1
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Masi S, Dalpiaz H, Borghi C. Gene editing of angiotensin for blood pressure management. INTERNATIONAL JOURNAL OF CARDIOLOGY. CARDIOVASCULAR RISK AND PREVENTION 2024; 23:200323. [PMID: 39258007 PMCID: PMC11382036 DOI: 10.1016/j.ijcrp.2024.200323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 08/05/2024] [Accepted: 08/15/2024] [Indexed: 09/12/2024]
Abstract
Arterial hypertension has remained the world's leading cause of morbidity and mortality for more than 20 years. While early Genome-Wide Association Studies raised the hypothesis that a precision medicine approach could be implemented in the treatment of hypertension, the large number of single nucleotide polymorphisms that were found to be associated with blood pressure and their limited impact on the blood pressure values have initially hampered these expectations. With the development and refinement of gene-editing and RNA-based approaches allowing selective and organ-specific modulation of critical systems involved in blood pressure regulation, a renewed interest in genetic treatments for hypertension has emerged. The CRISPR-Cas9 system, antisense oligonucleotides (ASO) and small interfering RNA (siRNA) have been used to specifically target the hepatic angiotensinogen (AGT) production, with the scope of safely but effectively reducing the activation of the renin-angiotensin system, ultimately leading to an effective reduction of the blood pressure with extremely simplified treatment regimens that involve weekly, monthly or even once-in-life injection of the drugs. Among the various approaches, siRNA and ASO that reduce hepatic AGT production are in advanced development, with phase I and II clinical trials showing their safety and effectiveness. In the current manuscript, we review the mode of action of these new approaches to hypertension treatment, discussing the results of the clinical trials and their potential to revolutionize the management of hypertension.
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Affiliation(s)
- Stefano Masi
- Department of Clinical and Experimental Medicine, University of Pisa, Italy
| | - Hermann Dalpiaz
- Department of Clinical and Experimental Medicine, University of Pisa, Italy
| | - Claudio Borghi
- Hypertension and Cardiovascular Disease Research Center, Medical and Surgical Sciences Department, Alma Mater Studiorum University of Bologna, 40126, Bologna, Italy
- Cardiovascular Medicine Unit, Heart-Chest-Vascular Department, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40126, Bologna, Italy
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2
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Aguirre Rivera J, Mao G, Sabantsev A, Panfilov M, Hou Q, Lindell M, Chanez C, Ritort F, Jinek M, Deindl S. Massively parallel analysis of single-molecule dynamics on next-generation sequencing chips. Science 2024; 385:892-898. [PMID: 39172826 DOI: 10.1126/science.adn5371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 06/12/2024] [Indexed: 08/24/2024]
Abstract
Single-molecule techniques are ideally poised to characterize complex dynamics but are typically limited to investigating a small number of different samples. However, a large sequence or chemical space often needs to be explored to derive a comprehensive understanding of complex biological processes. Here we describe multiplexed single-molecule characterization at the library scale (MUSCLE), a method that combines single-molecule fluorescence microscopy with next-generation sequencing to enable highly multiplexed observations of complex dynamics. We comprehensively profiled the sequence dependence of DNA hairpin properties and Cas9-induced target DNA unwinding-rewinding dynamics. The ability to explore a large sequence space for Cas9 allowed us to identify a number of target sequences with unexpected behaviors. We envision that MUSCLE will enable the mechanistic exploration of many fundamental biological processes.
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Affiliation(s)
- J Aguirre Rivera
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75105 Uppsala, Sweden
| | - G Mao
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75105 Uppsala, Sweden
| | - A Sabantsev
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75105 Uppsala, Sweden
| | - M Panfilov
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75105 Uppsala, Sweden
| | - Q Hou
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75105 Uppsala, Sweden
| | - M Lindell
- Department of Medical Sciences, Science for Life Laboratory, Uppsala University, 75144 Uppsala, Sweden
| | - C Chanez
- Department of Biochemistry, University of Zürich, 8057 Zürich, Switzerland
| | - F Ritort
- Small Biosystems Lab, Condensed Matter Physics Department, Universitat de Barcelona, 08028 Barcelona, Spain
- Institut de Nanociència i Nanotecnologia (IN2UB), Universitat de Barcelona, 08028 Barcelona, Spain
| | - M Jinek
- Department of Biochemistry, University of Zürich, 8057 Zürich, Switzerland
| | - S Deindl
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75105 Uppsala, Sweden
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3
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Chua GNL, Liu S. When Force Met Fluorescence: Single-Molecule Manipulation and Visualization of Protein-DNA Interactions. Annu Rev Biophys 2024; 53:169-191. [PMID: 38237015 DOI: 10.1146/annurev-biophys-030822-032904] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Myriad DNA-binding proteins undergo dynamic assembly, translocation, and conformational changes while on DNA or alter the physical configuration of the DNA substrate to control its metabolism. It is now possible to directly observe these activities-often central to the protein function-thanks to the advent of single-molecule fluorescence- and force-based techniques. In particular, the integration of fluorescence detection and force manipulation has unlocked multidimensional measurements of protein-DNA interactions and yielded unprecedented mechanistic insights into the biomolecular processes that orchestrate cellular life. In this review, we first introduce the different experimental geometries developed for single-molecule correlative force and fluorescence microscopy, with a focus on optical tweezers as the manipulation technique. We then describe the utility of these integrative platforms for imaging protein dynamics on DNA and chromatin, as well as their unique capabilities in generating complex DNA configurations and uncovering force-dependent protein behaviors. Finally, we give a perspective on the future directions of this emerging research field.
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Affiliation(s)
- Gabriella N L Chua
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, New York, USA;
- Tri-Institutional PhD Program in Chemical Biology, New York, New York, USA
| | - Shixin Liu
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, New York, USA;
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4
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Vasconcelos Komninakis S, Domingues W, Saeed Sanabani S, Angelo Folgosi V, Neves Barbosa I, Casseb J. CRISPR/CAS as a Powerful Tool for Human Immunodeficiency Virus Cure: A Review. AIDS Res Hum Retroviruses 2024; 40:363-375. [PMID: 38164106 DOI: 10.1089/aid.2022.0148] [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: 01/03/2024] Open
Abstract
Despite care and the availability of effective antiretroviral treatment, some human immunodeficiency virus (HIV)-infected individuals suffer from neurocognitive disorders associated with HIV (HAND) that significantly affect their quality of life. The different types of HAND can be divided into asymptomatic neurocognitive impairment, mild neurocognitive disorder, and the most severe form known as HIV-associated dementia. Little is known about the mechanisms of HAND, but it is thought to be related to infection of astrocytes, microglial cells, and macrophages in the human brain. The formation of a viral reservoir that lies dormant as a provirus in resting CD4+ T lymphocytes and in refuge tissues such as the brain contributes significantly to HIV eradication. In recent years, a new set of tools have emerged: the gene editing based on the clustered regularly interspaced palindromic repeats (CRISPR)/Cas9 system, which can alter genome segments by insertion, deletion, and replacement and has great therapeutic potential. This technology has been used in research to treat HIV and appears to offer hope for a possible cure for HIV infection and perhaps prevention of HAND. This approach has the potential to directly impact the quality of life of HIV-infected individuals, which is a very important topic to be known and discussed.
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Affiliation(s)
- Shirley Vasconcelos Komninakis
- Laboratory of Medical Investigation (LIM56) of the School of Medicine/Institute de Tropical Medicine, Department of Dermatology, São Paulo University, São Paulo, São Paulo, Brazil
| | - Wilson Domingues
- Laboratory of Medical Investigation (LIM56) of the School of Medicine/Institute de Tropical Medicine, Department of Dermatology, São Paulo University, São Paulo, São Paulo, Brazil
| | - Sabri Saeed Sanabani
- Laboratory of Medical Investigation (LIM56) of the School of Medicine/Institute de Tropical Medicine, Department of Dermatology, São Paulo University, São Paulo, São Paulo, Brazil
| | - Victor Angelo Folgosi
- Laboratory of Medical Investigation (LIM56) of the School of Medicine/Institute de Tropical Medicine, Department of Dermatology, São Paulo University, São Paulo, São Paulo, Brazil
| | - Igor Neves Barbosa
- Institute of Genetic Biology at the Biological Institute of São Paulo University, São Paulo, São Paulo, Brazil
| | - Jorge Casseb
- Laboratory of Medical Investigation (LIM56) of the School of Medicine/Institute de Tropical Medicine, Department of Dermatology, São Paulo University, São Paulo, São Paulo, Brazil
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5
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Olivi L, Bagchus C, Pool V, Bekkering E, Speckner K, Offerhaus H, Wu W, Depken M, Martens KA, Staals RJ, Hohlbein J. Live-cell imaging reveals the trade-off between target search flexibility and efficiency for Cas9 and Cas12a. Nucleic Acids Res 2024; 52:5241-5256. [PMID: 38647045 PMCID: PMC11109954 DOI: 10.1093/nar/gkae283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 03/25/2024] [Accepted: 04/04/2024] [Indexed: 04/25/2024] Open
Abstract
CRISPR-Cas systems have widely been adopted as genome editing tools, with two frequently employed Cas nucleases being SpyCas9 and LbCas12a. Although both nucleases use RNA guides to find and cleave target DNA sites, the two enzymes differ in terms of protospacer-adjacent motif (PAM) requirements, guide architecture and cleavage mechanism. In the last years, rational engineering led to the creation of PAM-relaxed variants SpRYCas9 and impLbCas12a to broaden the targetable DNA space. By employing their catalytically inactive variants (dCas9/dCas12a), we quantified how the protein-specific characteristics impact the target search process. To allow quantification, we fused these nucleases to the photoactivatable fluorescent protein PAmCherry2.1 and performed single-particle tracking in cells of Escherichia coli. From our tracking analysis, we derived kinetic parameters for each nuclease with a non-targeting RNA guide, strongly suggesting that interrogation of DNA by LbdCas12a variants proceeds faster than that of SpydCas9. In the presence of a targeting RNA guide, both simulations and imaging of cells confirmed that LbdCas12a variants are faster and more efficient in finding a specific target site. Our work demonstrates the trade-off of relaxing PAM requirements in SpydCas9 and LbdCas12a using a powerful framework, which can be applied to other nucleases to quantify their DNA target search.
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Affiliation(s)
- Lorenzo Olivi
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Cleo Bagchus
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
- Laboratory of Biophysics, Wageningen University & Research, Wageningen, The Netherlands
| | - Victor Pool
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
- Laboratory of Biophysics, Wageningen University & Research, Wageningen, The Netherlands
| | - Ezra Bekkering
- Laboratory of Biophysics, Wageningen University & Research, Wageningen, The Netherlands
| | - Konstantin Speckner
- Laboratory of Biophysics, Wageningen University & Research, Wageningen, The Netherlands
| | - Hidde Offerhaus
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Wen Y Wu
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Martin Depken
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Koen J A Martens
- Laboratory of Biophysics, Wageningen University & Research, Wageningen, The Netherlands
| | - Raymond H J Staals
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Johannes Hohlbein
- Laboratory of Biophysics, Wageningen University & Research, Wageningen, The Netherlands
- Microspectroscopy Research Facility, Wageningen University & Research, Wageningen, The Netherlands
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6
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Liu Z, van Veen E, Sánchez H, Solano B, Palmero Moya FJ, McCluskey KA, Ramírez Montero D, van Laar T, Dekker NH. A Biophysics Toolbox for Reliable Data Acquisition and Processing in Integrated Force-Confocal Fluorescence Microscopy. ACS PHOTONICS 2024; 11:1592-1603. [PMID: 38645993 PMCID: PMC11027178 DOI: 10.1021/acsphotonics.3c01739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 03/01/2024] [Accepted: 03/01/2024] [Indexed: 04/23/2024]
Abstract
Integrated single-molecule force-fluorescence spectroscopy setups allow for simultaneous fluorescence imaging and mechanical force manipulation and measurements on individual molecules, providing comprehensive dynamic and spatiotemporal information. Dual-beam optical tweezers (OT) combined with a confocal scanning microscope form a force-fluorescence spectroscopy apparatus broadly used to investigate various biological processes, in particular, protein:DNA interactions. Such experiments typically involve imaging of fluorescently labeled proteins bound to DNA and force spectroscopy measurements of trapped individual DNA molecules. Here, we present a versatile state-of-the-art toolbox including the preparation of protein:DNA complex samples, design of a microfluidic flow cell incorporated with OT, automation of OT-confocal scanning measurements, and the development and implementation of a streamlined data analysis package for force and fluorescence spectroscopy data processing. Its components can be adapted to any commercialized or home-built dual-beam OT setup equipped with a confocal scanning microscope, which will facilitate single-molecule force-fluorescence spectroscopy studies on a large variety of biological systems.
