1
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Mandal S, Ganesh KN, Maiti PK. Dynamics of terminal fraying-peeling and hydrogen bonds dictates the sequential vs. cooperative melting pathways of nanoscale DNA and PNA triplexes. NANOSCALE 2024; 16:13029-13040. [PMID: 38904319 DOI: 10.1039/d4nr01104j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
Peptide nucleic acids (PNAs) are charge-neutral synthetic DNA/RNA analogues. In many aspects of biology and biotechnology, the details of DNA and PNA melting reaction coordinates are crucial, and their associative/dissociative details remain inadequately understood. In the current study, we have attempted to gain insights into comparative melting pathways and binding affinity of iso-sequences of an 18-mer PNA-DNA-PNA triplex and the analogous DNA-DNA-DNA triplex, and DNA-DNA and PNA-DNA duplexes. It is intriguing that while the DNA-DNA-DNA triplex melts in two sequential steps, the PNA-DNA-PNA triplex melts in a single step and the mechanistic aspects for this difference are still not clear. We report an all-atom molecular dynamics simulation of both complexes in the temperature range of 300 to 500 K with 20 K intervals. Based on the trajectory analysis, we provide evidence that the association and dissociation are dictated by the differences in fraying-peeling effects from either terminus to the center in a zipper pattern among the PNA-DNA-PNA triplex and DNA-DNA-DNA triplexes. These are shown to be governed by the different characteristics of H-bonding, RMSD, and Free Energy Landscape (FEL) as analyzed by PCA, leading to the DNA-DNA-DNA triplex exhibiting sequential melting, while the PNA-DNA-PNA triplex shows cooperative melting of the whole fragment in a single-step. The PNA-DNA-PNA triplex base pairs are thermodynamically more stable than the DNA-DNA-DNA triplex, with the binding affinity of PNA-TFO to the PNA : DNA duplex being higher than that of DNA-TFO to the DNA : DNA duplex. The investigation of the association/dissociation of PNA-TFO to the PNA-DNA duplex has relevance and importance in the emerging effective applications of oligonucleotide therapy.
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Affiliation(s)
- Sandip Mandal
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India.
| | - Krishna N Ganesh
- Jawaharlal Nehru Center for Advanced Scientific Research (JNCASR), Jakkur, Bengaluru 560064, India.
| | - Prabal K Maiti
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India.
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2
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Zhou Y, Tang Q, Zhao X, Zeng X, Chong C, Yan J. A novel design for magnetic tweezers with wide-range temperature control. Biophys J 2023; 122:3860-3868. [PMID: 37563833 PMCID: PMC10560670 DOI: 10.1016/j.bpj.2023.08.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 06/19/2023] [Accepted: 08/07/2023] [Indexed: 08/12/2023] Open
Abstract
Single-molecule manipulation technologies have proven to be powerful tools for studying the molecular mechanisms and physical principles underlying many essential biological processes. However, achieving wide-range temperature control has been challenging due to thermal drift that undermines the stability of the instrument. This limitation has made it difficult to study biomolecules from thermophiles at their physiologically relevant temperatures and has also hindered the convenient measurement of temperature-sensitive biomolecular interactions and the fundamental thermodynamic properties of biomolecules. In this work, we present a novel design of magnetic tweezers that uses a reflective coverslip and dry objective lens to insulate the heat conductance between the sample and the objective lens, enabling stable temperature changes from ambient up to 70°C during experiments without significant thermal drift of the instrument. The performance of the technology is demonstrated through the quantification of the free energy change of a DNA hairpin over a temperature range of 22°C-72°C, from which the entropy and enthalpy changes are determined.
