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Abrosimova LA, Kuznetsov NA, Astafurova NA, Samsonova AR, Karpov AS, Perevyazova TA, Oretskaya TS, Fedorova OS, Kubareva EA. Kinetic Analysis of the Interaction of Nicking Endonuclease BspD6I with DNA. Biomolecules 2021; 11:1420. [PMID: 34680052 PMCID: PMC8533099 DOI: 10.3390/biom11101420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 12/03/2022] Open
Abstract
Nicking endonucleases (NEs) are enzymes that incise only one strand of the duplex to produce a DNA molecule that is 'nicked' rather than cleaved in two. Since these precision tools are used in genetic engineering and genome editing, information about their mechanism of action at all stages of DNA recognition and phosphodiester bond hydrolysis is essential. For the first time, fast kinetics of the Nt.BspD6I interaction with DNA were studied by the stopped-flow technique, and changes of optical characteristics were registered for the enzyme or DNA molecules. The role of divalent metal cations was estimated at all steps of Nt.BspD6I-DNA complex formation. It was demonstrated that divalent metal ions are not required for the formation of a non-specific complex of the protein with DNA. Nt.BspD6I bound five-fold more efficiently to its recognition site in DNA than to a random DNA. DNA bending was confirmed during the specific binding of Nt.BspD6I to a substrate. The optimal size of Nt.BspD6I's binding site in DNA as determined in this work should be taken into account in methods of detection of nucleic acid sequences and/or even various base modifications by means of NEs.
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Affiliation(s)
- Liudmila A. Abrosimova
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia; (N.A.A.); (A.S.K.)
| | - Nikita A. Kuznetsov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Lavrentiev Avenue 8, 630090 Novosibirsk, Russia;
| | - Natalia A. Astafurova
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia; (N.A.A.); (A.S.K.)
| | | | - Andrey S. Karpov
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia; (N.A.A.); (A.S.K.)
| | - Tatiana A. Perevyazova
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Institutskaya Str. 3, 142290 Puschino, Russia;
| | - Tatiana S. Oretskaya
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia; (T.S.O.); (E.A.K.)
| | - Olga S. Fedorova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Lavrentiev Avenue 8, 630090 Novosibirsk, Russia;
| | - Elena A. Kubareva
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia; (T.S.O.); (E.A.K.)
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Barnes HE, Liu G, Weston CQ, King P, Pham LK, Waltz S, Helzer KT, Day L, Sphar D, Yamamoto RT, Forsyth RA. Selective microbial genomic DNA isolation using restriction endonucleases. PLoS One 2014; 9:e109061. [PMID: 25279840 PMCID: PMC4184833 DOI: 10.1371/journal.pone.0109061] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 08/28/2014] [Indexed: 11/25/2022] Open
Abstract
To improve the metagenomic analysis of complex microbiomes, we have repurposed restriction endonucleases as methyl specific DNA binding proteins. As an example, we use DpnI immobilized on magnetic beads. The ten minute extraction technique allows specific binding of genomes containing the DpnI Gm6ATC motif common in the genomic DNA of many bacteria including γ-proteobacteria. Using synthetic genome mixtures, we demonstrate 80% recovery of Escherichia coli genomic DNA even when only femtogram quantities are spiked into 10 µg of human DNA background. Binding is very specific with less than 0.5% of human DNA bound. Next Generation Sequencing of input and enriched synthetic mixtures results in over 100-fold enrichment of target genomes relative to human and plant DNA. We also show comparable enrichment when sequencing complex microbiomes such as those from creek water and human saliva. The technique can be broadened to other restriction enzymes allowing for the selective enrichment of trace and unculturable organisms from complex microbiomes and the stratification of organisms according to restriction enzyme enrichment.
