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Ivanovaitė ŠRN, Paksaitė J, Kopu Stas A, Karzaitė G, Rutkauskas D, Silanskas A, Sasnauskas G, Zaremba M, Jones SK, Tutkus M. smFRET Detection of Cis and Trans DNA Interactions by the BfiI Restriction Endonuclease. J Phys Chem B 2023. [PMID: 37452775 PMCID: PMC10388346 DOI: 10.1021/acs.jpcb.3c03269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
Protein-DNA interactions are fundamental to many biological processes. Proteins must find their target site on a DNA molecule to perform their function, and mechanisms for target search differ across proteins. Especially challenging phenomena to monitor and understand are transient binding events that occur across two DNA target sites, whether occurring in cis or trans. Type IIS restriction endonucleases rely on such interactions. They play a crucial role in safeguarding bacteria against foreign DNA, including viral genetic material. BfiI, a type IIS restriction endonuclease, acts upon a specific asymmetric sequence, 5-ACTGGG-3, and precisely cuts both upper and lower DNA strands at fixed locations downstream of this sequence. Here, we present two single-molecule Förster resonance energy-transfer-based assays to study such interactions in a BfiI-DNA system. The first assay focuses on DNA looping, detecting both "Phi"- and "U"-shaped DNA looping events. The second assay only allows in trans BfiI-target DNA interactions, improving the specificity and reducing the limits on observation time. With total internal reflection fluorescence microscopy, we directly observe on- and off-target binding events and characterize BfiI binding events. Our results show that BfiI binds longer to target sites and that BfiI rarely changes conformations during binding. This newly developed assay could be employed for other DNA-interacting proteins that bind two targets and for the dsDNA substrate BfiI-PAINT, a useful strategy for DNA stretch assays and other super-resolution fluorescence microscopy studies.
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Affiliation(s)
- Ša Ru Nė Ivanovaitė
- Department of Molecular Compound Physics, Center for Physical Sciences and Technology, Savanorių 231, Vilnius LT-02300, Lithuania
- Vilnius University, Life Sciences Center, Institute of Biotechnology, Saulėtekio av. 7, Vilnius LT-10257, Lithuania
| | - Justė Paksaitė
- Vilnius University, Life Sciences Center, Institute of Biotechnology, Saulėtekio av. 7, Vilnius LT-10257, Lithuania
| | - Aurimas Kopu Stas
- Department of Molecular Compound Physics, Center for Physical Sciences and Technology, Savanorių 231, Vilnius LT-02300, Lithuania
- Vilnius University, Life Sciences Center, Institute of Biotechnology, Saulėtekio av. 7, Vilnius LT-10257, Lithuania
| | - Giedrė Karzaitė
- Department of Molecular Compound Physics, Center for Physical Sciences and Technology, Savanorių 231, Vilnius LT-02300, Lithuania
| | - Danielis Rutkauskas
- Department of Molecular Compound Physics, Center for Physical Sciences and Technology, Savanorių 231, Vilnius LT-02300, Lithuania
| | - Arunas Silanskas
- Vilnius University, Life Sciences Center, Institute of Biotechnology, Saulėtekio av. 7, Vilnius LT-10257, Lithuania
| | - Giedrius Sasnauskas
- Vilnius University, Life Sciences Center, Institute of Biotechnology, Saulėtekio av. 7, Vilnius LT-10257, Lithuania
| | - Mindaugas Zaremba
- Vilnius University, Life Sciences Center, Institute of Biotechnology, Saulėtekio av. 7, Vilnius LT-10257, Lithuania
| | - Stephen K Jones
- VU LSC-EMBL Partnership for Genome Editing Technologies, Life Sciences Center, Vilnius University, Vilnius LT-10257, Lithuania
| | - Marijonas Tutkus
- Department of Molecular Compound Physics, Center for Physical Sciences and Technology, Savanorių 231, Vilnius LT-02300, Lithuania
- Vilnius University, Life Sciences Center, Institute of Biotechnology, Saulėtekio av. 7, Vilnius LT-10257, Lithuania
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Uyar A, Kurkcuoglu O, Nilsson L, Doruker P. The elastic network model reveals a consistent picture on intrinsic functional dynamics of type II restriction endonucleases. Phys Biol 2011; 8:056001. [PMID: 21791727 DOI: 10.1088/1478-3975/8/5/056001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The vibrational dynamics of various type II restriction endonucleases, in complex with cognate/non-cognate DNA and in the apo form, are investigated with the elastic network model in order to reveal common functional mechanisms in this enzyme family. Scissor-like and tong-like motions observed in the slowest modes of all enzymes and their complexes point to common DNA recognition and cleavage mechanisms. Normal mode analysis further points out that the scissor-like motion has an important role in differentiating between cognate and non-cognate sequences at the recognition site, thus implying its catalytic relevance. Flexible regions observed around the DNA-binding site of the enzyme usually concentrate on the highly conserved β-strands, especially after DNA binding. These β-strands may have a structurally stabilizing role in functional dynamics for target site recognition and cleavage. In addition, hot spot residues based on high-frequency modes reveal possible communication pathways between the two distant cleavage sites in the enzyme family. Some of these hot spots also exist on the shortest path between the catalytic sites and are highly conserved.
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Affiliation(s)
- A Uyar
- Department of Chemical Engineering and Polymer Research Center, Bogazici University, 34342 Bebek, Istanbul, Turkey
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Gowers DM, Wilson GG, Halford SE. Measurement of the contributions of 1D and 3D pathways to the translocation of a protein along DNA. Proc Natl Acad Sci U S A 2005; 102:15883-8. [PMID: 16243975 PMCID: PMC1262116 DOI: 10.1073/pnas.0505378102] [Citation(s) in RCA: 205] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Proteins that act at specific DNA sequences bind DNA randomly and then translocate to the target site. The translocation is often ascribed to the protein sliding along the DNA while maintaining continuous contact with it. Proteins also can move on DNA by multiple cycles of dissociation/reassociation within the same chain. To distinguish these pathways, a strategy was developed to analyze protein motion between DNA sites. The strategy reveals whether the protein maintains contact with the DNA as it transfers from one site to another by sliding or whether it loses contact by a dissociation/reassociation step. In reactions at low salt, the test protein stayed on the DNA as it traveled between sites, but only when the sites were <50 bp apart. Transfers of >30 bp at in vivo salt, and over distances of >50 bp at any salt, always included at least one dissociation step. Hence, for this enzyme, 1D sliding operates only over short distances at low salt, and 3D dissociation/reassociation is its main mode of translocation.
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Affiliation(s)
- Darren M Gowers
- Department of Biochemistry, School of Medical Sciences, University of Bristol, Bristol BS8 1TD, United Kingdom
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