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Affiliation(s)
- Yu Zhou
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore
| | - Qingnan Tang
- Department of Physics, National University of Singapore, Singapore, Singapore
| | - Xiaodan Zhao
- Department of Physics, National University of Singapore, Singapore, Singapore; Centre for Bioimaging Sciences, National University of Singapore, Singapore, Singapore
| | - Xiangjun Zeng
- Department of Physics, National University of Singapore, Singapore, Singapore
| | - Clarence Chong
- Department of Physics, National University of Singapore, Singapore, Singapore
| | - Jie Yan
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore; Department of Physics, National University of Singapore, Singapore, Singapore; Centre for Bioimaging Sciences, National University of Singapore, Singapore, Singapore; Joint School of National University of Singapore and Tianjin University, International Campus of Tianjin University, Binhai New City, Fuzhou, China.
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3
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Qiao YP, Ren CL, Ma YQ. Two Different Ways of Stress Release in Supercoiled DNA Minicircles under DNA Nick. J Phys Chem B 2023; 127:4015-4021. [PMID: 37126597 DOI: 10.1021/acs.jpcb.2c08618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
It is generally believed that DNA nick is an effective way to release stress in supercoiled DNA, resulting from the twisting motion that individual strands rotate around the axis of the DNA helix. Here, we use MD simulations based on the oxDNA model to investigate the relaxation of 336 bp supercoiled minicircular DNA under DNA nick. Our simulations show that stress release, characterized by the abrupt decrease in linking number, may be induced by two types of DNA motion depending on the nick position. Except for the twisting motion, there is a writhing motion, that is, double strands collectively rotating with one plectoneme removal, which may occur in the process of DNA relaxation with the nick position in the loop region. Moreover, the writhing motion is more likely to occur in the DNA with relatively high hardness, such as C-G pairs. Our simulation results uncover the relationship between structural transformation, stress release, and DNA motion during the dynamic process under DNA nick, indicating the influence of nick position on the relaxation of the supercoiled DNA.
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Affiliation(s)
- Ye-Peng Qiao
- National Laboratory of Solid State Microstructures and Department of Physics, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Chun-Lai Ren
- National Laboratory of Solid State Microstructures and Department of Physics, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Yu-Qiang Ma
- National Laboratory of Solid State Microstructures and Department of Physics, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
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4
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Salerno D, Marrano CA, Cassina V, Cristofalo M, Shao Q, Finzi L, Mantegazza F, Dunlap D. Nanomechanics of negatively supercoiled diaminopurine-substituted DNA. Nucleic Acids Res 2021; 49:11778-11786. [PMID: 34718727 PMCID: PMC8599871 DOI: 10.1093/nar/gkab982] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 10/05/2021] [Accepted: 10/13/2021] [Indexed: 11/25/2022] Open
Abstract
Single molecule experiments have demonstrated a progressive transition from a B- to an L-form helix as DNA is gently stretched and progressively unwound. The particular sequence of a DNA segment defines both base stacking and hydrogen bonding that affect the partitioning and conformations of the two phases. Naturally or artificially modified bases alter H-bonds and base stacking and DNA with diaminopurine (DAP) replacing adenine was synthesized to produce linear fragments with triply hydrogen-bonded DAP:T base pairs. Both unmodified and DAP-substituted DNA transitioned from a B- to an L-helix under physiological conditions of mild tension and unwinding. This transition avoids writhing and the ease of this transition may prevent cumbersome topological rearrangements in genomic DNA that would require topoisomerase activity to resolve. L-DNA displayed about tenfold lower persistence length than B-DNA. However, left-handed DAP-substituted DNA was twice as stiff as unmodified L-DNA. Unmodified DNA and DAP-substituted DNA have very distinct mechanical characteristics at physiological levels of negative supercoiling and tension.
