TY - JOUR
T1 - Site-search process for synaptic protein-dna complexes
AU - Vemulapalli, Sridhar
AU - Hashemi, Mohtadin
AU - Lyubchenko, Yuri L.
N1 - Funding Information:
Acknowledgments: We thank L. Shlyakhtenko (University of Nebraska Medical Center) for valuable insights and all the Y.L.L lab members for their fruitful discussions. The authors thank Tommy Stormberg (University of Nebraska Medical Center) for proofreading the manuscript. The authors thank the UNMC Genomics Core Facility, which receives partial support from the NIGMS INBRE— P20GM103427-19 and the NCI center grant for Fred & Pamela Buffett Cancer Center P30CA036727.
Funding Information:
Funding: This work was supported by NSF grants MCB-1941049 and MCB-2123637 to Y.L.L.
Publisher Copyright:
© 2021 by the authors. Licensee MDPI, Basel, Switzerland.
PY - 2022/1/1
Y1 - 2022/1/1
N2 - 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 (HS-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 visualised sliding and jumping pathways for the loop dissociated complexes. Based on our data, we propose the site-search model for synaptic protein-DNA systems.
AB - 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 (HS-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 visualised sliding and jumping pathways for the loop dissociated complexes. Based on our data, we propose the site-search model for synaptic protein-DNA systems.
KW - High-speed AFM
KW - SFiI
KW - Site-bound segment transfer
KW - Site-search
KW - Synaptic complexes
KW - Threading
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U2 - 10.3390/ijms23010212
DO - 10.3390/ijms23010212
M3 - Article
C2 - 35008637
AN - SCOPUS:85121628705
VL - 23
JO - International Journal of Molecular Sciences
JF - International Journal of Molecular Sciences
SN - 1661-6596
IS - 1
M1 - 212
ER -