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Bowater RP, Bohálová N, Brázda V. Interaction of Proteins with Inverted Repeats and Cruciform Structures in Nucleic Acids. Int J Mol Sci 2022; 23:ijms23116171. [PMID: 35682854 PMCID: PMC9180970 DOI: 10.3390/ijms23116171] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/26/2022] [Accepted: 05/30/2022] [Indexed: 01/27/2023] Open
Abstract
Cruciforms occur when inverted repeat sequences in double-stranded DNA adopt intra-strand hairpins on opposing strands. Biophysical and molecular studies of these structures confirm their characterization as four-way junctions and have demonstrated that several factors influence their stability, including overall chromatin structure and DNA supercoiling. Here, we review our understanding of processes that influence the formation and stability of cruciforms in genomes, covering the range of sequences shown to have biological significance. It is challenging to accurately sequence repetitive DNA sequences, but recent advances in sequencing methods have deepened understanding about the amounts of inverted repeats in genomes from all forms of life. We highlight that, in the majority of genomes, inverted repeats are present in higher numbers than is expected from a random occurrence. It is, therefore, becoming clear that inverted repeats play important roles in regulating many aspects of DNA metabolism, including replication, gene expression, and recombination. Cruciforms are targets for many architectural and regulatory proteins, including topoisomerases, p53, Rif1, and others. Notably, some of these proteins can induce the formation of cruciform structures when they bind to DNA. Inverted repeat sequences also influence the evolution of genomes, and growing evidence highlights their significance in several human diseases, suggesting that the inverted repeat sequences and/or DNA cruciforms could be useful therapeutic targets in some cases.
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Affiliation(s)
- Richard P. Bowater
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK;
| | - Natália Bohálová
- Department of Biophysical Chemistry and Molecular Oncology, Institute of Biophysics of the Czech Academy of Sciences, 61265 Brno, Czech Republic;
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | - Václav Brázda
- Department of Biophysical Chemistry and Molecular Oncology, Institute of Biophysics of the Czech Academy of Sciences, 61265 Brno, Czech Republic;
- Correspondence:
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Bell NAW, Molloy JE. Efficient golden gate assembly of DNA constructs for single molecule force spectroscopy and imaging. Nucleic Acids Res 2022; 50:e77. [PMID: 35489063 PMCID: PMC9303394 DOI: 10.1093/nar/gkac300] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 03/18/2022] [Accepted: 04/13/2022] [Indexed: 01/01/2023] Open
Abstract
Single-molecule techniques such as optical tweezers and fluorescence imaging are powerful tools for probing the biophysics of DNA and DNA-protein interactions. The application of these methods requires efficient approaches for creating designed DNA structures with labels for binding to a surface or microscopic beads. In this paper, we develop a simple and fast technique for making a diverse range of such DNA constructs by combining PCR amplicons and synthetic oligonucleotides using golden gate assembly rules. We demonstrate high yield fabrication of torsionally-constrained duplex DNA up to 10 kbp in length and a variety of DNA hairpin structures. We also show how tethering to a cross-linked antibody substrate significantly enhances measurement lifetime under high force. This rapid and adaptable fabrication method streamlines the assembly of DNA constructs for single molecule biophysics.
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Bell NAW, Haynes PJ, Brunner K, de Oliveira TM, Flocco MM, Hoogenboom BW, Molloy JE. Single-molecule measurements reveal that PARP1 condenses DNA by loop stabilization. SCIENCE ADVANCES 2021; 7:7/33/eabf3641. [PMID: 34380612 PMCID: PMC8357241 DOI: 10.1126/sciadv.abf3641] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 06/22/2021] [Indexed: 05/11/2023]
Abstract
Poly(ADP-ribose) polymerase 1 (PARP1) is an abundant nuclear enzyme that plays important roles in DNA repair, chromatin organization and transcription regulation. Although binding and activation of PARP1 by DNA damage sites has been extensively studied, little is known about how PARP1 binds to long stretches of undamaged DNA and how it could shape chromatin architecture. Here, using single-molecule techniques, we show that PARP1 binds and condenses undamaged, kilobase-length DNA subject to sub-piconewton mechanical forces. Stepwise decondensation at high force and DNA braiding experiments show that the condensation activity is due to the stabilization of DNA loops by PARP1. PARP inhibitors do not affect the level of condensation of undamaged DNA but act to block condensation reversal for damaged DNA in the presence of NAD+ Our findings suggest a mechanism for PARP1 in the organization of chromatin structure.