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Affiliation(s)
- Domenico Salerno
- School of Medicine and Surgery, BioNanoMedicine Center NANOMIB, Università di Milano-Bicocca, via R. Follereau 3, Vedano al Lambro (MB), Italy
| | - Claudia Adriana Marrano
- School of Medicine and Surgery, BioNanoMedicine Center NANOMIB, Università di Milano-Bicocca, via R. Follereau 3, Vedano al Lambro (MB), Italy
| | - Valeria Cassina
- School of Medicine and Surgery, BioNanoMedicine Center NANOMIB, Università di Milano-Bicocca, via R. Follereau 3, Vedano al Lambro (MB), Italy
| | - Matteo Cristofalo
- School of Medicine and Surgery, BioNanoMedicine Center NANOMIB, Università di Milano-Bicocca, via R. Follereau 3, Vedano al Lambro (MB), Italy
| | - Qing Shao
- Department of Physics, Emory University, Atlanta, GA USA
| | - Laura Finzi
- Department of Physics, Emory University, Atlanta, GA USA
| | - Francesco Mantegazza
- School of Medicine and Surgery, BioNanoMedicine Center NANOMIB, Università di Milano-Bicocca, via R. Follereau 3, Vedano al Lambro (MB), Italy
| | - David Dunlap
- Department of Physics, Emory University, Atlanta, GA USA
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5
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Buglione E, Salerno D, Marrano CA, Cassina V, Vesco G, Nardo L, Dacasto M, Rigo R, Sissi C, Mantegazza F. Nanomechanics of G-quadruplexes within the promoter of the KIT oncogene. Nucleic Acids Res 2021; 49:4564-4573. [PMID: 33849064 PMCID: PMC8096272 DOI: 10.1093/nar/gkab079] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 01/07/2021] [Accepted: 04/09/2021] [Indexed: 12/31/2022] Open
Abstract
G-quadruplexes (G4s) are tetrahelical DNA structures stabilized by four guanines paired via Hoogsteen hydrogen bonds into quartets. While their presence within eukaryotic DNA is known to play a key role in regulatory processes, their functional mechanisms are still under investigation. In the present work, we analysed the nanomechanical properties of three G4s present within the promoter of the KIT proto-oncogene from a single-molecule point of view through the use of magnetic tweezers (MTs). The study of DNA extension fluctuations under negative supercoiling allowed us to identify a characteristic fingerprint of G4 folding. We further analysed the energetic contribution of G4 to the double-strand denaturation process in the presence of negative supercoiling, and we observed a reduction in the energy required for strands separation.
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Affiliation(s)
- Enrico Buglione
- School of Medicine and Surgery, BioNanoMedicine Center NANOMIB, University of Milano-Bicocca, 20854 Vedano al Lambro (MB), Italy
| | - Domenico Salerno
- School of Medicine and Surgery, BioNanoMedicine Center NANOMIB, University of Milano-Bicocca, 20854 Vedano al Lambro (MB), Italy
| | - Claudia Adriana Marrano
- School of Medicine and Surgery, BioNanoMedicine Center NANOMIB, University of Milano-Bicocca, 20854 Vedano al Lambro (MB), Italy
| | - Valeria Cassina
- School of Medicine and Surgery, BioNanoMedicine Center NANOMIB, University of Milano-Bicocca, 20854 Vedano al Lambro (MB), Italy
| | - Guglielmo Vesco
- School of Medicine and Surgery, BioNanoMedicine Center NANOMIB, University of Milano-Bicocca, 20854 Vedano al Lambro (MB), Italy
| | - Luca Nardo
- School of Medicine and Surgery, BioNanoMedicine Center NANOMIB, University of Milano-Bicocca, 20854 Vedano al Lambro (MB), Italy
| | - Mauro Dacasto
- Department of Comparative Biomedicine and Food Science, University of Padova, 35020 Legnaro (PD), Italy
| | - Riccardo Rigo
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, 35131 Padova (PD), Italy
| | - Claudia Sissi
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, 35131 Padova (PD), Italy.,Interdepartmental Research Center for Innovative Biotechnologies (CRIBI), University of Padova, 35121 Padova (PD), Italy
| | - Francesco Mantegazza
- School of Medicine and Surgery, BioNanoMedicine Center NANOMIB, University of Milano-Bicocca, 20854 Vedano al Lambro (MB), Italy
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6
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Seifert M, van Nies P, Papini FS, Arnold JJ, Poranen MM, Cameron CE, Depken M, Dulin D. Temperature controlled high-throughput magnetic tweezers show striking difference in activation energies of replicating viral RNA-dependent RNA polymerases. Nucleic Acids Res 2020; 48:5591-5602. [PMID: 32286652 PMCID: PMC7261197 DOI: 10.1093/nar/gkaa233] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 03/10/2020] [Accepted: 03/30/2020] [Indexed: 01/05/2023] Open
Abstract