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Affiliation(s)
- Zhaowei Liu
- Department
of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Edo van Veen
- Department
of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Humberto Sánchez
- Department
of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Belén Solano
- Department
of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Francisco J. Palmero Moya
- Department
of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Kaley A. McCluskey
- Department
of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Daniel Ramírez Montero
- Department
of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Theo van Laar
- Department
of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Nynke H. Dekker
- Department
of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, The Netherlands
- Clarendon
Laboratory, Department of Physics, University
of Oxford, Oxford OX1 3PU, U.K.
- Kavli
Institute of Nanoscience Discovery, University
of Oxford, Dorothy Crowfoot
Hodgkin Building, Oxford OX1 3QU, U.K.
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7
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Chatterjee S, Chaubet L, van den Berg A, Mukhortava A, Gulkis M, Çağlayan M. Uncovering nick DNA binding by LIG1 at the single-molecule level. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.28.587287. [PMID: 38586032 PMCID: PMC10996606 DOI: 10.1101/2024.03.28.587287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
DNA ligases repair the strand breaks are made continually and naturally throughout the genome, if left unrepaired and allowed to persist, they can lead to genome instability in the forms of lethal double-strand (ds) breaks, deletions, and duplications. DNA ligase 1 (LIG1) joins Okazaki fragments during the replication machinery and seals nicks at the end of most DNA repair pathways. Yet, how LIG1 recognizes its target substrate is entirely missing. Here, we uncover the dynamics of nick DNA binding by LIG1 at the single-molecule level. Our findings reveal that LIG1 binds to dsDNA both specifically and non-specifically and exhibits diffusive behavior to form a stable complex at the nick. Furthermore, by comparing with the LIG1 C-terminal protein, we demonstrate that the N-terminal non-catalytic region promotes binding enriched at nick sites and facilitates an efficient nick search process by promoting 1D diffusion along the DNA. Our findings provide a novel single-molecule insight into the nick binding by LIG1, which is critical to repair broken phosphodiester bonds in the DNA backbone to maintain genome integrity.
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8
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Halma MTJ, Xu L. Life under tension: the relevance of force on biological polymers. BIOPHYSICS REPORTS 2024; 10:48-56. [PMID: 38737478 PMCID: PMC11079598 DOI: 10.52601/bpr.2023.230019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 12/06/2023] [Indexed: 05/14/2024] Open
Abstract
Optical tweezers have elucidated numerous biological processes, particularly by enabling the precise manipulation and measurement of tension. One question concerns the biological relevance of these experiments and the generalizability of these experiments to wider biological systems. Here, we categorize the applicability of the information garnered from optical tweezers in two distinct categories: the direct relevance of tension in biological systems, and what experiments under tension can tell us about biological systems, while these systems do not reach the same tension as the experiment, still, these artificial experimental systems reveal insights into the operations of biological machines and life processes.
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Affiliation(s)
- Matthew T. J. Halma
- Department of Physics and Astronomy and LaserLab, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV, Amsterdam, the Netherlands
- LUMICKS B. V., 1081 HV, Amsterdam, the Netherlands
| | - Longfu Xu
- Department of Physics and Astronomy and LaserLab, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV, Amsterdam, the Netherlands
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9
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Pacesa M, Pelea O, Jinek M. Past, present, and future of CRISPR genome editing technologies. Cell 2024; 187:1076-1100. [PMID: 38428389 DOI: 10.1016/j.cell.2024.01.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/23/2024] [Accepted: 01/26/2024] [Indexed: 03/03/2024]
Abstract
Genome editing has been a transformative force in the life sciences and human medicine, offering unprecedented opportunities to dissect complex biological processes and treat the underlying causes of many genetic diseases. CRISPR-based technologies, with their remarkable efficiency and easy programmability, stand at the forefront of this revolution. In this Review, we discuss the current state of CRISPR gene editing technologies in both research and therapy, highlighting limitations that constrain them and the technological innovations that have been developed in recent years to address them. Additionally, we examine and summarize the current landscape of gene editing applications in the context of human health and therapeutics. Finally, we outline potential future developments that could shape gene editing technologies and their applications in the coming years.
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Affiliation(s)
- Martin Pacesa
- Laboratory of Protein Design and Immunoengineering, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Station 19, CH-1015 Lausanne, Switzerland
| | - Oana Pelea
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Martin Jinek
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
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10
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Schaich MA, Weaver TM, Roginskaya V, Freudenthal BD, Van Houten B. Single-molecule analysis of purified proteins and nuclear extracts: Insights from 8-oxoguanine glycosylase 1. DNA Repair (Amst) 2024; 134:103625. [PMID: 38237481 PMCID: PMC11287474 DOI: 10.1016/j.dnarep.2024.103625] [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: 10/13/2023] [Revised: 12/15/2023] [Accepted: 01/02/2024] [Indexed: 01/30/2024]
Abstract
By observing one molecule at a time, single-molecule studies can offer detailed insights about biomolecular processes including on rates, off rates, and diffusivity of molecules on strands of DNA. A recent technological advance (Single-molecule Analysis of DNA-binding proteins from Nuclear Extracts, SMADNE) has lowered the barrier to entry for single-molecule studies, and single-molecule dynamics can now be determined directly out of nuclear extracts, providing information in an intermediate environment between purified proteins in isolation and the heterogeneity of a nucleus. To compare and contrast the single-molecule DNA binding dynamics in nuclear extracts versus purified proteins, combined optical tweezers and fluorescence microscopy experiments were performed with purified GFP-tagged 8-oxoguanine glycosylase 1 (OGG1), purified GFP-OGG1 spiked into nuclear extracts, and nuclear extracts from human cells overexpressing GFP-OGG1. We observed differences in undamaged DNA binding during DNA damage search in each of the three conditions. Purified GFP-OGG1 engaged undamaged DNA for a weighted average lifetime of 5.7 s and 21% of these events underwent DNA diffusion after binding. However, unlike other glycosylases studied by SMADNE, OGG1 does not bind non-damaged DNA efficiently in nuclear extracts. In contrast, GFP-OGG1 binding dynamics on DNA substrates containing oxidative damage were relatively similar in all three conditions, with the weighted average binding lifetimes varying from 2.2 s in nuclear extracts to 7.8 s with purified GFP-OGG1 in isolation. Finally, we compared the purified protein and nuclear extract approaches for a catalytically dead OGG1 variant (GFP-OGG1-K249Q). This variant greatly increased the binding lifetime for oxidative DNA damage, with the weighted average lifetime for GFP-OGG1-249Q in nuclear extracts at 15.4 s vs 10.7 s for the purified protein. SMADNE will provide a new window of observation into the behavior of nucleic acid binding proteins only accessible by biophysicists trained in protein purification and protein labeling.
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Affiliation(s)
- Matthew A Schaich
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; UPMC-Hillman Cancer Center, USA
| | - Tyler M Weaver
- Department of Biochemistry and Molecular Biology, Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | | | - Bret D Freudenthal
- Department of Biochemistry and Molecular Biology, Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA; University of Kansas Cancer Center, Kansas City, KS 66160, USA
| | - Bennett Van Houten
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; UPMC-Hillman Cancer Center, USA.
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11
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Ramírez Montero D, Liu Z, Dekker NH. De novo fabrication of custom-sequence plasmids for the synthesis of long DNA constructs with extrahelical features. Biophys J 2024; 123:31-41. [PMID: 37968907 PMCID: PMC10808024 DOI: 10.1016/j.bpj.2023.11.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 10/06/2023] [Accepted: 11/13/2023] [Indexed: 11/17/2023] Open
Abstract
DNA constructs for single-molecule experiments often require specific sequences and/or extrahelical/noncanonical structures to study DNA-processing mechanisms. The precise introduction of such structures requires extensive control of the sequence of the initial DNA substrate. A commonly used substrate in the synthesis of DNA constructs is plasmid DNA. Nevertheless, the controlled introduction of specific sequences and extrahelical/noncanonical structures into plasmids often requires several rounds of cloning on pre-existing plasmids whose sequence one cannot fully control. Here, we describe a simple and efficient way to synthesize 10.1-kb plasmids de novo using synthetic gBlocks that provides full control of the sequence. Using these plasmids, we developed a 1.5-day protocol to assemble 10.1-kb linear DNA constructs with end and internal modifications. As a proof of principle, we synthesize two different DNA constructs with biotinylated ends and one or two internal 3' single-stranded DNA flaps, characterize them using single-molecule force and fluorescence spectroscopy, and functionally validate them by showing that the eukaryotic replicative helicase Cdc45/Mcm2-7/GINS (CMG) binds the 3' single-stranded DNA flap and translocates in the expected direction. We anticipate that our approach can be used to synthesize custom-sequence DNA constructs for a variety of force and fluorescence single-molecule spectroscopy experiments to interrogate DNA replication, DNA repair, and transcription.
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Affiliation(s)
- Daniel Ramírez Montero
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Zhaowei Liu
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Nynke H Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands.
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12
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Sharma M, de Alba E. Assembly mechanism of the inflammasome sensor AIM2 revealed by single molecule analysis. Nat Commun 2023; 14:7957. [PMID: 38042863 PMCID: PMC10693601 DOI: 10.1038/s41467-023-43691-4] [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: 08/18/2022] [Accepted: 11/06/2023] [Indexed: 12/04/2023] Open
Abstract
Pathogenic dsDNA prompts AIM2 assembly leading to the formation of the inflammasome, a multimeric complex that triggers the inflammatory response. The recognition of foreign dsDNA involves AIM2 self-assembly concomitant with dsDNA binding. However, we lack mechanistic and kinetic information on the formation and propagation of the assembly, which can shed light on innate immunity's time response and specificity. Combining optical traps and confocal fluorescence microscopy, we determine here the association and dissociation rates of the AIM2-DNA complex at the single molecule level. We identify distinct mechanisms for oligomer growth via the binding of incoming AIM2 molecules to adjacent dsDNA or direct interaction with bound AIM2 assemblies, resembling primary and secondary nucleation. Through these mechanisms, the size of AIM2 oligomers can increase fourfold in seconds. Finally, our data indicate that single AIM2 molecules do not diffuse/scan along the DNA, suggesting that oligomerization depends on stochastic encounters with DNA and/or DNA-bound AIM2.
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Affiliation(s)
- Meenakshi Sharma
- Department of Bioengineering, School of Engineering, University of California Merced, Merced, California, USA
| | - Eva de Alba
- Department of Bioengineering, School of Engineering, University of California Merced, Merced, California, USA.
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13
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Overton MS, Guy SE, Chen X, Martsul A, Carolino K, Akbari OS, Meyer JR, Kryazhimskiy S. Upper Bound on the Mutational Burden Imposed by a CRISPR-Cas9 Gene-Drive Element. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.28.569142. [PMID: 38076841 PMCID: PMC10705488 DOI: 10.1101/2023.11.28.569142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
CRISPR-Cas9 gene drives (CCGDs) are powerful tools for genetic control of wild populations, useful for eradication of disease vectors, conservation of endangered species and other applications. However, Cas9 alone and in a complex with gRNA can cause double-stranded DNA breaks at off-target sites, which could increase the mutational load and lead to loss of heterozygosity (LOH). These undesired effects raise potential concerns about the long-term evolutionary safety of CCGDs, but the magnitude of these effects is unknown. To estimate how the presence of a CCGD or a Cas9 alone in the genome affects the rates of LOH events and de novo mutations, we carried out a mutation accumulation experiment in yeast Saccharomyces cerevisiae. Despite its substantial statistical power, our experiment revealed no detectable effect of CCGD or Cas9 alone on the genome-wide rates of mutations or LOH events, suggesting that these rates are affected by less than 30%. Nevertheless, we found that Cas9 caused a slight but significant shift towards more interstitial and fewer terminal LOH events, and the CCGD caused a significant difference in the distribution of LOH events on Chromosome V. Taken together, our results show that these genetic elements impose a weak and likely localized additional mutational burden in the yeast model. Although the mutagenic effects of CCGDs need to be further evaluated in other systems, our results suggest that the effect of CCGDs on off-target mutation rates and genetic diversity may be acceptable.
