three other dNTPs and additional triphosphates found in the cell. The rarity of misincorporations in vivo, then, belies the high tolerance for dNTP analogs observed in vitro. Advances over the last 10 years in single-molecule fluorescence and electronic detection of dNTP analog incorporation enable exploration of the mechanism and limits to base discrimination by DNA polymerases. Such studies reveal transient motions of DNA polymerase during substrate recognition and mutagenesis in the context of erroneous dNTP incorporation that can lead to evolution and genetic disease. Further improvements in time resolution and noise reduction of single-molecule studies will uncover deeper mechanistic understanding of this critical, first step in evolution.
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24
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Vyas R, Reed AJ, Raper AT, Zahurancik WJ, Wallenmeyer PC, Suo Z. Structural basis for the D-stereoselectivity of human DNA polymerase β. Nucleic Acids Res 2017; 45:6228-6237. [PMID: 28402499 PMCID: PMC5449621 DOI: 10.1093/nar/gkx252] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 03/24/2017] [Accepted: 04/03/2017] [Indexed: 12/20/2022] Open
Abstract
Nucleoside reverse transcriptase inhibitors (NRTIs) with L-stereochemistry have long been an effective treatment for viral infections because of the strong D-stereoselectivity exhibited by human DNA polymerases relative to viral reverse transcriptases. The D-stereoselectivity of DNA polymerases has only recently been explored structurally and all three DNA polymerases studied to date have demonstrated unique stereochemical selection mechanisms. Here, we have solved structures of human DNA polymerase β (hPolβ), in complex with single-nucleotide gapped DNA and L-nucleotides and performed pre-steady-state kinetic analysis to determine the D-stereoselectivity mechanism of hPolβ. Beyond a similar 180° rotation of the L-nucleotide ribose ring seen in other studies, the pre-catalytic ternary crystal structures of hPolβ, DNA and L-dCTP or the triphosphate forms of antiviral drugs lamivudine ((-)3TC-TP) and emtricitabine ((-)FTC-TP) provide little structural evidence to suggest that hPolβ follows the previously characterized mechanisms of D-stereoselectivity. Instead, hPolβ discriminates against L-stereochemistry through accumulation of several active site rearrangements that lead to a decreased nucleotide binding affinity and incorporation rate. The two NRTIs escape some of the active site selection through the base and sugar modifications but are selected against through the inability of hPolβ to complete thumb domain closure.
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Affiliation(s)
- Rajan Vyas
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Andrew J. Reed
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- The Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
| | - Austin T. Raper
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- The Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
| | - Walter J. Zahurancik
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- The Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
| | - Petra C. Wallenmeyer
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Zucai Suo
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- The Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
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25
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Gardini S, Furini S, Santucci A, Niccolai N. A structural bioinformatics investigation on protein–DNA complexes delineates their modes of interaction. MOLECULAR BIOSYSTEMS 2017; 13:1010-1017. [DOI: 10.1039/c7mb00071e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
A non-redundant dataset of 629 protein–DNA complexes has been used to investigate on amino acid composition of protein-DNA interfaces. Structural proteins, transcription factors and DNA-related enzymes show specific patterns accounting for different modes of their interaction with DNA.
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Affiliation(s)
- Simone Gardini
- Department of Biotechnology
- Chemistry and Pharmacy
- University of Siena
- Italy
| | - Simone Furini
- Department of Medical Biotechnologies
- University of Siena
- Siena
- Italy
| | - Annalisa Santucci
- Department of Biotechnology
- Chemistry and Pharmacy
- University of Siena
- Italy
| | - Neri Niccolai
- Department of Biotechnology
- Chemistry and Pharmacy
- University of Siena
- Italy
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26
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Meli M, Sustarsic M, Craggs TD, Kapanidis AN, Colombo G. DNA Polymerase Conformational Dynamics and the Role of Fidelity-Conferring Residues: Insights from Computational Simulations. Front Mol Biosci 2016; 3:20. [PMID: 27303671 PMCID: PMC4882331 DOI: 10.3389/fmolb.2016.00020] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 05/10/2016] [Indexed: 12/11/2022] Open
Abstract
Herein we investigate the molecular bases of DNA polymerase I conformational dynamics that underlie the replication fidelity of the enzyme. Such fidelity is determined by conformational changes that promote the rejection of incorrect nucleotides before the chemical ligation step. We report a comprehensive atomic resolution study of wild type and mutant enzymes in different bound states and starting from different crystal structures, using extensive molecular dynamics (MD) simulations that cover a total timespan of ~5 ms. The resulting trajectories are examined via a combination of novel methods of internal dynamics and energetics analysis, aimed to reveal the principal molecular determinants for the (de)stabilization of a certain conformational state. Our results show that the presence of fidelity-decreasing mutations or the binding of incorrect nucleotides in ternary complexes tend to favor transitions from closed toward open structures, passing through an ensemble of semi-closed intermediates. The latter ensemble includes the experimentally observed ajar conformation which, consistent with previous experimental observations, emerges as a molecular checkpoint for the selection of the correct nucleotide to incorporate. We discuss the implications of our results for the understanding of the relationships between the structure, dynamics, and function of DNA polymerase I at the atomistic level.
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Affiliation(s)
- Massimiliano Meli
- Computational Biochemistry Group, Istituto di Chimica del Riconoscimento Molecolare, National Research Council of Italy Milano, Italy
| | - Marko Sustarsic
- Clarendon Laboratory, Department of Physics, Biological Physics Research Group, University of Oxford Oxford, UK
| | - Timothy D Craggs
- Clarendon Laboratory, Department of Physics, Biological Physics Research Group, University of Oxford Oxford, UK
| | - Achillefs N Kapanidis
- Clarendon Laboratory, Department of Physics, Biological Physics Research Group, University of Oxford Oxford, UK
| | - Giorgio Colombo
- Computational Biochemistry Group, Istituto di Chimica del Riconoscimento Molecolare, National Research Council of Italy Milano, Italy
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Assembly, translocation, and activation of XerCD-dif recombination by FtsK translocase analyzed in real-time by FRET and two-color tethered fluorophore motion. Proc Natl Acad Sci U S A 2015; 112:E5133-41. [PMID: 26324908 DOI: 10.1073/pnas.1510814112] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The FtsK dsDNA translocase functions in bacterial chromosome unlinking by activating XerCD-dif recombination in the replication terminus region. To analyze FtsK assembly and translocation, and the subsequent activation of XerCD-dif recombination, we extended the tethered fluorophore motion technique, using two spectrally distinct fluorophores to monitor two effective lengths along the same tethered DNA molecule. We observed that FtsK assembled stepwise on DNA into a single hexamer, and began translocation rapidly (∼ 0.25 s). Without extruding DNA loops, single FtsK hexamers approached XerCD-dif and resided there for ∼ 0.5 s irrespective of whether XerCD-dif was synapsed or unsynapsed. FtsK then dissociated, rather than reversing. Infrequently, FtsK activated XerCD-dif recombination when it encountered a preformed synaptic complex, and dissociated before the completion of recombination, consistent with each FtsK-XerCD-dif encounter activating only one round of recombination.
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