RNA virus survival depends on efficient viral genome replication, which is performed by the viral RNA dependent RNA polymerase (RdRp). The recent development of high throughput magnetic tweezers has enabled the simultaneous observation of dozens of viral RdRp elongation traces on kilobases long templates, and this has shown that RdRp nucleotide addition kinetics is stochastically interrupted by rare pauses of 1-1000 s duration, of which the short-lived ones (1-10 s) are the temporal signature of a low fidelity catalytic pathway. We present a simple and precise temperature controlled system for magnetic tweezers to characterize the replication kinetics temperature dependence between 25°C and 45°C of RdRps from three RNA viruses, i.e. the double-stranded RNA bacteriophage Φ6, and the positive-sense single-stranded RNA poliovirus (PV) and human rhinovirus C (HRV-C). We found that Φ6 RdRp is largely temperature insensitive, while PV and HRV-C RdRps replication kinetics are activated by temperature. Furthermore, the activation energies we measured for PV RdRp catalytic state corroborate previous estimations from ensemble pre-steady state kinetic studies, further confirming the catalytic origin of the short pauses and their link to temperature independent RdRp fidelity. This work will enable future temperature controlled study of biomolecular complex at the single molecule level.
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Affiliation(s)
- Mona Seifert
- Junior Research Group 2, Interdisciplinary Center for Clinical Research, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Cauerstr. 3, 91058 Erlangen, Germany
| | - Pauline van Nies
- Junior Research Group 2, Interdisciplinary Center for Clinical Research, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Cauerstr. 3, 91058 Erlangen, Germany
| | - Flávia S Papini
- Junior Research Group 2, Interdisciplinary Center for Clinical Research, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Cauerstr. 3, 91058 Erlangen, Germany
| | - Jamie J Arnold
- Department of Microbiology and Immunology, School of Medicine, The University of North Carolina Chapel Hill, 6012 Marsico Hall, CB 7290 Mason Farm Road, NC 27599, USA
| | - Minna M Poranen
- Molecular and Integrative Biosciences Research Program, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikki Biocenter 1, P.O. Box 56 (Viikinkaari 9), 00014 Helsinki, Finland
| | - Craig E Cameron
- Department of Microbiology and Immunology, School of Medicine, The University of North Carolina Chapel Hill, 6012 Marsico Hall, CB 7290 Mason Farm Road, NC 27599, USA
| | - Martin Depken
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands,Correspondence may also be addressed to Martin Depken. Tel: +31 15 27 81305;
| | - David Dulin
- Junior Research Group 2, Interdisciplinary Center for Clinical Research, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Cauerstr. 3, 91058 Erlangen, Germany,To whom correspondence should be addressed. Tel: +49 9131 85 70347; Fax: +49 9131 85 35903;
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7
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Kriegel F, Matek C, Dršata T, Kulenkampff K, Tschirpke S, Zacharias M, Lankaš F, Lipfert J. The temperature dependence of the helical twist of DNA. Nucleic Acids Res 2018; 46:7998-8009. [PMID: 30053087 PMCID: PMC6125625 DOI: 10.1093/nar/gky599] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 06/08/2018] [Accepted: 07/20/2018] [Indexed: 01/11/2023] Open
Abstract
DNA is the carrier of all cellular genetic information and increasingly used in nanotechnology. Quantitative understanding and optimization of its functions requires precise experimental characterization and accurate modeling of DNA properties. A defining feature of DNA is its helicity. DNA unwinds with increasing temperature, even for temperatures well below the melting temperature. However, accurate quantitation of DNA unwinding under external forces and a microscopic understanding of the corresponding structural changes are currently lacking. Here we combine single-molecule magnetic tweezers measurements with atomistic molecular dynamics and coarse-grained simulations to obtain a comprehensive view of the temperature dependence of DNA twist. Experimentally, we find that DNA twist changes by ΔTw(T) = (-11.0 ± 1.2)°/(°C·kbp), independent of applied force, in the range of forces where torque-induced melting is negligible. Our atomistic simulations predict ΔTw(T) = (-11.1 ± 0.3)°/(°C·kbp), in quantitative agreement with experiments, and suggest that the untwisting of DNA with temperature is predominantly due to changes in DNA structure for defined backbone substates, while the effects of changes in substate populations are minor. Coarse-grained simulations using the oxDNA framework yield a value of ΔTw(T) = (-6.4 ± 0.2)°/(°C·kbp) in semi-quantitative agreement with experiments.