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Affiliation(s)
- Michael S. Overton
- Department of Ecology, Behavior and Evolution, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093
| | - Sean E. Guy
- Department of Ecology, Behavior and Evolution, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093
- Current address: Bionano Genomics, San Diego, CA 92121
| | - Xingsen Chen
- Department of Ecology, Behavior and Evolution, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093
- Current address: Department of Entomology, University of Arizona, Tucson, Arizona, USA
| | - Alena Martsul
- Department of Ecology, Behavior and Evolution, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093
- Current address: Illumina Inc., San Diego, CA 92122
| | - Krypton Carolino
- Department of Ecology, Behavior and Evolution, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093
| | - Omar S. Akbari
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Justin R. Meyer
- Department of Ecology, Behavior and Evolution, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093
| | - Sergey Kryazhimskiy
- Department of Ecology, Behavior and Evolution, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093
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14
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Schaich MA, Weaver TM, Roginskaya V, Freudenthal BD, Van Houten B. Single-molecule analysis of purified proteins and nuclear extracts: insights from 8-oxoguanine glycosylase 1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.01.565178. [PMID: 37961208 PMCID: PMC10635064 DOI: 10.1101/2023.11.01.565178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
By observing one molecule at a time, single-molecule studies can offer detailed insights about biomolecular processes including on rates, off rates, and diffusivity of molecules on strands of DNA. A recent technological advance (Single-molecule Analysis of DNA-binding proteins from Nuclear Extracts, SMADNE) has lowered the barrier to entry for single-molecule studies, and single-molecule dynamics can now be determined directly out of nuclear extracts, providing information in an intermediate environment between purified proteins in isolation and the heterogeneity of a nucleus. To compare and contrast the single-molecule DNA binding dynamics in nuclear extracts versus purified proteins, combined optical tweezers and fluorescence microscopy experiments were performed with purified GFP-tagged 8-oxoguanine glycosylase 1 (OGG1), purified GFP-OGG1 spiked into nuclear extracts, and nuclear extracts from human cells overexpressing GFP-OGG1. We observed differences in undamaged DNA binding during DNA damage search in each of the three conditions. Purified GFP-OGG1 engaged undamaged DNA for a weighted average lifetime of 5.7 s and 21% of these events underwent DNA diffusion after binding. However, unlike other glycosylases studied by SMADNE, OGG1 does not bind non-damaged DNA efficiently in nuclear extracts. In contrast, GFP-OGG1 binding dynamics on DNA substrates containing oxidative damage were relatively similar in all three conditions, with the weighted average binding lifetimes varying from 2.2 s in nuclear extracts to 7.8 s with purified GFP-OGG1 in isolation. Finally, we compared the purified protein and nuclear extract approaches for a catalytically dead OGG1 variant (GFP-OGG1-K249Q). This variant greatly increased the binding lifetime for oxidative DNA damage, with the weighted average lifetime for GFP-OGG1-249Q in nuclear extracts at 15.4 s vs 10.7 s for the purified protein. SMADNE will provide a new window of observation into the behavior of nucleic acid binding proteins only accessible by biophysicists trained in protein purification and protein labeling.
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15
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Newton MD, Losito M, Smith QM, Parnandi N, Taylor BJ, Akcakaya P, Maresca M, van Eijk P, Reed SH, Boulton SJ, King GA, Cuomo ME, Rueda DS. Negative DNA supercoiling induces genome-wide Cas9 off-target activity. Mol Cell 2023; 83:3533-3545.e5. [PMID: 37802026 DOI: 10.1016/j.molcel.2023.09.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 05/30/2023] [Accepted: 09/07/2023] [Indexed: 10/08/2023]
Abstract
CRISPR-Cas9 is a powerful gene-editing technology; however, off-target activity remains an important consideration for therapeutic applications. We have previously shown that force-stretching DNA induces off-target activity and hypothesized that distortions of the DNA topology in vivo, such as negative DNA supercoiling, could reduce Cas9 specificity. Using single-molecule optical-tweezers, we demonstrate that negative supercoiling λ-DNA induces sequence-specific Cas9 off-target binding at multiple sites, even at low forces. Using an adapted CIRCLE-seq approach, we detect over 10,000 negative-supercoiling-induced Cas9 off-target double-strand breaks genome-wide caused by increased mismatch tolerance. We further demonstrate in vivo that directed local DNA distortion increases off-target activity in cells and that induced off-target events can be detected during Cas9 genome editing. These data demonstrate that Cas9 off-target activity is regulated by DNA topology in vitro and in vivo, suggesting that cellular processes, such as transcription and replication, could induce off-target activity at previously overlooked sites.
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Affiliation(s)
- Matthew D Newton
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0HS, UK; Single Molecule Imaging, MRC-London Institute of Medical Sciences, Du Cane Road, London W12 0HS, UK; DSB Repair Metabolism Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Marialucrezia Losito
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0HS, UK; Single Molecule Imaging, MRC-London Institute of Medical Sciences, Du Cane Road, London W12 0HS, UK; Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB2 0AA, UK
| | - Quentin M Smith
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0HS, UK; Single Molecule Imaging, MRC-London Institute of Medical Sciences, Du Cane Road, London W12 0HS, UK
| | - Nishita Parnandi
- DSB Repair Metabolism Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Benjamin J Taylor
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB2 0AA, UK
| | - Pinar Akcakaya
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, 43183 Gothenburg, Sweden
| | - Marcello Maresca
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, 43183 Gothenburg, Sweden
| | - Patrick van Eijk
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff CF14 4AW, UK
| | - Simon H Reed
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff CF14 4AW, UK
| | - Simon J Boulton
- DSB Repair Metabolism Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Graeme A King
- Institute of Structural and Molecular Biology, University College London, London WC1E 6BT, UK.
| | | | - David S Rueda
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0HS, UK; Single Molecule Imaging, MRC-London Institute of Medical Sciences, Du Cane Road, London W12 0HS, UK.
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16
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Li Y, Cooper BH, Liu Y, Wu D, Zhang X, Rohs R, Qin PZ. CRISPR-Cas9 Activities with Truncated 16-Nucleotide RNA Guides Are Tuned by Target Duplex Stability Beyond the RNA/DNA Hybrid. Biochemistry 2023; 62:2541-2548. [PMID: 37552860 PMCID: PMC10578059 DOI: 10.1021/acs.biochem.3c00250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2023]
Abstract
CRISPR-Cas9 has been adapted as a readily programmable genome manipulation agent, and continuing technological advances rely on an in-depth mechanistic understanding of Cas9 target discrimination. Cas9 interrogates a target by unwinding the DNA duplex to form an R-loop, where the RNA guide hybridizes with one of the DNA strands. It has been shown that RNA guides shorter than the normal length of 20-nucleotide (-nt) support Cas9 cleavage activity by enabling partial unwinding beyond the RNA/DNA hybrid. To investigate whether DNA segment beyond the RNA/DNA hybrid can impact Cas9 target discrimination with truncated guides, Cas9 double-stranded DNA cleavage rates (kcat) were measured with 16-nt guides on targets with varying sequences at +17 to +20 positions distal to the protospacer-adjacent-motif (PAM). The data reveal a log-linear inverse correlation between kcat and the PAM+(17-20) DNA duplex dissociation free energy (ΔGNN(17-20)0), with sequences having smaller ΔGNN(17-20)0 showing faster cleavage and a higher degree of unwinding. The results indicate that, with a 16-nt guide, "peripheral" DNA sequences beyond the RNA/DNA hybrid contribute to target discrimination by tuning the cleavage reaction transition state through the modulation of PAM-distal unwinding. The finding provides mechanistic insights for the further development of strategies that use RNA guide truncation to enhance Cas9 specificity.
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Affiliation(s)
- Yue Li
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Brendon H Cooper
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California 90089, United States
| | - Yukang Liu
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Difei Wu
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Xiaojun Zhang
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Remo Rohs
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California 90089, United States
| | - Peter Z Qin
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
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17
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Chu J, Romero A, Taulbee J, Aran K. Development of Single Molecule Techniques for Sensing and Manipulation of CRISPR and Polymerase Enzymes. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2300328. [PMID: 37226388 PMCID: PMC10524706 DOI: 10.1002/smll.202300328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 03/20/2023] [Indexed: 05/26/2023]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) and polymerases are powerful enzymes and their diverse applications in genomics, proteomics, and transcriptomics have revolutionized the biotechnology industry today. CRISPR has been widely adopted for genomic editing applications and Polymerases can efficiently amplify genomic transcripts via polymerase chain reaction (PCR). Further investigations into these enzymes can reveal specific details about their mechanisms that greatly expand their use. Single-molecule techniques are an effective way to probe enzymatic mechanisms because they may resolve intermediary conformations and states with greater detail than ensemble or bulk biosensing techniques. This review discusses various techniques for sensing and manipulation of single biomolecules that can help facilitate and expedite these discoveries. Each platform is categorized as optical, mechanical, or electronic. The methods, operating principles, outputs, and utility of each technique are briefly introduced, followed by a discussion of their applications to monitor and control CRISPR and Polymerases at the single molecule level, and closing with a brief overview of their limitations and future prospects.
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Affiliation(s)
- Josephine Chu
- Henry E. Riggs School of Applied Life Sciences, Keck Graduate Institute, Claremont, CA, 91711, USA
| | - Andres Romero
- Henry E. Riggs School of Applied Life Sciences, Keck Graduate Institute, Claremont, CA, 91711, USA
| | - Jeffrey Taulbee
- Henry E. Riggs School of Applied Life Sciences, Keck Graduate Institute, Claremont, CA, 91711, USA
| | - Kiana Aran
- Henry E. Riggs School of Applied Life Sciences, Keck Graduate Institute, Claremont, CA, 91711, USA
- Cardea, San Diego, CA, 92121, USA
- University of California Berkeley, Berkeley, CA, 94720, USA
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18
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Kauert DJ, Madariaga-Marcos J, Rutkauskas M, Wulfken A, Songailiene I, Sinkunas T, Siksnys V, Seidel R. The energy landscape for R-loop formation by the CRISPR-Cas Cascade complex. Nat Struct Mol Biol 2023:10.1038/s41594-023-01019-2. [PMID: 37415009 DOI: 10.1038/s41594-023-01019-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 05/11/2023] [Indexed: 07/08/2023]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) sequences and CRISPR-associated (Cas) genes comprise CIRSPR-Cas effector complexes, which have revolutionized gene editing with their ability to target specific genomic loci using CRISPR RNA (crRNA) complementarity. Recognition of double-stranded DNA targets proceeds via DNA unwinding and base pairing between crRNA and the DNA target strand, forming an R-loop structure. Full R-loop extension is a prerequisite for subsequent DNA cleavage. However, the recognition of unintended sequences with multiple mismatches has limited therapeutic applications and is still poorly understood on a mechanistic level. Here we set up ultrafast DNA unwinding experiments on the basis of plasmonic DNA origami nanorotors to study R-loop formation by the Cascade effector complex in real time, close to base-pair resolution. We resolve a weak global downhill bias of the forming R-loop, followed by a steep uphill bias for the final base pairs. We also show that the energy landscape is modulated by base flips and mismatches. These findings suggest that Cascade-mediated R-loop formation occurs on short timescales in submillisecond single base-pair steps, but on longer timescales in six base-pair intermediate steps, in agreement with the structural periodicity of the crRNA-DNA hybrid.
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Affiliation(s)
- Dominik J Kauert
- Peter Debye Institute for Soft Matter Physics, Universität Leipzig, Leipzig, Germany
| | | | - Marius Rutkauskas
- Peter Debye Institute for Soft Matter Physics, Universität Leipzig, Leipzig, Germany
| | - Alexander Wulfken
- Peter Debye Institute for Soft Matter Physics, Universität Leipzig, Leipzig, Germany
| | - Inga Songailiene
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Tomas Sinkunas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Virginijus Siksnys
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Ralf Seidel
- Peter Debye Institute for Soft Matter Physics, Universität Leipzig, Leipzig, Germany.
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19
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Yu T, Liu T, Wang Y, Zhao X, Zhang W. Effect of Cas9 Protein on the Seed-Target Base Pair of the sgRNA/DNA Hybrid Duplex. J Phys Chem B 2023. [PMID: 37243666 DOI: 10.1021/acs.jpcb.3c00997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
CRISPR (clustered regularly interspaced short palindromic repeats)/CRISPR-associated protein (Cas9) has been widely used for gene editing. Not all guide RNAs can cleave the DNA efficiently remains a major challenge to CRISPR/Cas9-mediated genome engineering. Therefore, understanding how the Cas9 complex successfully and efficiently identifies specific functional targets through base-pairing has great implications for such applications. The 10-nt seed sequence at the 3' end of the guide RNA is critical to target recognition and cleavage. Here, through stretching molecular dynamics simulation, we studied the thermodynamics and kinetics of the binding-dissociation process of the seed base and the target DNA base with the Cas9 protein. The results showed that in the presence of Cas9 protein, the enthalpy change and entropy change in binding-dissociation of the seed base with the target are smaller than those without the Cas9 protein. The reduction of entropy penalty upon association with the protein resulted from the pre-organization of the seed base in an A-form helix, and the reduction of enthalpy change was due to the electrostatic attraction of the positively charged channel with the negative target DNA. The binding barrier coming from the entropy loss and the dissociation barrier resulting from the destruction of the base pair in the presence of Cas9 protein were lower than those without protein, which indicates that the seed region is crucial for efficiently searching the correct target by accelerating the binding rate and dissociating fast from the wrong target.