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Affiliation(s)
- Nicholas A W Bell
- The Francis Crick Institute, London NW1 1AT, UK.
- London Centre for Nanotechnology, University College London, London WC1H 0AH, UK
| | - Philip J Haynes
- London Centre for Nanotechnology, University College London, London WC1H 0AH, UK
- Molecular Sciences Research Hub, Department of Chemistry, Imperial College London, London W12 0BZ, UK
- Department of Physics and Astronomy, University College London, London WC1E 6BT, UK
| | - Katharina Brunner
- The Francis Crick Institute, London NW1 1AT, UK
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
| | - Taiana Maia de Oliveira
- Mechanistic and Structural Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Maria M Flocco
- Mechanistic and Structural Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Bart W Hoogenboom
- London Centre for Nanotechnology, University College London, London WC1H 0AH, UK
- Department of Physics and Astronomy, University College London, London WC1E 6BT, UK
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Bell NAW, Molloy JE. Microfluidic flow-cell with passive flow control for microscopy applications. PLoS One 2020; 15:e0244103. [PMID: 33320916 PMCID: PMC7737957 DOI: 10.1371/journal.pone.0244103] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 12/02/2020] [Indexed: 11/19/2022] Open
Abstract
We present a fast, inexpensive and robust technique for constructing thin, optically transparent flow-cells with pump-free flow control. Using layers of glass, patterned adhesive tape and polydimethylsiloxane (PDMS) connections, we demonstrate the fabrication of planar devices with chamber height as low as 25 μm and with millimetre-scale (x,y) dimensions for wide-field microscope observation. The method relies on simple benchtop equipment and does not require microfabrication facilities, glass drilling or other workshop infrastructure. We also describe a gravity perfusion system that exploits the strong capillary action in the flow chamber as a passive limit-valve. Our approach allows simple sequential sample exchange with controlled flow rates, sub-5 μL sample chamber size and zero dead volume. We demonstrate the system in a single-molecule force spectroscopy experiment using magnetic tweezers.
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Carrasco C, Pastrana CL, Aicart-Ramos C, Leuba SH, Khan S, Moreno-Herrero F. Dynamics of DNA nicking and unwinding by the RepC-PcrA complex. Nucleic Acids Res 2020; 48:2013-2025. [PMID: 31930301 PMCID: PMC7038956 DOI: 10.1093/nar/gkz1200] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 12/10/2019] [Accepted: 12/18/2019] [Indexed: 01/22/2023] Open
Abstract
The rolling-circle replication is the most common mechanism for the replication of small plasmids carrying antibiotic resistance genes in Gram-positive bacteria. It is initiated by the binding and nicking of double-stranded origin of replication by a replication initiator protein (Rep). Duplex unwinding is then performed by the PcrA helicase, whose processivity is critically promoted by its interaction with Rep. How Rep and PcrA proteins interact to nick and unwind the duplex is not fully understood. Here, we have used magnetic tweezers to monitor PcrA helicase unwinding and its relationship with the nicking activity of Staphylococcus aureus plasmid pT181 initiator RepC. Our results indicate that PcrA is a highly processive helicase prone to stochastic pausing, resulting in average translocation rates of 30 bp s-1, while a typical velocity of 50 bp s-1 is found in the absence of pausing. Single-strand DNA binding protein did not affect PcrA translocation velocity but slightly increased its processivity. Analysis of the degree of DNA supercoiling required for RepC nicking, and the time between RepC nicking and DNA unwinding, suggests that RepC and PcrA form a protein complex on the DNA binding site before nicking. A comprehensive model that rationalizes these findings is presented.
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Affiliation(s)
- Carolina Carrasco
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, CSIC, Darwin 3, 28049 Cantoblanco, Madrid, Spain
| | - Cesar L Pastrana
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, CSIC, Darwin 3, 28049 Cantoblanco, Madrid, Spain
| | - Clara Aicart-Ramos
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, CSIC, Darwin 3, 28049 Cantoblanco, Madrid, Spain
| | - Sanford H Leuba
- Departments of Cell Biology and Bioengineering, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, 5117 Centre Avenue, Pittsburgh, PA 15213, USA
| | - Saleem A Khan
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, 450 Technology Drive, Pittsburgh, PA 15219, USA
| | - Fernando Moreno-Herrero
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, CSIC, Darwin 3, 28049 Cantoblanco, Madrid, Spain
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