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Affiliation(s)
- Franziska Kriegel
- Department of Physics, Nanosystems Initiative Munich, and Center for Nanoscience, LMU Munich, Amalienstr. 54, 80799 Munich, Germany
| | - Christian Matek
- Technical University of Munich and Institute of Computational Biology, Helmholtz Zentrum München-German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
| | - Tomáš Dršata
- Department of Informatics and Chemistry, University of Chemistry and Technology Prague, Technická 5, 166 28 Prague, Czech Republic
| | - Klara Kulenkampff
- Department of Physics, Nanosystems Initiative Munich, and Center for Nanoscience, LMU Munich, Amalienstr. 54, 80799 Munich, Germany
| | - Sophie Tschirpke
- Department of Physics, Nanosystems Initiative Munich, and Center for Nanoscience, LMU Munich, Amalienstr. 54, 80799 Munich, Germany
| | - Martin Zacharias
- Physics-Department T38, Technical University of Munich, James-Franck-Strasse 1, 85748 Garching, Germany
| | - Filip Lankaš
- Department of Informatics and Chemistry, University of Chemistry and Technology Prague, Technická 5, 166 28 Prague, Czech Republic
| | - Jan Lipfert
- Department of Physics, Nanosystems Initiative Munich, and Center for Nanoscience, LMU Munich, Amalienstr. 54, 80799 Munich, Germany
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8
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TFIIH generates a six-base-pair open complex during RNAP II transcription initiation and start-site scanning. Nat Struct Mol Biol 2017; 24:1139-1145. [PMID: 29106413 PMCID: PMC5741190 DOI: 10.1038/nsmb.3500] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 10/09/2017] [Indexed: 12/23/2022]
Abstract
Eukaryotic mRNA transcription initiation is directed by the formation of the megaDalton-sized pre-initiation complex (PIC). After PIC formation, double-stranded DNA is unwound to form a single-stranded DNA bubble and the template strand is loaded into the polymerase active site. DNA opening is catalyzed by Ssl2(XPB), the dsDNA translocase subunit of the basal transcription factor TFIIH. In yeast, transcription initiation proceeds through a scanning phase where downstream DNA is searched for optimal start-sites. Here, to test models for initial DNA opening and start-site scanning, we measure the DNA bubble sizes generated by Saccharomyces cerevisiae PICs in real time using single-molecule magnetic tweezers. We show that ATP hydrolysis by Ssl2 opens a 6 base-pair (bp) bubble that grows to 13 bp in the presence of NTPs. These observations support a two-step model wherein ATP-dependent Ssl2 translocation leads to a 6 bp open complex which RNA polymerase II expands via NTP-dependent RNA transcription.