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Affiliation(s)
- Ting Yu
- Department of Physics, Wuhan University, Wuhan, Hubei 430072, PR China
| | - Taigang Liu
- Department of Physics, Wuhan University, Wuhan, Hubei 430072, PR China
- School of Medical Engineering, Xinxiang Medical University, Xinxiang, Henan 453003, PR China
| | - Yujie Wang
- Department of Physics, Wuhan University, Wuhan, Hubei 430072, PR China
- Department of Physics and Telecommunication Engineering, Zhoukou Normal University, Zhoukou, Henan 466000, PR China
| | - Xuanlin Zhao
- Department of Physics, Wuhan University, Wuhan, Hubei 430072, PR China
| | - Wenbing Zhang
- Department of Physics, Wuhan University, Wuhan, Hubei 430072, PR China
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20
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Sufyan M, Daraz U, Hyder S, Zulfiqar U, Iqbal R, Eldin SM, Rafiq F, Mahmood N, Shahzad K, Uzair M, Fiaz S, Ali I. An overview of genome engineering in plants, including its scope, technologies, progress and grand challenges. Funct Integr Genomics 2023; 23:119. [PMID: 37022538 DOI: 10.1007/s10142-023-01036-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 03/20/2023] [Accepted: 03/21/2023] [Indexed: 04/07/2023]
Abstract
Genome editing is a useful, adaptable, and favored technique for both functional genomics and crop enhancement. Over the years, rapidly evolving genome editing technologies, including clustered regularly interspaced short palindromic repeats/CRISPR-associated protein (CRISPR/Cas), transcription activator-like effector nucleases (TALENs), and zinc finger nucleases (ZFNs), have shown broad application prospects in gene function research and improvement of critical agronomic traits in many crops. These technologies have also opened up opportunities for plant breeding. These techniques provide excellent chances for the quick modification of crops and the advancement of plant science in the future. The current review describes various genome editing techniques and how they function, particularly CRISPR/Cas9 systems, which can contribute significantly to the most accurate characterization of genomic rearrangement and plant gene functions as well as the enhancement of critical traits in field crops. To accelerate the use of gene-editing technologies for crop enhancement, the speed editing strategy of gene-family members was designed. As it permits genome editing in numerous biological systems, the CRISPR technology provides a valuable edge in this regard that particularly captures the attention of scientists.
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Affiliation(s)
- Muhammad Sufyan
- College of Biological Sciences, China Agricultural University, Beijing, 100083, China
| | - Umar Daraz
- State Key Laboratory of Grassland Agro-Ecosystems, Center for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, China
| | - Sajjad Hyder
- Department of Botant, Government College Women University, Sialkot, Pakistan
| | - Usman Zulfiqar
- Department of Agronomy, Faculty of Agriculture and Environment, The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan
| | - Rashid Iqbal
- Department of Agronomy, Faculty of Agriculture and Environment, The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan.
| | - Sayed M Eldin
- Center of Research, Faculty of Engineering, Future University in Egypt, New Cairo, 11835, Egypt
| | - Farzana Rafiq
- School of Environmental Sciences and Engineering, NCEPU, Beijing, China
| | - Naveed Mahmood
- College of Biological Sciences, China Agricultural University, Beijing, 100083, China
| | - Khurram Shahzad
- Institute of Geographic Sciences and Natural Resources Research, CAS, Beijing, China
| | - Muhammad Uzair
- National Institute for Genomics and Advanced Biotechnology, Park Road, Islamabad, Pakistan
| | - Sajid Fiaz
- Department of Plant Breeding and Genetics, The University of Haripur, Haripur, 22620, Pakistan
| | - Iftikhar Ali
- Center for Plant Sciences and Biodiversity, University of Swat, Charbagh, 19120, Pakistan.
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, 10032, USA.
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21
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Lostao A, Lim K, Pallarés MC, Ptak A, Marcuello C. Recent advances in sensing the inter-biomolecular interactions at the nanoscale - A comprehensive review of AFM-based force spectroscopy. Int J Biol Macromol 2023; 238:124089. [PMID: 36948336 DOI: 10.1016/j.ijbiomac.2023.124089] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/13/2023] [Accepted: 03/15/2023] [Indexed: 03/24/2023]
Abstract
Biomolecular interactions underpin most processes inside the cell. Hence, a precise and quantitative understanding of molecular association and dissociation events is crucial, not only from a fundamental perspective, but also for the rational design of biomolecular platforms for state-of-the-art biomedical and industrial applications. In this context, atomic force microscopy (AFM) appears as an invaluable experimental technique, allowing the measurement of the mechanical strength of biomolecular complexes to provide a quantitative characterization of their interaction properties from a single molecule perspective. In the present review, the most recent methodological advances in this field are presented with special focus on bioconjugation, immobilization and AFM tip functionalization, dynamic force spectroscopy measurements, molecular recognition imaging and theoretical modeling. We expect this work to significantly aid in grasping the principles of AFM-based force spectroscopy (AFM-FS) technique and provide the necessary tools to acquaint the type of data that can be achieved from this type of experiments. Furthermore, a critical assessment is done with other nanotechnology techniques to better visualize the future prospects of AFM-FS.
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Affiliation(s)
- Anabel Lostao
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, Zaragoza 50009, Spain; Laboratorio de Microscopias Avanzadas (LMA), Universidad de Zaragoza, Zaragoza 50018, Spain; Fundación ARAID, Aragón, Spain.
| | - KeeSiang Lim
- WPI-Nano Life Science Institute, Kanazawa University, Ishikawa 920-1192, Japan
| | - María Carmen Pallarés
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, Zaragoza 50009, Spain; Laboratorio de Microscopias Avanzadas (LMA), Universidad de Zaragoza, Zaragoza 50018, Spain
| | - Arkadiusz Ptak
- Institute of Physics, Faculty of Materials Engineering and Technical Physics, Poznan University of Technology, Poznan 60-925, Poland
| | - Carlos Marcuello
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, Zaragoza 50009, Spain; Laboratorio de Microscopias Avanzadas (LMA), Universidad de Zaragoza, Zaragoza 50018, Spain.
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22
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Nierzwicki Ł, Ahsan M, Palermo G. The Electronic Structure of Genome Editors from the First Principles. ELECTRONIC STRUCTURE (BRISTOL, ENGLAND) 2023; 5:014003. [PMID: 36926635 PMCID: PMC10016068 DOI: 10.1088/2516-1075/acb410] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Genome editing based on the CRISPR-Cas9 system has paved new avenues for medicine, pharmaceutics, biotechnology, and beyond. This article reports the role of first-principles (ab-initio) molecular dynamics (MD) in the CRISPR-Cas9 revolution, achieving a profound understanding of the enzymatic function and offering valuable insights for enzyme engineering. We introduce the methodologies and explain the use of ab-initio MD simulations to characterize the two-metal dependent mechanism of DNA cleavage in the RuvC domain of the Cas9 enzyme, and how a second catalytic domain, HNH, cleaves the target DNA with the aid of a single metal ion. A detailed description of how ab-initio MD is combined with free-energy methods - i.e., thermodynamic integration and metadynamics - to break and form chemical bonds is given, explaining the use of these methods to determine the chemical landscape and establish the catalytic mechanism in CRISPR-Cas9. The critical role of classical methods is also discussed, explaining theory and application of constant pH MD simulations, used to accurately predict the catalytic residues' protonation states. Overall, first-principles methods are shown to unravel the electronic structure of the Cas9 enzyme, providing valuable insights that can serve for the design of genome editing tools with improved catalytic efficiency or controllable activity.
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Affiliation(s)
- Łukasz Nierzwicki
- Department of Bioengineering, University of California Riverside, 900 University Avenue, Riverside, CA 52512, United States
| | - Mohd Ahsan
- Department of Bioengineering, University of California Riverside, 900 University Avenue, Riverside, CA 52512, United States
| | - Giulia Palermo
- Department of Bioengineering, University of California Riverside, 900 University Avenue, Riverside, CA 52512, United States
- Department of Chemistry, University of California Riverside, 900 University Avenue, Riverside, CA 52512, United States
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23
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Bekkouche I, Shishonin AY, Vetcher AA. Recent Development in Biomedical Applications of Oligonucleotides with Triplex-Forming Ability. Polymers (Basel) 2023; 15:858. [PMID: 36850142 PMCID: PMC9964087 DOI: 10.3390/polym15040858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 01/31/2023] [Accepted: 02/02/2023] [Indexed: 02/12/2023] Open
Abstract
A DNA structure, known as triple-stranded DNA, is made up of three oligonucleotide chains that wind around one another to form a triple helix (TFO). Hoogsteen base pairing describes how triple-stranded DNA may be built at certain conditions by the attachment of the third strand to an RNA, PNA, or DNA, which might all be employed as oligonucleotide chains. In each of these situations, the oligonucleotides can be employed as an anchor, in conjunction with a specific bioactive chemical, or as a messenger that enables switching between transcription and replication through the triplex-forming zone. These data are also considered since various illnesses have been linked to the expansion of triplex-prone sequences. In light of metabolic acidosis and associated symptoms, some consideration is given to the impact of several low-molecular-weight compounds, including pH on triplex production in vivo. The review is focused on the development of biomedical oligonucleotides with triplexes.
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Affiliation(s)
- Incherah Bekkouche
- Nanotechnology Scientific and Educational Center, Institute of Biochemical Technology and Nanotechnology, Peoples’ Friendship University of Russia (RUDN), Miklukho-Maklaya Str. 6, Moscow 117198, Russia
| | - Alexander Y. Shishonin
- Complementary and Integrative Health Clinic of Dr. Shishonin, 5, Yasnogorskaya Str., Moscow 117588, Russia
| | - Alexandre A. Vetcher
- Nanotechnology Scientific and Educational Center, Institute of Biochemical Technology and Nanotechnology, Peoples’ Friendship University of Russia (RUDN), Miklukho-Maklaya Str. 6, Moscow 117198, Russia
- Complementary and Integrative Health Clinic of Dr. Shishonin, 5, Yasnogorskaya Str., Moscow 117588, Russia
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Haghizadeh A, Iftikhar M, Dandpat SS, Simpson T. Looking at Biomolecular Interactions through the Lens of Correlated Fluorescence Microscopy and Optical Tweezers. Int J Mol Sci 2023; 24:2668. [PMID: 36768987 PMCID: PMC9916863 DOI: 10.3390/ijms24032668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/19/2022] [Accepted: 01/26/2023] [Indexed: 02/01/2023] Open
Abstract
Understanding complex biological events at the molecular level paves the path to determine mechanistic processes across the timescale necessary for breakthrough discoveries. While various conventional biophysical methods provide some information for understanding biological systems, they often lack a complete picture of the molecular-level details of such dynamic processes. Studies at the single-molecule level have emerged to provide crucial missing links to understanding complex and dynamic pathways in biological systems, which are often superseded by bulk biophysical and biochemical studies. Latest developments in techniques combining single-molecule manipulation tools such as optical tweezers and visualization tools such as fluorescence or label-free microscopy have enabled the investigation of complex and dynamic biomolecular interactions at the single-molecule level. In this review, we present recent advances using correlated single-molecule manipulation and visualization-based approaches to obtain a more advanced understanding of the pathways for fundamental biological processes, and how this combination technique is facilitating research in the dynamic single-molecule (DSM), cell biology, and nanomaterials fields.
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25
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Wang J, Arantes PR, Ahsan M, Sinha S, Kyro GW, Maschietto F, Allen B, Skeens E, Lisi GP, Batista VS, Palermo G. Twisting and swiveling domain motions in Cas9 to recognize target DNA duplexes, make double-strand breaks, and release cleaved duplexes. Front Mol Biosci 2023; 9:1072733. [PMID: 36699705 PMCID: PMC9868570 DOI: 10.3389/fmolb.2022.1072733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 12/12/2022] [Indexed: 01/11/2023] Open
Abstract
The CRISPR-associated protein 9 (Cas9) has been engineered as a precise gene editing tool to make double-strand breaks. CRISPR-associated protein 9 binds the folded guide RNA (gRNA) that serves as a binding scaffold to guide it to the target DNA duplex via a RecA-like strand-displacement mechanism but without ATP binding or hydrolysis. The target search begins with the protospacer adjacent motif or PAM-interacting domain, recognizing it at the major groove of the duplex and melting its downstream duplex where an RNA-DNA heteroduplex is formed at nanomolar affinity. The rate-limiting step is the formation of an R-loop structure where the HNH domain inserts between the target heteroduplex and the displaced non-target DNA strand. Once the R-loop structure is formed, the non-target strand is rapidly cleaved by RuvC and ejected from the active site. This event is immediately followed by cleavage of the target DNA strand by the HNH domain and product release. Within CRISPR-associated protein 9, the HNH domain is inserted into the RuvC domain near the RuvC active site via two linker loops that provide allosteric communication between the two active sites. Due to the high flexibility of these loops and active sites, biophysical techniques have been instrumental in characterizing the dynamics and mechanism of the CRISPR-associated protein 9 nucleases, aiding structural studies in the visualization of the complete active sites and relevant linker structures. Here, we review biochemical, structural, and biophysical studies on the underlying mechanism with emphasis on how CRISPR-associated protein 9 selects the target DNA duplex and rejects non-target sequences.
