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Site-Search Process for Synaptic Protein-DNA Complexes

The assembly of synaptic protein-DNA complexes by specialized proteins is critical for bringing together two distant sites within a DNA molecule or bridging two DNA molecules. The assembly of such synaptosomes is needed in numerous genetic processes requiring the interactions of two or more sites. T...

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Autores principales: Vemulapalli, Sridhar, Hashemi, Mohtadin, Lyubchenko, Yuri L.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8745619/
https://www.ncbi.nlm.nih.gov/pubmed/35008637
http://dx.doi.org/10.3390/ijms23010212
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author Vemulapalli, Sridhar
Hashemi, Mohtadin
Lyubchenko, Yuri L.
author_facet Vemulapalli, Sridhar
Hashemi, Mohtadin
Lyubchenko, Yuri L.
author_sort Vemulapalli, Sridhar
collection PubMed
description The assembly of synaptic protein-DNA complexes by specialized proteins is critical for bringing together two distant sites within a DNA molecule or bridging two DNA molecules. The assembly of such synaptosomes is needed in numerous genetic processes requiring the interactions of two or more sites. The molecular mechanisms by which the protein brings the sites together, enabling the assembly of synaptosomes, remain unknown. Such proteins can utilize sliding, jumping, and segmental transfer pathways proposed for the single-site search process, but none of these pathways explains how the synaptosome assembles. Here we used restriction enzyme SfiI, that requires the assembly of synaptosome for DNA cleavage, as our experimental system and applied time-lapse, high-speed AFM to directly visualize the site search process accomplished by the SfiI enzyme. For the single-site SfiI-DNA complexes, we were able to directly visualize such pathways as sliding, jumping, and segmental site transfer. However, within the synaptic looped complexes, we visualized the threading and site-bound segment transfer as the synaptosome-specific search pathways for SfiI. In addition, we visualized sliding and jumping pathways for the loop dissociated complexes. Based on our data, we propose the site-search model for synaptic protein-DNA systems.
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spelling pubmed-87456192022-01-11 Site-Search Process for Synaptic Protein-DNA Complexes Vemulapalli, Sridhar Hashemi, Mohtadin Lyubchenko, Yuri L. Int J Mol Sci Article The assembly of synaptic protein-DNA complexes by specialized proteins is critical for bringing together two distant sites within a DNA molecule or bridging two DNA molecules. The assembly of such synaptosomes is needed in numerous genetic processes requiring the interactions of two or more sites. The molecular mechanisms by which the protein brings the sites together, enabling the assembly of synaptosomes, remain unknown. Such proteins can utilize sliding, jumping, and segmental transfer pathways proposed for the single-site search process, but none of these pathways explains how the synaptosome assembles. Here we used restriction enzyme SfiI, that requires the assembly of synaptosome for DNA cleavage, as our experimental system and applied time-lapse, high-speed AFM to directly visualize the site search process accomplished by the SfiI enzyme. For the single-site SfiI-DNA complexes, we were able to directly visualize such pathways as sliding, jumping, and segmental site transfer. However, within the synaptic looped complexes, we visualized the threading and site-bound segment transfer as the synaptosome-specific search pathways for SfiI. In addition, we visualized sliding and jumping pathways for the loop dissociated complexes. Based on our data, we propose the site-search model for synaptic protein-DNA systems. MDPI 2021-12-25 /pmc/articles/PMC8745619/ /pubmed/35008637 http://dx.doi.org/10.3390/ijms23010212 Text en © 2021 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Vemulapalli, Sridhar
Hashemi, Mohtadin
Lyubchenko, Yuri L.
Site-Search Process for Synaptic Protein-DNA Complexes
title Site-Search Process for Synaptic Protein-DNA Complexes
title_full Site-Search Process for Synaptic Protein-DNA Complexes
title_fullStr Site-Search Process for Synaptic Protein-DNA Complexes
title_full_unstemmed Site-Search Process for Synaptic Protein-DNA Complexes
title_short Site-Search Process for Synaptic Protein-DNA Complexes
title_sort site-search process for synaptic protein-dna complexes
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8745619/
https://www.ncbi.nlm.nih.gov/pubmed/35008637
http://dx.doi.org/10.3390/ijms23010212
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