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9
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Salerno D, Beretta GL, Zanchetta G, Brioschi S, Cristofalo M, Missana N, Nardo L, Cassina V, Tempestini A, Giovannoni R, Cerrito MG, Zaffaroni N, Bellini T, Mantegazza F. Platinum-Based Drugs and DNA Interactions Studied by Single-Molecule and Bulk Measurements. Biophys J 2017; 110:2151-61. [PMID: 27224480 DOI: 10.1016/j.bpj.2016.02.030] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 01/07/2016] [Accepted: 02/09/2016] [Indexed: 11/24/2022] Open
Abstract
Platinum-containing molecules are widely used as anticancer drugs. These molecules exert cytotoxic effects by binding to DNA through various mechanisms. The binding between DNA and platinum-based drugs hinders the opening of DNA, and therefore, DNA duplication and transcription are severely hampered. Overall, impeding the above-mentioned important DNA mechanisms results in irreversible DNA damage and the induction of apoptosis. Several molecules, including multinuclear platinum compounds, belong to the family of platinum drugs, and there is a body of research devoted to developing more efficient and less toxic versions of these compounds. In this study, we combined different biophysical methods, including single-molecule assays (magnetic tweezers) and bulk experiments (ultraviolet absorption for thermal denaturation) to analyze the differential stability of double-stranded DNA in complex with either cisplatin or multinuclear platinum agents. Specifically, we analyzed how the binding of BBR3005 and BBR3464, two representative multinuclear platinum-based compounds, to DNA affects its stability as compared with cisplatin binding. Our results suggest that single-molecule approaches can provide insights into the drug-DNA interactions that underlie drug potency and provide information that is complementary to that generated from bulk analysis; thus, single-molecule approaches have the potential to facilitate the selection and design of optimized drug compounds. In particular, relevant differences in DNA stability at the single-molecule level are demonstrated by analyzing nanomechanically induced DNA denaturation. On the basis of the comparison between the single-molecule and bulk analyses, we suggest that transplatinated drugs are able to locally destabilize small portions of the DNA chain, whereas other regions are stabilized.
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Affiliation(s)
| | - Giovanni L Beretta
- Dipartimento di Oncologia Sperimentale e Medicina Molecolare, Fondazione IRCCS Istituto Nazionale Tumori, Milano, Italy
| | - Giuliano Zanchetta
- Dipartimento di Biotecnologie Mediche e Medicina Translazionale, Università degli Studi di Milano, Segrate, Italy
| | - Simone Brioschi
- School of Medicine, Università di Milano-Bicocca, Monza, Italy
| | | | - Natalia Missana
- School of Medicine, Università di Milano-Bicocca, Monza, Italy
| | - Luca Nardo
- School of Medicine, Università di Milano-Bicocca, Monza, Italy
| | - Valeria Cassina
- School of Medicine, Università di Milano-Bicocca, Monza, Italy
| | | | - Roberto Giovannoni
- Dipartimento di Scienze Chirurgiche, Università di Milano-Bicocca, Monza, Italy
| | | | - Nadia Zaffaroni
- Dipartimento di Oncologia Sperimentale e Medicina Molecolare, Fondazione IRCCS Istituto Nazionale Tumori, Milano, Italy
| | - Tommaso Bellini
- Dipartimento di Biotecnologie Mediche e Medicina Translazionale, Università degli Studi di Milano, Segrate, Italy
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10
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Kemmerich FE, Kasaciunaite K, Seidel R. Modular magnetic tweezers for single-molecule characterizations of helicases. Methods 2016; 108:4-13. [PMID: 27402355 DOI: 10.1016/j.ymeth.2016.07.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 07/05/2016] [Accepted: 07/06/2016] [Indexed: 01/09/2023] Open
Abstract
Magnetic tweezers provide a versatile toolkit supporting the mechanistic investigation of helicases. In the present article, we show that custom magnetic tweezers setups are straightforward to construct and can easily be extended to provide adaptable platforms, capable of addressing a multitude of enquiries regarding the functions of these fascinating molecular machines. We first address the fundamental components of a basic magnetic tweezers scheme and review some previous results to demonstrate the versatility of this instrument. We then elaborate on several extensions to the basic magnetic tweezers scheme, and demonstrate their applications with data from ongoing research. As our methodological overview illustrates, magnetic tweezers are an extremely useful tool for the characterization of helicases and a custom built instrument can be specifically tailored to suit the experimenter's needs.