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Affiliation(s)
- Jimin Wang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - Pablo R. Arantes
- Department of Bioengineering and Department of Chemistry, University of California, Riverside, Riverside, CA, United States
| | - Mohd Ahsan
- Department of Bioengineering and Department of Chemistry, University of California, Riverside, Riverside, CA, United States
| | - Souvik Sinha
- Department of Bioengineering and Department of Chemistry, University of California, Riverside, Riverside, CA, United States
| | - Gregory W. Kyro
- Department of Chemistry, Yale University, New Haven, CT, United States
| | | | - Brandon Allen
- Department of Chemistry, Yale University, New Haven, CT, United States
| | - Erin Skeens
- Department of Molecular and Cell Biology and Biochemistry, Brown University, Providence, RI, United States
| | - George P. Lisi
- Department of Molecular and Cell Biology and Biochemistry, Brown University, Providence, RI, United States
| | - Victor S. Batista
- Department of Chemistry, Yale University, New Haven, CT, United States
| | - Giulia Palermo
- Department of Bioengineering and Department of Chemistry, University of California, Riverside, Riverside, CA, United States
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26
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Halma MTJ, Tuszynski JA, Wuite GJL. Optical tweezers for drug discovery. Drug Discov Today 2023; 28:103443. [PMID: 36396117 DOI: 10.1016/j.drudis.2022.103443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 09/23/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022]
Abstract
The time taken and the cost of producing novel therapeutic drugs presents a significant burden - a typical target-based drug discovery process involves computational screening of drug libraries, compound assays and expensive clinical trials. This review summarises the value of dynamic conformational information obtained by optical tweezers and how this information can target 'undruggable' proteins. Optical tweezers provide insights into the link between biological mechanisms and structural conformations, which can be used in drug discovery. Developing workflows including software and sample preparation will improve throughput, enabling adoption of optical tweezers in biopharma. As a complementary tool, optical tweezers increase the number of drug candidates, improve the understanding of a target's complex structural dynamics and elucidate interactions between compounds and their targets.
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Affiliation(s)
- Matthew T J Halma
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands; LUMICKS B.V, Paalbergweg 3, 1105 AG Amsterdam, The Netherlands
| | - Jack A Tuszynski
- Department of Physics, University of Alberta, 116 St 85 Ave, Edmonton, Alberta T6G 2R3, Canada
| | - Gijs J L Wuite
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands.
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27
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Parker D. Neurobiological reduction: From cellular explanations of behavior to interventions. Front Psychol 2022; 13:987101. [PMID: 36619115 PMCID: PMC9815460 DOI: 10.3389/fpsyg.2022.987101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 11/28/2022] [Indexed: 12/24/2022] Open
Abstract
Scientific reductionism, the view that higher level functions can be explained by properties at some lower-level or levels, has been an assumption of nervous system analyses since the acceptance of the neuron doctrine in the late 19th century, and became a dominant experimental approach with the development of intracellular recording techniques in the mid-20th century. Subsequent refinements of electrophysiological approaches and the continual development of molecular and genetic techniques have promoted a focus on molecular and cellular mechanisms in experimental analyses and explanations of sensory, motor, and cognitive functions. Reductionist assumptions have also influenced our views of the etiology and treatment of psychopathologies, and have more recently led to claims that we can, or even should, pharmacologically enhance the normal brain. Reductionism remains an area of active debate in the philosophy of science. In neuroscience and psychology, the debate typically focuses on the mind-brain question and the mechanisms of cognition, and how or if they can be explained in neurobiological terms. However, these debates are affected by the complexity of the phenomena being considered and the difficulty of obtaining the necessary neurobiological detail. We can instead ask whether features identified in neurobiological analyses of simpler aspects in simpler nervous systems support current molecular and cellular approaches to explaining systems or behaviors. While my view is that they do not, this does not invite the opposing view prevalent in dichotomous thinking that molecular and cellular detail is irrelevant and we should focus on computations or representations. We instead need to consider how to address the long-standing dilemma of how a nervous system that ostensibly functions through discrete cell to cell communication can generate population effects across multiple spatial and temporal scales to generate behavior.
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28
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Shi YJ, Duan M, Ding JM, Wang FQ, Bi LL, Zhang CX, Zhang YZ, Duan JY, Huang AH, Lei XL, Yin H, Zhang Y. DNA topology regulates PAM-Cas9 interaction and DNA unwinding to enable near-PAMless cleavage by thermophilic Cas9. Mol Cell 2022; 82:4160-4175.e6. [DOI: 10.1016/j.molcel.2022.09.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 08/04/2022] [Accepted: 09/27/2022] [Indexed: 11/06/2022]
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29
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Zagorski K, Stormberg T, Hashemi M, Kolomeisky AB, Lyubchenko YL. Nanorings to Probe Mechanical Stress of Single-Stranded DNA Mediated by the DNA Duplex. Int J Mol Sci 2022; 23:12916. [PMID: 36361704 PMCID: PMC9655958 DOI: 10.3390/ijms232112916] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 10/18/2022] [Accepted: 10/23/2022] [Indexed: 01/11/2024] Open
Abstract
The interplay between the mechanical properties of double-stranded and single-stranded DNA is a phenomenon that contributes to various genetic processes in which both types of DNA structures coexist. Highly stiff DNA duplexes can stretch single-stranded DNA (ssDNA) segments between the duplexes in a topologically constrained domain. To evaluate such an effect, we designed short DNA nanorings in which a DNA duplex with 160 bp is connected by a 30 nt single-stranded DNA segment. The stretching effect of the duplex in such a DNA construct can lead to the elongation of ssDNA, and this effect can be measured directly using atomic force microscopy (AFM) imaging. In AFM images of the nanorings, the ssDNA regions were identified, and the end-to-end distance of ssDNA was measured. The data revealed a stretching of the ssDNA segment with a median end-to-end distance which was 16% higher compared with the control. These data are in line with theoretical estimates of the stretching of ssDNA by the rigid DNA duplex holding the ssDNA segment within the nanoring construct. Time-lapse AFM data revealed substantial dynamics of the DNA rings, allowing for the formation of transient crossed nanoring formations with end-to-end distances as much as 30% larger than those of the longer-lived morphologies. The generated nanorings are an attractive model system for investigation of the effects of mechanical stretching of ssDNA on its biochemical properties, including interaction with proteins.
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Affiliation(s)
- Karen Zagorski
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Tommy Stormberg
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Mohtadin Hashemi
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | | | - Yuri L. Lyubchenko
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE 68198, USA
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30
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Kaczmarczyk AP, Déclais AC, Newton MD, Boulton SJ, Lilley DMJ, Rueda DS. Search and processing of Holliday junctions within long DNA by junction-resolving enzymes. Nat Commun 2022; 13:5921. [PMID: 36207294 PMCID: PMC9547003 DOI: 10.1038/s41467-022-33503-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 09/21/2022] [Indexed: 12/05/2022] Open
Abstract
Resolution of Holliday junctions is a critical intermediate step of homologous recombination in which junctions are processed by junction-resolving endonucleases. Although binding and cleavage are well understood, the question remains how the enzymes locate their substrate within long duplex DNA. Here we track fluorescent dimers of endonuclease I on DNA, presenting the complete single-molecule reaction trajectory for a junction-resolving enzyme finding and cleaving a Holliday junction. We show that the enzyme binds remotely to dsDNA and then undergoes 1D diffusion. Upon encountering a four-way junction, a catalytically-impaired mutant remains bound at that point. An active enzyme, however, cleaves the junction after a few seconds. Quantitative analysis provides a comprehensive description of the facilitated diffusion mechanism. We show that the eukaryotic junction-resolving enzyme GEN1 also undergoes facilitated diffusion on dsDNA until it becomes located at a junction, so that the general resolution trajectory is probably applicable to many junction resolving enzymes.
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Affiliation(s)
- Artur P Kaczmarczyk
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
- Single Molecule Imaging Group, MRC-London Institute of Medical Sciences, London, W12 0NN, UK
| | | | - Matthew D Newton
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
- Single Molecule Imaging Group, MRC-London Institute of Medical Sciences, London, W12 0NN, UK
- DSB Repair Metabolism Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Simon J Boulton
- DSB Repair Metabolism Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - David M J Lilley
- School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK.
| | - David S Rueda
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, W12 0NN, UK.
- Single Molecule Imaging Group, MRC-London Institute of Medical Sciences, London, W12 0NN, UK.
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Khurana A, Sayed N, Singh V, Khurana I, Allawadhi P, Rawat PS, Navik U, Pasumarthi SK, Bharani KK, Weiskirchen R. A comprehensive overview of CRISPR/Cas 9 technology and application thereof in drug discovery. J Cell Biochem 2022; 123:1674-1698. [PMID: 36128934 DOI: 10.1002/jcb.30329] [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] [Received: 04/24/2022] [Revised: 08/13/2022] [Accepted: 09/01/2022] [Indexed: 11/07/2022]
Abstract
Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-Cas technology possesses revolutionary potential to positively affect various domains of drug discovery. It has initiated a rise in the area of genetic engineering and its advantages range from classical science to translational medicine. These genome editing systems have given a new dimension to our capabilities to alter, detect and annotate specified gene sequences. Moreover, the ease, robustness and adaptability of the CRISPR/Cas9 technology have led to its extensive utilization in research areas in such a short period of time. The applications include the development of model cell lines, understanding disease mechanisms, discovering disease targets, developing transgenic animals and plants, and transcriptional modulation. Further, the technology is rapidly growing; hence, an overlook of progressive success is crucial. This review presents the current status of the CRISPR-Cas technology in a tailor-made format from its discovery to several advancements for drug discovery alongwith future trends associated with possibilities and hurdles including ethical concerns.
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Affiliation(s)
- Amit Khurana
- Institute of Molecular Pathobiochemistry, Experimental Gene Therapy and Clinical Chemistry (IFMPEGKC), RWTH Aachen University Hospital, Aachen, Germany
- Department of Veterinary Pharmacology and Toxicology, College of Veterinary Science (CVSc), PVNRTVU, Hyderabad, Telangana, India
- Department of Veterinary Pharmacology and Toxicology, College of Veterinary Science (CVSc), PVNRTVU, Mamnoor, Warangal, Telangana, India
| | - Nilofer Sayed
- Department of Pharmacy, Pravara Rural Education Society's (P.R.E.S.'s) College of Pharmacy, Shreemati Nathibai Damodar Thackersey (SNDT) Women's University, Nashik, Maharashtra, India
| | - Vishakha Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Isha Khurana
- Department of Pharmaceutical Chemistry, University Institute of Pharmaceutical Sciences (UIPS), Panjab University, Chandigarh, India
| | - Prince Allawadhi
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Pushkar Singh Rawat
- Department of Pharmacology, Central University of Punjab, Ghudda, Bathinda, Punjab, India
| | - Umashanker Navik
- Department of Pharmacology, Central University of Punjab, Ghudda, Bathinda, Punjab, India
| | | | - Kala Kumar Bharani
- Department of Veterinary Pharmacology and Toxicology, College of Veterinary Science (CVSc), PVNRTVU, Mamnoor, Warangal, Telangana, India
| | - Ralf Weiskirchen
- Institute of Molecular Pathobiochemistry, Experimental Gene Therapy and Clinical Chemistry (IFMPEGKC), RWTH Aachen University Hospital, Aachen, Germany
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32
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Pacesa M, Loeff L, Querques I, Muckenfuss LM, Sawicka M, Jinek M. R-loop formation and conformational activation mechanisms of Cas9. Nature 2022; 609:191-196. [PMID: 36002571 PMCID: PMC9433323 DOI: 10.1038/s41586-022-05114-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 07/14/2022] [Indexed: 12/25/2022]
Abstract
Cas9 is a CRISPR-associated endonuclease capable of RNA-guided, site-specific DNA cleavage1-3. The programmable activity of Cas9 has been widely utilized for genome editing applications4-6, yet its precise mechanisms of target DNA binding and off-target discrimination remain incompletely understood. Here we report a series of cryo-electron microscopy structures of Streptococcus pyogenes Cas9 capturing the directional process of target DNA hybridization. In the early phase of R-loop formation, the Cas9 REC2 and REC3 domains form a positively charged cleft that accommodates the distal end of the target DNA duplex. Guide-target hybridization past the seed region induces rearrangements of the REC2 and REC3 domains and relocation of the HNH nuclease domain to assume a catalytically incompetent checkpoint conformation. Completion of the guide-target heteroduplex triggers conformational activation of the HNH nuclease domain, enabled by distortion of the guide-target heteroduplex, and complementary REC2 and REC3 domain rearrangements. Together, these results establish a structural framework for target DNA-dependent activation of Cas9 that sheds light on its conformational checkpoint mechanism and may facilitate the development of novel Cas9 variants and guide RNA designs with enhanced specificity and activity.
