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Ahlqvist J, Tymecka-Mulik J, Burkiewicz K, Wallenberg R, Jasilionis A, Karlsson EN, Dabrowski S. DNA digestion and formation of DNA-network structures with Holliday junction-resolving enzyme Hjc_15-6 in conjunction with polymerase reactions. J Biotechnol 2024; 385:23-29. [PMID: 38408644 DOI: 10.1016/j.jbiotec.2024.02.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 02/11/2024] [Accepted: 02/22/2024] [Indexed: 02/28/2024]
Abstract
The recently identified novel Holliday junction-resolving enzyme, termed Hjc_15-6, activity investigation results imply DNA cleavage by Hjc_15-6 in a manner that potentially enhances the molecular self-assembly that may be exploited for creating DNA-networks and nanostructures. The study also demonstrates Pwo DNA polymerase acting in combination with Hjc_15-6 capability to produce large amounts of DNA that transforms into large DNA-network structures even without DNA template and primers. Furthermore, it is demonstrated that Hjc_15-6 prefers Holliday junction oligonucleotides as compared to Y-shaped oligonucleotides as well as efficiently cleaves typical branched products from isothermal DNA amplification of both linear and circular DNA templates amplified by phi29-like DNA polymerase. The assembly of large DNA network structures was observed in real time, by transmission electron microscopy, on negative stained grids that were freshly prepared, and also on the same grids after incubation for 4 days under constant cooling. Hence, Hjc_15-6 is a promising molecular tool for efficient production of various DNA origamis that may be implemented for a wide range of applications such as within medical biomaterials, catalytic materials, molecular devices and biosensors.
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Affiliation(s)
- Josefin Ahlqvist
- Division of Biotechnology, Department of Chemistry, Lund University, PO Box 124, Lund SE-221 00, Sweden.
| | | | | | - Reine Wallenberg
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University, PO Box 124, Lund SE-221 00, Sweden
| | - Andrius Jasilionis
- Division of Biotechnology, Department of Chemistry, Lund University, PO Box 124, Lund SE-221 00, Sweden
| | - Eva Nordberg Karlsson
- Division of Biotechnology, Department of Chemistry, Lund University, PO Box 124, Lund SE-221 00, Sweden
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Zhang S, Tang L, Zhang J, Sun W, Liu D, Chen J, Hu B, Huang Z. Single-Atom-Directed Inhibition of De Novo DNA Synthesis in Isothermal Amplifications. Anal Chem 2022; 94:15763-15771. [DOI: 10.1021/acs.analchem.2c03489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Shun Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, P. R. China
- SeNA Research Institute and Szostak-CDHT Large Nucleic Acids Institute, Chengdu, Sichuan 610095, China
| | - Ling Tang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, P. R. China
| | - Jun Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, P. R. China
| | - Wen Sun
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, P. R. China
| | - Dan Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, P. R. China
| | - Jiuyi Chen
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, P. R. China
| | - Bei Hu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, P. R. China
| | - Zhen Huang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, P. R. China
- SeNA Research Institute and Szostak-CDHT Large Nucleic Acids Institute, Chengdu, Sichuan 610095, China
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Garafutdinov RR, Gilvanov AR, Kupova OY, Sakhabutdinova AR. Effect of metal ions on isothermal amplification with Bst exo- DNA polymerase. Int J Biol Macromol 2020; 161:1447-1455. [DOI: 10.1016/j.ijbiomac.2020.08.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 08/02/2020] [Accepted: 08/04/2020] [Indexed: 01/28/2023]
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Antipova VN, Reveguk ZV, Kraynyukov ES, Zyrina NV. Structure of DNA obtained during the ab initio synthesis by Bst DNA polymerase in the presence of the nicking endonuclease from Bacillus stearothermophilus (Nt.BstNBI). J Biomol Struct Dyn 2018; 37:3314-3321. [PMID: 30146945 DOI: 10.1080/07391102.2018.1515662] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Valeriya N Antipova
- a Laboratory of Biophysics of Active Media , Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences , Pushchino , Moscow , Russia
| | - Zakhar V Reveguk
- b Centre for Diagnostics of Functional Materials for Medicine, Pharmacology and Nanoelectronics , St. Petersburg State University , St. Petersburg , Russia
| | - Evgeny S Kraynyukov
- b Centre for Diagnostics of Functional Materials for Medicine, Pharmacology and Nanoelectronics , St. Petersburg State University , St. Petersburg , Russia
| | - Nadezhda V Zyrina
- c Laboratory of Crystallophysics and X-ray Research , Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences , Pushchino , Moscow , Russia
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Antipova VN, Zheleznaya LA, Zyrina NV. Ab initio DNA synthesis by Bst polymerase in the presence of nicking endonucleases Nt.AlwI, Nb.BbvCI, and Nb.BsmI. FEMS Microbiol Lett 2014; 357:144-50. [PMID: 24965874 DOI: 10.1111/1574-6968.12511] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 06/13/2014] [Accepted: 06/14/2014] [Indexed: 01/08/2023] Open
Abstract
In the absence of added DNA, thermophilic DNA polymerases synthesize double-stranded DNA from free dNTPs, which consist of numerous repetitive units (ab initio DNA synthesis). The addition of thermophilic restriction endonuclease (REase), or nicking endonuclease (NEase), effectively stimulates ab initio DNA synthesis and determines the nucleotide sequence of reaction products. We have found that NEases Nt.AlwI, Nb.BbvCI, and Nb.BsmI with non-palindromic recognition sites stimulate the synthesis of sequences organized mainly as palindromes. Moreover, the nucleotide sequence of the palindromes appeared to be dependent on NEase recognition/cleavage modes. Thus, the heterodimeric Nb.BbvCI stimulated the synthesis of palindromes composed of two recognition sites of this NEase, which were separated by AT-reach sequences or (A)n (T)m spacers. Palindromic DNA sequences obtained in the ab initio DNA synthesis with the monomeric NEases Nb.BsmI and Nt.AlwI contained, along with the sites of these NEases, randomly synthesized sequences consisted of blocks of short repeats. These findings could help investigation of the potential abilities of highly productive ab initio DNA synthesis for the creation of DNA molecules with desirable sequence.
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Affiliation(s)
- Valeriya N Antipova
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
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Affiliation(s)
- Nadezhda V. Zyrina
- Institute of Theoretical and Experimental Biophysics; Russian Academy of Sciences; Pushchino Moscow Region Russia
| | - Valeriya N. Antipova
- Institute of Theoretical and Experimental Biophysics; Russian Academy of Sciences; Pushchino Moscow Region Russia
| | - Lyudmila A. Zheleznaya
- Institute of Theoretical and Experimental Biophysics; Russian Academy of Sciences; Pushchino Moscow Region Russia
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