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Affiliation(s)
- Felix E Kemmerich
- Molecular Biophysics Group, Institute of Experimental Physics I, Universität Leipzig, 04103 Leipzig, Germany
| | - Kristina Kasaciunaite
- Molecular Biophysics Group, Institute of Experimental Physics I, Universität Leipzig, 04103 Leipzig, Germany
| | - Ralf Seidel
- Molecular Biophysics Group, Institute of Experimental Physics I, Universität Leipzig, 04103 Leipzig, Germany.
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11
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Probing the mechanical properties, conformational changes, and interactions of nucleic acids with magnetic tweezers. J Struct Biol 2016; 197:26-36. [PMID: 27368129 DOI: 10.1016/j.jsb.2016.06.022] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 05/06/2016] [Accepted: 06/28/2016] [Indexed: 11/21/2022]
Abstract
Nucleic acids are central to the storage and transmission of genetic information. Mechanical properties, along with their sequence, both enable and fundamentally constrain the biological functions of DNA and RNA. For small deformations from the equilibrium conformations, nucleic acids are well described by an isotropic elastic rod model. However, external forces and torsional strains can induce conformational changes, giving rise to a complex force-torque phase diagram. This review focuses on magnetic tweezers as a powerful tool to precisely determine both the elastic parameters and conformational transitions of nucleic acids under external forces and torques at the single-molecule level. We review several variations of magnetic tweezers, in particular conventional magnetic tweezers, freely orbiting magnetic tweezers and magnetic torque tweezers, and discuss their characteristic capabilities. We then describe the elastic rod model for DNA and RNA and discuss conformational changes induced by mechanical stress. The focus lies on the responses to torque and twist, which are crucial in the mechanics and interactions of nucleic acids and can directly be measured using magnetic tweezers. We conclude by highlighting several recent studies of nucleic acid-protein and nucleic acid-small-molecule interactions as further applications of magnetic tweezers and give an outlook of some exciting developments to come.
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12
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Vlijm R, v.d. Torre J, Dekker C. Counterintuitive DNA Sequence Dependence in Supercoiling-Induced DNA Melting. PLoS One 2015; 10:e0141576. [PMID: 26513573 PMCID: PMC4625975 DOI: 10.1371/journal.pone.0141576] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 10/09/2015] [Indexed: 11/19/2022] Open
Abstract
The metabolism of DNA in cells relies on the balance between hybridized double-stranded DNA (dsDNA) and local de-hybridized regions of ssDNA that provide access to binding proteins. Traditional melting experiments, in which short pieces of dsDNA are heated up until the point of melting into ssDNA, have determined that AT-rich sequences have a lower binding energy than GC-rich sequences. In cells, however, the double-stranded backbone of DNA is destabilized by negative supercoiling, and not by temperature. To investigate what the effect of GC content is on DNA melting induced by negative supercoiling, we studied DNA molecules with a GC content ranging from 38% to 77%, using single-molecule magnetic tweezer measurements in which the length of a single DNA molecule is measured as a function of applied stretching force and supercoiling density. At low force (<0.5pN), supercoiling results into twisting of the dsDNA backbone and loop formation (plectonemes), without inducing any DNA melting. This process was not influenced by the DNA sequence. When negative supercoiling is introduced at increasing force, local melting of DNA is introduced. We measured for the different DNA molecules a characteristic force Fchar, at which negative supercoiling induces local melting of the dsDNA. Surprisingly, GC-rich sequences melt at lower forces than AT-rich sequences: Fchar = 0.56pN for 77% GC but 0.73pN for 38% GC. An explanation for this counterintuitive effect is provided by the realization that supercoiling densities of a few percent only induce melting of a few percent of the base pairs. As a consequence, denaturation bubbles occur in local AT-rich regions and the sequence-dependent effect arises from an increased DNA bending/torsional energy associated with the plectonemes. This new insight indicates that an increased GC-content adjacent to AT-rich DNA regions will enhance local opening of the double-stranded DNA helix.