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Affiliation(s)
- Martin Pacesa
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Luuk Loeff
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Irma Querques
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Lena M Muckenfuss
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Marta Sawicka
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Martin Jinek
- Department of Biochemistry, University of Zurich, Zurich, Switzerland.
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Okafor IC, Choi J, Ha T. Single molecule methods for studying CRISPR Cas9-induced DNA unwinding. Methods 2022; 204:319-326. [PMID: 34767923 DOI: 10.1016/j.ymeth.2021.11.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 10/12/2021] [Accepted: 11/03/2021] [Indexed: 12/12/2022] Open
Abstract
Like helicases, CRISPR proteins such as Cas9 and Cas12a unwind DNA, but unlike helicases, these CRISPR proteins do not use ATP. Instead, they use binding energy to melt DNA locally and then utilize basepairing between guide (g) RNA and target strand to continue to unwind the DNA. CRISPR Cas9 is the most widely used tool for genome editing applications. The Cas9 endonuclease forms a complex with gRNA that can be programmed to bind a specific 20 bp segment of DNA, the protospacer. If there is enough of a sequence match between sgRNA and protospacer, Cas9 undergoes a conformational change, which activates the two nuclease domains, causing a double strand break in the DNA. We can use single-molecule FRET (smFRET) to probe the state of DNA unwinding as a function of mismatches between sgRNA and DNA. This approach can also be used to probe the position of Cas9's HNH domain before and after cleavage.
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Affiliation(s)
- Ikenna C Okafor
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Janice Choi
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA; Howard Hughes Medical Institute, Baltimore, MD, USA.
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Liu SC, Feng YL, Sun XN, Chen RD, Liu Q, Xiao JJ, Zhang JN, Huang ZC, Xiang JF, Chen GQ, Yang Y, Lou C, Li HD, Cai Z, Xu SM, Lin H, Xie AY. Target residence of Cas9-sgRNA influences DNA double-strand break repair pathway choices in CRISPR/Cas9 genome editing. Genome Biol 2022; 23:165. [PMID: 35915475 PMCID: PMC9341079 DOI: 10.1186/s13059-022-02736-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 07/22/2022] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND Due to post-cleavage residence of the Cas9-sgRNA complex at its target, Cas9-induced DNA double-strand breaks (DSBs) have to be exposed to engage DSB repair pathways. Target interaction of Cas9-sgRNA determines its target binding affinity and modulates its post-cleavage target residence duration and exposure of Cas9-induced DSBs. This exposure, via different mechanisms, may initiate variable DNA damage responses, influencing DSB repair pathway choices and contributing to mutational heterogeneity in genome editing. However, this regulation of DSB repair pathway choices is poorly understood. RESULTS In repair of Cas9-induced DSBs, repair pathway choices vary widely at different target sites and classical nonhomologous end joining (c-NHEJ) is not even engaged at some sites. In mouse embryonic stem cells, weakening the target interaction of Cas9-sgRNA promotes bias towards c-NHEJ and increases target dissociation and reduces target residence of Cas9-sgRNAs in vitro. As an important strategy for enhancing homology-directed repair, inactivation of c-NHEJ aggravates off-target activities of Cas9-sgRNA due to its weak interaction with off-target sites. By dislodging Cas9-sgRNA from its cleaved targets, DNA replication alters DSB end configurations and suppresses c-NHEJ in favor of other repair pathways, whereas transcription has little effect on c-NHEJ engagement. Dissociation of Cas9-sgRNA from its cleaved target by DNA replication may generate three-ended DSBs, resulting in palindromic fusion of sister chromatids, a potential source for CRISPR/Cas9-induced on-target chromosomal rearrangements. CONCLUSIONS Target residence of Cas9-sgRNA modulates DSB repair pathway choices likely through varying dissociation of Cas9-sgRNA from cleaved DNA, thus widening on-target and off-target mutational spectra in CRISPR/Cas9 genome editing.
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Affiliation(s)
- Si-Cheng Liu
- Innovation Center for Minimally Invasive Technique and Device, Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310019, People's Republic of China
- Institute of Translational Medicine, Zhejiang University School of Medicine and Zhejiang University Cancer Center, Hangzhou, Zhejiang, 310029, People's Republic of China
| | - Yi-Li Feng
- Innovation Center for Minimally Invasive Technique and Device, Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310019, People's Republic of China
- Institute of Translational Medicine, Zhejiang University School of Medicine and Zhejiang University Cancer Center, Hangzhou, Zhejiang, 310029, People's Republic of China
- Department of Biochemistry and Molecular Biology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310058, People's Republic of China
| | - Xiu-Na Sun
- Innovation Center for Minimally Invasive Technique and Device, Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310019, People's Republic of China
- Institute of Translational Medicine, Zhejiang University School of Medicine and Zhejiang University Cancer Center, Hangzhou, Zhejiang, 310029, People's Republic of China
| | - Ruo-Dan Chen
- Innovation Center for Minimally Invasive Technique and Device, Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310019, People's Republic of China
- Institute of Translational Medicine, Zhejiang University School of Medicine and Zhejiang University Cancer Center, Hangzhou, Zhejiang, 310029, People's Republic of China
- Department of Biochemistry and Molecular Biology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310058, People's Republic of China
| | - Qian Liu
- Innovation Center for Minimally Invasive Technique and Device, Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310019, People's Republic of China
- Institute of Translational Medicine, Zhejiang University School of Medicine and Zhejiang University Cancer Center, Hangzhou, Zhejiang, 310029, People's Republic of China
| | - Jing-Jing Xiao
- Innovation Center for Minimally Invasive Technique and Device, Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310019, People's Republic of China
- Institute of Translational Medicine, Zhejiang University School of Medicine and Zhejiang University Cancer Center, Hangzhou, Zhejiang, 310029, People's Republic of China
| | - Jin-Na Zhang
- Institute of Translational Medicine, Zhejiang University School of Medicine and Zhejiang University Cancer Center, Hangzhou, Zhejiang, 310029, People's Republic of China
- The First affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310019, People's Republic of China
| | - Zhi-Cheng Huang
- Innovation Center for Minimally Invasive Technique and Device, Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310019, People's Republic of China
- Institute of Translational Medicine, Zhejiang University School of Medicine and Zhejiang University Cancer Center, Hangzhou, Zhejiang, 310029, People's Republic of China
| | - Ji-Feng Xiang
- Innovation Center for Minimally Invasive Technique and Device, Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310019, People's Republic of China
- Institute of Translational Medicine, Zhejiang University School of Medicine and Zhejiang University Cancer Center, Hangzhou, Zhejiang, 310029, People's Republic of China
- Institute of Hepatopancreatobiliary Surgery, Chongqing General Hospital, University of Chinese Academy of Sciences, Chongqing, 400013, People's Republic of China
| | - Guo-Qiao Chen
- Innovation Center for Minimally Invasive Technique and Device, Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310019, People's Republic of China
- Institute of Translational Medicine, Zhejiang University School of Medicine and Zhejiang University Cancer Center, Hangzhou, Zhejiang, 310029, People's Republic of China
| | - Yi Yang
- Institute of Translational Medicine, Zhejiang University School of Medicine and Zhejiang University Cancer Center, Hangzhou, Zhejiang, 310029, People's Republic of China
| | - Chao Lou
- Shurui Tech Ltd, Hangzhou, Zhejiang, 310005, People's Republic of China
| | - Hao-Dan Li
- Shurui Tech Ltd, Hangzhou, Zhejiang, 310005, People's Republic of China
| | - Zhen Cai
- The First affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310019, People's Republic of China
| | - Shi-Ming Xu
- Institute of Translational Medicine, Zhejiang University School of Medicine and Zhejiang University Cancer Center, Hangzhou, Zhejiang, 310029, People's Republic of China
| | - Hui Lin
- Innovation Center for Minimally Invasive Technique and Device, Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310019, People's Republic of China
| | - An-Yong Xie
- Innovation Center for Minimally Invasive Technique and Device, Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310019, People's Republic of China.
- Institute of Translational Medicine, Zhejiang University School of Medicine and Zhejiang University Cancer Center, Hangzhou, Zhejiang, 310029, People's Republic of China.
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Saha A, Arantes PR, Palermo G. Dynamics and mechanisms of CRISPR-Cas9 through the lens of computational methods. Curr Opin Struct Biol 2022; 75:102400. [PMID: 35689914 PMCID: PMC9398989 DOI: 10.1016/j.sbi.2022.102400] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 04/25/2022] [Accepted: 05/07/2022] [Indexed: 12/24/2022]
Abstract
The clustered regularly interspaced short palindromic repeat (CRISPR) genome-editing revolution established the beginning of a new era in life sciences. Here, we review the role of state-of-the-art computations in the CRISPR-Cas9 revolution, from the early refinement of cryo-EM data to enhanced simulations of large-scale conformational transitions. Molecular simulations reported a mechanism for RNA binding and the formation of a catalytically competent Cas9 enzyme, in agreement with subsequent structural studies. Inspired by single-molecule experiments, molecular dynamics offered a rationale for the onset of off-target effects, while graph theory unveiled the allosteric regulation. Finally, the use of a mixed quantum-classical approach established the catalytic mechanism of DNA cleavage. Overall, molecular simulations have been instrumental in understanding the dynamics and mechanism of CRISPR-Cas9, contributing to understanding function, catalysis, allostery, and specificity.
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Affiliation(s)
- Aakash Saha
- Department of Bioengineering, University of California Riverside, 900 University Avenue, Riverside, CA, 52512, United States. https://twitter.com/@aakashsahha
| | - Pablo R Arantes
- Department of Bioengineering, University of California Riverside, 900 University Avenue, Riverside, CA, 52512, United States. https://twitter.com/@pablitoarantes
| | - Giulia Palermo
- Department of Bioengineering, University of California Riverside, 900 University Avenue, Riverside, CA, 52512, United States; Department of Chemistry, University of California Riverside, 900 University Avenue, Riverside, CA, 52512, United States.
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36
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Carcamo CC, Poyton MF, Ranjan A, Park G, Louder RK, Feng XA, Kim JM, Dzu T, Wu C, Ha T. ATP binding facilitates target search of SWR1 chromatin remodeler by promoting one-dimensional diffusion on DNA. eLife 2022; 11:e77352. [PMID: 35876491 PMCID: PMC9365391 DOI: 10.7554/elife.77352] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 07/22/2022] [Indexed: 12/01/2022] Open
Abstract
One-dimensional (1D) target search is a well-characterized phenomenon for many DNA-binding proteins but is poorly understood for chromatin remodelers. Herein, we characterize the 1D scanning properties of SWR1, a conserved yeast chromatin remodeler that performs histone exchange on +1 nucleosomes adjacent to a nucleosome-depleted region (NDR) at gene promoters. We demonstrate that SWR1 has a kinetic binding preference for DNA of NDR length as opposed to gene-body linker length DNA. Using single and dual color single-particle tracking on DNA stretched with optical tweezers, we directly observe SWR1 diffusion on DNA. We found that various factors impact SWR1 scanning, including ATP which promotes diffusion through nucleotide binding rather than ATP hydrolysis. A DNA-binding subunit, Swc2, plays an important role in the overall diffusive behavior of the complex, as the subunit in isolation retains similar, although faster, scanning properties as the whole remodeler. ATP-bound SWR1 slides until it encounters a protein roadblock, of which we tested dCas9 and nucleosomes. The median diffusion coefficient, 0.024 μm2/s, in the regime of helical sliding, would mediate rapid encounter of NDR-flanking nucleosomes at length scales found in cellular chromatin.
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Affiliation(s)
- Claudia C Carcamo
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins UniversityBaltimoreUnited States
| | - Matthew F Poyton
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins UniversityBaltimoreUnited States
| | - Anand Ranjan
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Giho Park
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Robert K Louder
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Xinyu A Feng
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins UniversityBaltimoreUnited States
| | - Jee Min Kim
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Thuc Dzu
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Carl Wu
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins UniversityBaltimoreUnited States
- Howard Hughes Medical InstituteBaltimoreUnited States
- Johns Hopkins University, Department of Biomedical EngineeringBaltimoreUnited States
- Johns Hopkins University, Department of BiophysicsBaltimoreUnited States
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37
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In vitro single molecule and bulk phase studies reveal the AP-1 transcription factor cFos binds to DNA without its partner cJun. J Biol Chem 2022; 298:102229. [PMID: 35787376 PMCID: PMC9364023 DOI: 10.1016/j.jbc.2022.102229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 06/27/2022] [Accepted: 06/29/2022] [Indexed: 11/23/2022] Open
Abstract
The AP-1 transcription factor family crucially regulates progression of the cell cycle, as well as playing roles in proliferation, differentiation, and the stress response. The two best described AP-1 family members, cFos and cJun, are known to dimerize to form a functional AP-1 heterodimer that binds to a consensus response element sequence. Although cJun can also homodimerize and bind to DNA, the canonical view is that cFos cannot bind DNA without heterodimerizing with cJun. Here, we show that cFos can actually bind to DNA in the absence of cJun in vitro. Using dual color single molecule imaging of cFos alone, we directly visualize binding to and movement on DNA. Of all these DNA-bound proteins, detailed analysis suggested 30 to 46% were homodimers. Furthermore, we constructed fluorescent protein fusions of cFos and cJun for Förster resonance energy transfer experiments. These constructs indicated complete dimerization of cJun, but although cFos could dimerize, its extent was reduced. Finally, to provide orthogonal confirmation of cFos binding to DNA, we performed bulk-phase circular dichroism experiments that showed clear structural changes in DNA; these were found to be specific to the AP-1 consensus sequence. Taken together, our results clearly show cFos can interact with DNA both as monomers and dimers independently of its archetypal partner, cJun.