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Affiliation(s)
- Helen E. Barnes
- FLIR Systems, Inc., La Jolla, California, United States of America
| | - Guohong Liu
- FLIR Systems, Inc., La Jolla, California, United States of America
| | | | - Paula King
- FLIR Systems, Inc., La Jolla, California, United States of America
| | - Long K. Pham
- FLIR Systems, Inc., La Jolla, California, United States of America
| | - Shannon Waltz
- FLIR Systems, Inc., La Jolla, California, United States of America
| | | | - Laura Day
- FLIR Systems, Inc., La Jolla, California, United States of America
| | - Dan Sphar
- FLIR Systems, Inc., La Jolla, California, United States of America
| | | | - R. Allyn Forsyth
- FLIR Systems, Inc., La Jolla, California, United States of America
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Abrosimova LA, Monakhova MV, Migur AY, Wolfgang W, Pingoud A, Kubareva EA, Oretskaya TS. Thermo-switchable activity of the restriction endonuclease SsoII achieved by site-directed enzyme modification. IUBMB Life 2013; 65:1012-6. [PMID: 24376208 DOI: 10.1002/iub.1222] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Revised: 10/02/2013] [Accepted: 10/02/2013] [Indexed: 12/30/2022]
Abstract
In this work, the possibility of constructing a thermo-switchable enzyme according to the "molecular gate" strategy is demonstrated. The approach is based on the covalent attachment of oligodeoxyribonucleotides to cysteine residues of an enzyme adjacent to its active center to form a temporal barrier for enzyme-substrate complex formation. The activity of the modified enzyme that had been studied here-the restriction endonuclease SsoII (R.SsoII)-was diminished by a factor of 180 at 25 °С that almost abolished the enzymatic activity when compared with the unmodified enzyme. However, heating of the modified enzyme to 45 °С resulted in a 30-fold increase of activity. The activity of unmodified R.SsoII also increased on heating from 25 to 45 °; however, the difference did not exceed a factor of 3-4. The changes in enzymatic activity observed were shown to be reversible for both the unmodified and the modified R.SsoII. Variation of the length and the sequence of the attached oligodeoxyribonucleotides might allow greater modulation of the activity of DNA-protein conjugates.
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Affiliation(s)
- Liudmila A Abrosimova
- Department of Bioengineering and Bioinformatics, M. V. Lomonosov Moscow State University, Moscow, Russian Federation; Department of Chemistry, and Belozersky Institute of Physico-Chemical Biology, M. V. Lomonosov Moscow State University, Moscow, Russian Federation
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Romanenkov AS, Kisil OV, Zatsepin TS, Iamskova OV, Kariagina AS, Metelev VG, Oretskaia TS, Kubareva EA. DNA-methyltransferase SsoII as a bifunctional protein: Features of the interaction with the promoter region of SsoII restriction-modification genes. BIOCHEMISTRY (MOSCOW) 2006; 71:1341-9. [PMID: 17223787 DOI: 10.1134/s0006297906120091] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
DNA duplexes bearing an aldehyde group at the 2'-position of the sugar moiety were used for affinity modification of (cytosine-5)-DNA methyltransferase SsoII. It is shown that lysine residues of M.SsoII N-terminal region are located in proximity to DNA sugar-phosphate backbone of a regulatory sequence of promoter region of SsoII restriction-modification enzyme coding genes. The ability of the two M.SsoII subunits to interact with DNA regulatory sequence has been demonstrated by affinity modification using DNA duplexes with two 2'-aldehyde groups. Changes in nucleotide sequence of one half of the regulatory region prevented cross-linking of the second M.SsoII subunit. The results on sequential affinity modification of M.SsoII by two types of modified DNA ligands (i.e. by 2'-aldehyde-containing and phosphoryldisulfide-containing) have demonstrated the possibility of covalent attachment of the protein to two different DNA recognition sites: regulatory sequence and methylation site.
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Affiliation(s)
- A S Romanenkov
- Chemical Faculty, Lomonosov Moscow State University, Moscow, 119992, Russia
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