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Affiliation(s)
- Rifka Vlijm
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands
| | - Jaco v.d. Torre
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands
- * E-mail:
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Gollnick B, Carrasco C, Zuttion F, Gilhooly NS, Dillingham MS, Moreno-Herrero F. Probing DNA helicase kinetics with temperature-controlled magnetic tweezers. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2015; 11:1273-84. [PMID: 25400244 PMCID: PMC4473356 DOI: 10.1002/smll.201402686] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Indexed: 05/04/2023]
Abstract
Motor protein functions like adenosine triphosphate (ATP) hydrolysis or translocation along molecular substrates take place at nanometric scales and consequently depend on the amount of available thermal energy. The associated rates can hence be investigated by actively varying the temperature conditions. In this article, a thermally controlled magnetic tweezers (MT) system for single-molecule experiments at up to 40 °C is presented. Its compact thermostat module yields a precision of 0.1 °C and can in principle be tailored to any other surface-coupled microscopy technique, such as tethered particle motion (TPM), nanopore-based sensing of biomolecules, or super-resolution fluorescence imaging. The instrument is used to examine the temperature dependence of translocation along double-stranded (ds)DNA by individual copies of the protein complex AddAB, a helicase-nuclease motor involved in dsDNA break repair. Despite moderately lower mean velocities measured at sub-saturating ATP concentrations, almost identical estimates of the enzymatic reaction barrier (around 21-24 k(B)T) are obtained by comparing results from MT and stopped-flow bulk assays. Single-molecule rates approach ensemble values at optimized chemical energy conditions near the motor, which can withstand opposing loads of up to 14 piconewtons (pN). Having proven its reliability, the temperature-controlled MT described herein will eventually represent a routinely applied method within the toolbox for nano-biotechnology.
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Affiliation(s)
- Benjamin Gollnick
- Centro Nacional de Biotecnología, CSIC, Darwin 3, Campus de Cantoblanco, 28049, Madrid, Spain
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Driessen RPC, Sitters G, Laurens N, Moolenaar GF, Wuite GJL, Goosen N, Dame RT. Effect of temperature on the intrinsic flexibility of DNA and its interaction with architectural proteins. Biochemistry 2014; 53:6430-8. [PMID: 25291500 PMCID: PMC5451147 DOI: 10.1021/bi500344j] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
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The
helical structure of double-stranded DNA is destabilized by
increasing temperature. Above a critical temperature (the melting
temperature), the two strands in duplex DNA become fully separated.
Below this temperature, the structural effects are localized. Using
tethered particle motion in a temperature-controlled sample chamber,
we systematically investigated the effect of increasing temperature
on DNA structure and the interplay between this effect and protein
binding. Our measurements revealed that (1) increasing temperature
enhances DNA flexibility, effectively leading to more compact folding
of the double-stranded DNA chain, and (2) temperature differentially
affects different types of DNA-bending chromatin proteins from mesophilic
and thermophilic organisms. Thus, our findings aid in understanding
genome organization in organisms thriving at moderate as well as extreme
temperatures. Moreover, our results underscore the importance of carefully
controlling and measuring temperature in single-molecule DNA (micromanipulation)
experiments.
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Affiliation(s)
- Rosalie P C Driessen
- Molecular Genetics, Leiden Institute of Chemistry and Cell Observatory, Leiden University , 2333 CC Leiden, The Netherlands
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