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38
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Zhao M, Gao M, Xiong L, Liu Y, Tao X, Gao B, Liu M, Wang FQ, Wei DZ. CRISPR-Cas Assisted Shotgun Mutagenesis Method for Evolutionary Genome Engineering. ACS Synth Biol 2022; 11:1958-1970. [PMID: 35500195 DOI: 10.1021/acssynbio.2c00112] [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: 11/29/2022]
Abstract
Genome mutagenesis drives the evolution of organisms. Here, we developed a CRISPR-Cas assisted random mutation (CARM) technique for whole-genome mutagenesis. The method leverages an entirely random gRNA library and SpCas9-NG to randomly damage genomes in a controllable shotgunlike manner that then triggers diverse and abundant mutations via low-fidelity repair. As a proof of principle, CARM was applied to evolve the capacity of Saccharomyces cerevisiae BY4741 to produce β-carotene. After seven rounds of iterative evolution over two months, a β-carotene hyperproducing strain, C7-143, was isolated with a 10.5-fold increase in β-carotene production and 857 diverse genomic mutations that comprised indels, duplications, inversions, and chromosomal rearrangements. Transcriptomic analysis revealed that the expression of 2541 genes of strain C7-143 was significantly altered, suggesting that the metabolic landscape of the strain was deeply reconstructed. In addition, CARM was applied to evolve industrially relevant S. cerevisiae CEN.PK2-1C for S-adenosyl-L-methionine production, which was increased 2.28 times after just one round. Thus, CARM can contribute to increasing genetic diversity to identify new phenotypes that could further be investigated by reverse engineering.
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Affiliation(s)
- Ming Zhao
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
- Anhui Engineering Laboratory for Industrial Microbiology Molecular Breeding, College of Biological and Food Engineering, Anhui Polytechnic University, Wuhu 241000, China
| | - Miaomiao Gao
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Liangbin Xiong
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
- Shanghai Key Laboratory of Molecular Imaging, Shanghai University of Medicine and Health Sciences, Shanghai 201318, China
| | - Yongjun Liu
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Xinyi Tao
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Bei Gao
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Min Liu
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Feng-Qing Wang
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Dong-Zhi Wei
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
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Paul B, Chaubet L, Verver DE, Montoya G. Mechanics of CRISPR-Cas12a and engineered variants on λ-DNA. Nucleic Acids Res 2022; 50:5208-5225. [PMID: 34951457 PMCID: PMC9122593 DOI: 10.1093/nar/gkab1272] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 12/10/2021] [Accepted: 12/13/2021] [Indexed: 12/26/2022] Open
Abstract
Cas12a is an RNA-guided endonuclease that is emerging as a powerful genome-editing tool. Here, we selected a target site on bacteriophage λ-DNA and used optical tweezers combined with fluorescence to provide mechanistic insight into wild type Cas12a and three engineered variants, where the specific dsDNA and the unspecific ssDNA cleavage are dissociated (M1 and M2) and a third one which nicks the target DNA (M3). At low forces wtCas12a and the variants display two main off-target binding sites, while on stretched dsDNA at higher forces numerous binding events appear driven by the mechanical distortion of the DNA and partial matches to the crRNA. The multiple binding events onto dsDNA at high tension do not lead to cleavage, which is observed on the target site at low forces when the DNA is flexible. In addition, activity assays also show that the preferential off-target sites for this crRNA are not cleaved by wtCas12a, indicating that λ-DNA is only severed at the target site. Our single molecule data indicate that the Cas12a scaffold presents singular mechanical properties, which could be used to generate new endonucleases with biomedical and biotechnological applications.
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Affiliation(s)
- Bijoya Paul
- Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences University of Copenhagen, Blegdamsvej 3-B, Copenhagen 2200, Denmark
| | - Loïc Chaubet
- LUMICKS, Pilotenstraat 41, 1059 CH, Amsterdam, The Netherlands
| | | | - Guillermo Montoya
- Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences University of Copenhagen, Blegdamsvej 3-B, Copenhagen 2200, Denmark
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40
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Hormeno S, Wilkinson OJ, Aicart-Ramos C, Kuppa S, Antony E, Dillingham MS, Moreno-Herrero F. Human HELB is a processive motor protein that catalyzes RPA clearance from single-stranded DNA. Proc Natl Acad Sci U S A 2022; 119:e2112376119. [PMID: 35385349 PMCID: PMC9169624 DOI: 10.1073/pnas.2112376119] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 03/01/2022] [Indexed: 01/17/2023] Open
Abstract
Human DNA helicase B (HELB) is a poorly characterized helicase suggested to play both positive and negative regulatory roles in DNA replication and recombination. In this work, we used bulk and single-molecule approaches to characterize the biochemical activities of HELB protein with a particular focus on its interactions with Replication Protein A (RPA) and RPA–single-stranded DNA (ssDNA) filaments. HELB is a monomeric protein that binds tightly to ssDNA with a site size of ∼20 nucleotides. It couples ATP hydrolysis to translocation along ssDNA in the 5′ to 3′ direction accompanied by the formation of DNA loops. HELB also displays classical helicase activity, but this is very weak in the absence of an assisting force. HELB binds specifically to human RPA, which enhances its ATPase and ssDNA translocase activities but inhibits DNA unwinding. Direct observation of HELB on RPA nucleoprotein filaments shows that translocating HELB concomitantly clears RPA from ssDNA. This activity, which can allow other proteins access to ssDNA intermediates despite their shielding by RPA, may underpin the diverse roles of HELB in cellular DNA transactions.
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Affiliation(s)
- Silvia Hormeno
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain
| | - Oliver J. Wilkinson
- DNA:Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol BS8 1TD, United Kingdom
| | - Clara Aicart-Ramos
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain
| | - Sahiti Kuppa
- Department of Biochemistry, Saint Louis University, St. Louis, MO 63104
| | - Edwin Antony
- Department of Biochemistry, Saint Louis University, St. Louis, MO 63104
| | - Mark S. Dillingham
- DNA:Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol BS8 1TD, United Kingdom
| | - Fernando Moreno-Herrero
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain
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41
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Cofsky JC, Soczek KM, Knott GJ, Nogales E, Doudna JA. CRISPR-Cas9 bends and twists DNA to read its sequence. Nat Struct Mol Biol 2022; 29:395-402. [PMID: 35422516 PMCID: PMC9189902 DOI: 10.1038/s41594-022-00756-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 03/01/2022] [Indexed: 12/28/2022]
Abstract
In bacterial defense and genome editing applications, the CRISPR-associated protein Cas9 searches millions of DNA base pairs to locate a 20-nucleotide, guide RNA-complementary target sequence that abuts a protospacer-adjacent motif (PAM). Target capture requires Cas9 to unwind DNA at candidate sequences using an unknown ATP-independent mechanism. Here we show that Cas9 sharply bends and undertwists DNA on PAM binding, thereby flipping DNA nucleotides out of the duplex and toward the guide RNA for sequence interrogation. Cryogenic-electron microscopy (cryo-EM) structures of Cas9-RNA-DNA complexes trapped at different states of the interrogation pathway, together with solution conformational probing, reveal that global protein rearrangement accompanies formation of an unstacked DNA hinge. Bend-induced base flipping explains how Cas9 'reads' snippets of DNA to locate target sites within a vast excess of nontarget DNA, a process crucial to both bacterial antiviral immunity and genome editing. This mechanism establishes a physical solution to the problem of complementarity-guided DNA search and shows how interrogation speed and local DNA geometry may influence genome editing efficiency.
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Affiliation(s)
- Joshua C Cofsky
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Katarzyna M Soczek
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Gavin J Knott
- Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria, Australia
| | - Eva Nogales
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
- MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA.
- Innovative Genomics Institute, University of California, Berkeley, CA, USA.
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA.
- MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Department of Chemistry, University of California, Berkeley, CA, USA.
- Gladstone Institutes, University of California, San Francisco, CA, USA.
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA.
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42
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Roy RK, Debashree I, Srivastava S, Rishi N, Srivastava A. CRISPR/ Cas9 Off-targets: Computational Analysis of Causes, Prediction,
Detection, and Overcoming Strategies. Curr Bioinform 2022. [DOI: 10.2174/1574893616666210708150439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
:
CRISPR/Cas9 technology is a highly flexible RNA-guided endonuclease (RGEN)
based gene-editing tool that has transformed the field of genomics, gene therapy, and genome/
epigenome imaging. Its wide range of applications provides immense scope for understanding
as well as manipulating genetic/epigenetic elements. However, the RGEN is prone to
off-target mutagenesis that leads to deleterious effects. This review details the molecular and cellular
mechanisms underlying the off-target activity, various available detection tools and prediction
methodology ranging from sequencing to machine learning approaches, and the strategies to
overcome/minimise off-targets. A coherent and concise method increasing target precision would
prove indispensable to concrete manipulation and interpretation of genome editing results that
can revolutionise therapeutics, including clarity in genome regulatory mechanisms during development.
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Affiliation(s)
- Roshan Kumar Roy
- Amity Institute of Virology and Immunology, Amity University Uttar Pradesh, Noida 201313, India
| | - Ipsita Debashree
- Amity Institute of Virology and Immunology, Amity University Uttar Pradesh, Noida 201313, India
| | - Sonal Srivastava
- Amity Institute of Virology and Immunology, Amity University Uttar Pradesh, Noida 201313,India
| | - Narayan Rishi
- Amity Institute of Virology and Immunology, Amity University Uttar Pradesh, Noida 201313,India
| | - Ashish Srivastava
- Amity Institute of Virology and Immunology, Amity University Uttar Pradesh, Noida 201313,India
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43
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Ha T, Kaiser C, Myong S, Wu B, Xiao J. Next generation single-molecule techniques: Imaging, labeling, and manipulation in vitro and in cellulo. Mol Cell 2022; 82:304-314. [PMID: 35063098 DOI: 10.1016/j.molcel.2021.12.019] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 12/14/2021] [Accepted: 12/14/2021] [Indexed: 12/24/2022]
Abstract
Owing to their unique abilities to manipulate, label, and image individual molecules in vitro and in cellulo, single-molecule techniques provide previously unattainable access to elementary biological processes. In imaging, single-molecule fluorescence resonance energy transfer (smFRET) and protein-induced fluorescence enhancement in vitro can report on conformational changes and molecular interactions, single-molecule pull-down (SiMPull) can capture and analyze the composition and function of native protein complexes, and single-molecule tracking (SMT) in live cells reveals cellular structures and dynamics. In labeling, the abilities to specifically label genomic loci, mRNA, and nascent polypeptides in cells have uncovered chromosome organization and dynamics, transcription and translation dynamics, and gene expression regulation. In manipulation, optical tweezers, integration of single-molecule fluorescence with force measurements, and single-molecule force probes in live cells have transformed our mechanistic understanding of diverse biological processes, ranging from protein folding, nucleic acids-protein interactions to cell surface receptor function.
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Affiliation(s)
- Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA; Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA; Howard Hughes Medical Institute, Baltimore, MD 21205, USA.
| | - Christian Kaiser
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Sua Myong
- Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Bin Wu
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Jie Xiao
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
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44
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Newton MD, Taylor BJ, Cuomo ME, Rueda DS. CRISPR/Cas9 On- and Off-Target Activity Using Correlative Force and Fluorescence Single-Molecule Microscopy. Methods Mol Biol 2022; 2478:349-378. [PMID: 36063327 DOI: 10.1007/978-1-0716-2229-2_13] [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] [Indexed: 06/15/2023]
Abstract
The discovery of CRISPR/Cas9 as an easily programmable endonuclease heralds a new era of genetic manipulation. With this comes the prospect of novel gene therapy approaches, and the potential to cure previously untreatable genetic diseases. However, reports of spurious off-target editing by CRISPR/Cas9 pose a significant hurdle to realizing this potential. A deeper understanding of the factors that affect Cas9 specificity is vital for development of safe and efficient therapeutics. Here, we describe methods for the use of optical tweezers combined with confocal fluorescence microscopy and microfluidics for the analysis of on- and off-target activity of Cas9 activity.
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Affiliation(s)
- Matthew D Newton
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
- Single Molecule Imaging Group, MRC-London Institute of Medical Sciences, London, UK
| | | | | | - David S Rueda
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK.
- Single Molecule Imaging Group, MRC-London Institute of Medical Sciences, London, UK.
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45
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King GA, Spakman D, Peterman EJG, Wuite GJL. Generating Negatively Supercoiled DNA Using Dual-Trap Optical Tweezers. Methods Mol Biol 2022; 2478:243-272. [PMID: 36063323 DOI: 10.1007/978-1-0716-2229-2_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Many genomic processes lead to the formation of underwound (negatively supercoiled) or overwound (positively supercoiled) DNA. These DNA topological changes regulate the interactions of DNA-binding proteins, including transcription factors, architectural proteins and topoisomerases. In order to advance our understanding of the structure and interactions of supercoiled DNA, we recently developed a single-molecule approach called Optical DNA Supercoiling (ODS). This method enables rapid generation of negatively supercoiled DNA (with between <5% and 70% lower helical twist than nonsupercoiled DNA) using a standard dual-trap optical tweezers instrument. ODS is advantageous as it allows for combined force spectroscopy, fluorescence imaging, and spatial control of the supercoiled substrate, which is difficult to achieve with most other approaches. Here, we describe how to generate negatively supercoiled DNA using dual-trap optical tweezers. To this end, we provide detailed instructions on the design and preparation of suitable DNA substrates, as well as a step-by-step guide for how to control and calibrate the supercoiling density produced.
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Affiliation(s)
- Graeme A King
- Institute of Structural and Molecular Biology, University College London, London, UK.
| | - Dian Spakman
- Department of Physics and Astronomy, and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Erwin J G Peterman
- Department of Physics and Astronomy, and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
| | - Gijs J L Wuite
- Department of Physics and Astronomy, and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
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46
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Anand R, Buechelmaier E, Belan O, Newton M, Vancevska A, Kaczmarczyk A, Takaki T, Rueda DS, Powell SN, Boulton SJ. HELQ is a dual-function DSB repair enzyme modulated by RPA and RAD51. Nature 2022; 601:268-273. [PMID: 34937945 PMCID: PMC8755542 DOI: 10.1038/s41586-021-04261-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 11/17/2021] [Indexed: 02/04/2023]
Abstract
DNA double-stranded breaks (DSBs) are deleterious lesions, and their incorrect repair can drive cancer development1. HELQ is a superfamily 2 helicase with 3' to 5' polarity, and its disruption in mice confers germ cells loss, infertility and increased predisposition to ovarian and pituitary tumours2-4. At the cellular level, defects in HELQ result in hypersensitivity to cisplatin and mitomycin C, and persistence of RAD51 foci after DNA damage3,5. Notably, HELQ binds to RPA and the RAD51-paralogue BCDX2 complex, but the relevance of these interactions and how HELQ functions in DSB repair remains unclear3,5,6. Here we show that HELQ helicase activity and a previously unappreciated DNA strand annealing function are differentially regulated by RPA and RAD51. Using biochemistry analyses and single-molecule imaging, we establish that RAD51 forms a complex with and strongly stimulates HELQ as it translocates during DNA unwinding. By contrast, RPA inhibits DNA unwinding by HELQ but strongly stimulates DNA strand annealing. Mechanistically, we show that HELQ possesses an intrinsic ability to capture RPA-bound DNA strands and then displace RPA to facilitate annealing of complementary sequences. Finally, we show that HELQ deficiency in cells compromises single-strand annealing and microhomology-mediated end-joining pathways and leads to bias towards long-tract gene conversion tracts during homologous recombination. Thus, our results implicate HELQ in multiple arms of DSB repair through co-factor-dependent modulation of intrinsic translocase and DNA strand annealing activities.
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Affiliation(s)
- Roopesh Anand
- DSB Repair Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Erika Buechelmaier
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Ondrej Belan
- DSB Repair Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Matthew Newton
- DSB Repair Metabolism Laboratory, The Francis Crick Institute, London, UK
| | | | - Artur Kaczmarczyk
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
- Single Molecule Imaging Group, MRC-London Institute of Medical Sciences, London, UK
| | - Tohru Takaki
- DSB Repair Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - David S Rueda
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK.
- Single Molecule Imaging Group, MRC-London Institute of Medical Sciences, London, UK.
| | - Simon N Powell
- Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Simon J Boulton
- DSB Repair Metabolism Laboratory, The Francis Crick Institute, London, UK.
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Losito M, Smith QM, Newton MD, Cuomo ME, Rueda DS. Cas12a target search and cleavage on force-stretched DNA. Phys Chem Chem Phys 2021; 23:26640-26644. [PMID: 34494640 PMCID: PMC8653695 DOI: 10.1039/d1cp03408a] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Using optical tweezers, we investigate target search and cleavage by CRISPR-Cas12a on force-stretched λ-DNA. Cas12a uses fast, one-dimensional hopping to locate its target. Binding and cleavage occur rapidly and specifically at low forces (≤5 pN), with a 1.8 nm rate-limiting conformational change. Mechanical distortion slows diffusion, increases off-target binding but hinders cleavage.
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Affiliation(s)
- Marialucrezia Losito
- Department of Infectious Disease, Section of Virology, Faculty of Medicine, Imperial College London, London W12 0NN, UK.
- Single Molecule Imaging Group, MRC London Institute of Medical Sciences, London W12 0NN, UK
- Discovery Sciences, AstraZeneca, Cambridge CB4 0WG, UK
| | - Quentin M Smith
- Department of Infectious Disease, Section of Virology, Faculty of Medicine, Imperial College London, London W12 0NN, UK.
- Single Molecule Imaging Group, MRC London Institute of Medical Sciences, London W12 0NN, UK
| | - Matthew D Newton
- Department of Infectious Disease, Section of Virology, Faculty of Medicine, Imperial College London, London W12 0NN, UK.
- Single Molecule Imaging Group, MRC London Institute of Medical Sciences, London W12 0NN, UK
| | | | - David S Rueda
- Department of Infectious Disease, Section of Virology, Faculty of Medicine, Imperial College London, London W12 0NN, UK.
- Single Molecule Imaging Group, MRC London Institute of Medical Sciences, London W12 0NN, UK
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Aldag P, Welzel F, Jakob L, Schmidbauer A, Rutkauskas M, Fettes F, Grohmann D, Seidel R. Probing the stability of the SpCas9-DNA complex after cleavage. Nucleic Acids Res 2021; 49:12411-12421. [PMID: 34792162 PMCID: PMC8643700 DOI: 10.1093/nar/gkab1072] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 10/14/2021] [Accepted: 10/20/2021] [Indexed: 12/26/2022] Open
Abstract
CRISPR-Cas9 is a ribonucleoprotein complex that sequence-specifically binds and cleaves double-stranded DNA. Wildtype Cas9 and its nickase and cleavage-incompetent mutants have been used in various biological techniques due to their versatility and programmable specificity. Cas9 has been shown to bind very stably to DNA even after cleavage of the individual DNA strands, inhibiting further turnovers and considerably slowing down in-vivo repair processes. This poses an obstacle in genome editing applications. Here, we employed single-molecule magnetic tweezers to investigate the binding stability of different Streptococcus pyogenes Cas9 variants after cleavage by challenging them with supercoiling. We find that different release mechanisms occur depending on which DNA strand is cleaved. After initial target strand cleavage, supercoils are only removed after the collapse of the R-loop. We identified several states with different stabilities of the R-loop. Most importantly, we find that the post-cleavage state of Cas9 exhibits a higher stability than the pre-cleavage state. After non-target strand cleavage, supercoils are immediately but slowly released by swiveling of the non-target strand around Cas9 bound to the target strand. Consequently, Cas9 and its non-target strand nicking mutant stay stably bound to the DNA for many hours even at elevated torsional stress.
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Affiliation(s)
- Pierre Aldag
- Peter Debye Institute for Soft Matter Physics, University of Leipzig, Leipzig 04103, Germany
| | - Fabian Welzel
- Peter Debye Institute for Soft Matter Physics, University of Leipzig, Leipzig 04103, Germany
| | - Leonhard Jakob
- Institute of Microbiology & Archaea Centre, Single-Molecule Biochemistry Lab, University of Regensburg, Regensburg 93053, Germany
| | - Andreas Schmidbauer
- Institute of Microbiology & Archaea Centre, Single-Molecule Biochemistry Lab, University of Regensburg, Regensburg 93053, Germany
| | - Marius Rutkauskas
- Peter Debye Institute for Soft Matter Physics, University of Leipzig, Leipzig 04103, Germany
| | - Fergus Fettes
- Peter Debye Institute for Soft Matter Physics, University of Leipzig, Leipzig 04103, Germany
| | - Dina Grohmann
- Institute of Microbiology & Archaea Centre, Single-Molecule Biochemistry Lab, University of Regensburg, Regensburg 93053, Germany
- Regensburg Center of Biochemistry (RCB), University of Regensburg, 93053 Regensburg, Germany
| | - Ralf Seidel
- Peter Debye Institute for Soft Matter Physics, University of Leipzig, Leipzig 04103, Germany
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Schaich MA, Van Houten B. Searching for DNA Damage: Insights From Single Molecule Analysis. Front Mol Biosci 2021; 8:772877. [PMID: 34805281 PMCID: PMC8602339 DOI: 10.3389/fmolb.2021.772877] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 10/18/2021] [Indexed: 01/26/2023] Open
Abstract
DNA is under constant threat of damage from a variety of chemical and physical insults, such as ultraviolet rays produced by sunlight and reactive oxygen species produced during respiration or inflammation. Because damaged DNA, if not repaired, can lead to mutations or cell death, multiple DNA repair pathways have evolved to maintain genome stability. Two repair pathways, nucleotide excision repair (NER) and base excision repair (BER), must sift through large segments of nondamaged nucleotides to detect and remove rare base modifications. Many BER and NER proteins share a common base-flipping mechanism for the detection of modified bases. However, the exact mechanisms by which these repair proteins detect their damaged substrates in the context of cellular chromatin remains unclear. The latest generation of single-molecule techniques, including the DNA tightrope assay, atomic force microscopy, and real-time imaging in cells, now allows for nearly direct visualization of the damage search and detection processes. This review describes several mechanistic commonalities for damage detection that were discovered with these techniques, including a combination of 3-dimensional and linear diffusion for surveying damaged sites within long stretches of DNA. We also discuss important findings that DNA repair proteins within and between pathways cooperate to detect damage. Finally, future technical developments and single-molecule studies are described which will contribute to the growing mechanistic understanding of DNA damage detection.
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Affiliation(s)
- Matthew A Schaich
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, United States.,Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Bennett Van Houten
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, United States.,Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States.,Molecular Biophysics and Structural Biology Graduate Program, University of Pittsburgh, Pittsburgh, PA, United States
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50
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Balaguer FDA, Aicart-Ramos C, Fisher GL, de Bragança S, Martin-Cuevas EM, Pastrana CL, Dillingham MS, Moreno-Herrero F. CTP promotes efficient ParB-dependent DNA condensation by facilitating one-dimensional diffusion from parS. eLife 2021; 10:67554. [PMID: 34250901 PMCID: PMC8299390 DOI: 10.7554/elife.67554] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 07/09/2021] [Indexed: 12/19/2022] Open
Abstract
Faithful segregation of bacterial chromosomes relies on the ParABS partitioning system and the SMC complex. In this work, we used single-molecule techniques to investigate the role of cytidine triphosphate (CTP) binding and hydrolysis in the critical interaction between centromere-like parS DNA sequences and the ParB CTPase. Using a combined optical tweezers confocal microscope, we observe the specific interaction of ParB with parS directly. Binding around parS is enhanced by the presence of CTP or the non-hydrolysable analogue CTPγS. However, ParB proteins are also detected at a lower density in distal non-specific DNA. This requires the presence of a parS loading site and is prevented by protein roadblocks, consistent with one-dimensional diffusion by a sliding clamp. ParB diffusion on non-specific DNA is corroborated by direct visualization and quantification of movement of individual quantum dot labelled ParB. Magnetic tweezers experiments show that the spreading activity, which has an absolute requirement for CTP binding but not hydrolysis, results in the condensation of parS-containing DNA molecules at low nanomolar protein concentrations.
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Affiliation(s)
- Francisco de Asis Balaguer
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Clara Aicart-Ramos
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Gemma Lm Fisher
- DNA:Protein Interactions Unit, School of Biochemistry, Biomedical Sciences Building, University of Bristol, University Walk, Bristol, United Kingdom
| | - Sara de Bragança
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Eva M Martin-Cuevas
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Cesar L Pastrana
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Mark Simon Dillingham
- DNA:Protein Interactions Unit, School of Biochemistry, Biomedical Sciences Building, University of Bristol, University Walk, Bristol, United Kingdom
| | - Fernando Moreno-Herrero
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain
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