1
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Gabashvili E, Kobakhidze S, Koulouris S, Robinson T, Kotetishvili M. Bi- and Multi-directional Gene Transfer in the Natural Populations of Polyvalent Bacteriophages, and Their Host Species Spectrum Representing Foodborne Versus Other Human and/or Animal Pathogens. FOOD AND ENVIRONMENTAL VIROLOGY 2021; 13:179-202. [PMID: 33484405 DOI: 10.1007/s12560-021-09460-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 01/06/2021] [Indexed: 06/12/2023]
Abstract
Unraveling the trends of phage-host versus phage-phage coevolution is critical for avoiding possible undesirable outcomes from the use of phage preparations intended for therapeutic, food safety or environmental safety purposes. We aimed to investigate a phenomenon of intergeneric recombination and its trajectories across the natural populations of phages predominantly linked to foodborne pathogens. The results from the recombination analyses, using a large array of the recombination detection algorithms imbedded in SplitsTree, RDP4, and Simplot software packages, provided strong evidence (fit: 100; P ≤ 0.014) for both bi- and multi-directional intergeneric recombination of the genetic loci involved collectively in phage morphogenesis, host specificity, virulence, replication, and persistence. Intergeneric recombination was determined to occur not only among conspecifics of the virulent versus temperate phages but also between the phages with these different lifestyles. The recombining polyvalent phages were suggested to interact with fairly large host species networks, including sometimes genetically very distinct species, such as e.g., Salmonella enterica and/or Escherichia coli versus Staphylococcus aureus or Yersinia pestis. Further studies are needed to understand whether phage-driven intergeneric recombination can lead to undesirable changes of intestinal and other microbiota in humans and animals.
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Affiliation(s)
- Ekaterine Gabashvili
- School of Natural Sciences and Medicine, Ilia State University, 1 Giorgi Tsereteli exit, 0162, Tbilisi, Georgia
- Division of Risk Assessment, Scientific-Research Center of Agriculture, 6 Marshal Gelovani ave., 0159, Tbilisi, Georgia
| | - Saba Kobakhidze
- Division of Risk Assessment, Scientific-Research Center of Agriculture, 6 Marshal Gelovani ave., 0159, Tbilisi, Georgia
| | - Stylianos Koulouris
- Engagement and Cooperation Unit, European Food Safety Authority, Via Carlo Magno 1A, 43126, Parma, Italy
| | - Tobin Robinson
- Scientific Committee, and Emerging Risks Unit, European Food Safety Authority, Via Carlo Magno 1A, 43126, Parma, Italy
| | - Mamuka Kotetishvili
- Division of Risk Assessment, Scientific-Research Center of Agriculture, 6 Marshal Gelovani ave., 0159, Tbilisi, Georgia.
- Hygiene and Medical Ecology, G. Natadze Scientific-Research Institute of Sanitation, 78 D. Uznadze St., 0102, Tbilisi, Georgia.
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2
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Chen H, Cheng K, Liu X, An R, Komiyama M, Liang X. Preferential production of RNA rings by T4 RNA ligase 2 without any splint through rational design of precursor strand. Nucleic Acids Res 2020; 48:e54. [PMID: 32232357 PMCID: PMC7229815 DOI: 10.1093/nar/gkaa181] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 02/04/2020] [Accepted: 03/11/2020] [Indexed: 12/04/2022] Open
Abstract
Rings of single-stranded RNA are promising for many practical applications, but the methods to prepare them in preparative scale have never been established. Previously, RNA circularization was achieved by T4 RNA ligase 2 (Rnl2, a dsRNA ligase) using splints, but the yield was low due to concurrent intermolecular polymerization. Here, various functional RNAs (siRNA, miRNA, ribozyme, etc.) are dominantly converted by Rnl2 to the rings without significant limitations in sizes and sequences. The key is to design a precursor RNA, which is highly activated for the efficient circularization without any splint. First, secondary structure of target RNA ring is simulated by Mfold, and then hypothetically cut at one site so that a few intramolecular base pairs are formed at the terminal. Simply by treating this RNA with Rnl2, the target ring was selectively and efficiently produced. Unexpectedly, circular RNA can be obtained in high yield (>90%), even when only 2 bp form in the 3'-OH side and no full match base pair forms in the 5'-phosphate side. Formation of polymeric by-products was further suppressed by diluting conventional Rnl2 buffer to abnormally low concentrations. Even at high-RNA concentrations (e.g. 50 μM), enormously high selectivity (>95%) was accomplished.
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Affiliation(s)
- Hui Chen
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Kai Cheng
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Xiaoli Liu
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Ran An
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266235, China
| | - Makoto Komiyama
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Xingguo Liang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266235, China
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3
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Gubu A, Wang J, Jin H, Tang X. Synthesis and "DNA Interlocks" Formation of Small Circular Oligodeoxynucleotides. ACS APPLIED MATERIALS & INTERFACES 2020; 12:12584-12590. [PMID: 32100989 DOI: 10.1021/acsami.0c00923] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Circular oligodeoxynucleotides (c-ODNs) have their particular characteristics in topological properties. However, different from oligoribonucleotides, enzymatic synthesis of small c-ODNs is still challenging using conventional methods. Herein, we successfully achieved highly efficient cyclization of linear single-stranded ODNs using T4 DNA ligase simply through the frozen/lyophilization/cyclization (FLC) method. We successfully shortened the cyclization length of linear ODNs to 20 nt (l-ODN 20) with up to 63% yield, which was never achieved before through normal enzymatic methods. With the efficient FLC method, we further developed "DNA interlocks" which were intercross-linked with multiple c-ODNs using the one-pot FLC method. This FLC strategy provides a powerful, cheap, and convenient method to synthesize small c-ODNs for studying DNA nanotechnology and paves the way to achieve future deciphering of c-ODN functions.
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Affiliation(s)
- Amu Gubu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38 Xueyuan Road, Beijing 100191, China
| | - Jing Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38 Xueyuan Road, Beijing 100191, China
| | - Hongwei Jin
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38 Xueyuan Road, Beijing 100191, China
| | - Xinjing Tang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38 Xueyuan Road, Beijing 100191, China
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4
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Wang J, Liu F, Su T, Chang Y, Guo Q, Wang Q, Liang Q, Qi Q. The phage T4 DNA ligase in vivo improves the survival-coupled bacterial mutagenesis. Microb Cell Fact 2019; 18:107. [PMID: 31196093 PMCID: PMC6567493 DOI: 10.1186/s12934-019-1160-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 06/09/2019] [Indexed: 01/09/2023] Open
Abstract
Background Microbial mutagenesis is an important avenue to acquire microbial strains with desirable traits for industry application. However, mutagens either chemical or physical used often leads narrow library pool due to high lethal rate. The T4 DNA ligase is one of the most widely utilized enzymes in modern molecular biology. Its contribution to repair chromosomal DNA damages, therefore cell survival during mutagenesis will be discussed. Results Expression of T4 DNA ligase in vivo could substantially increase cell survival to ionizing radiation in multiple species. A T4 mediated survival-coupled mutagenesis approach was proposed. When polyhydroxybutyrate (PHB)-producing E. coli with T4 DNA ligase expressed in vivo was subjected to ionizing radiation, mutants with improved PHB production were acquired quickly owing to a large viable mutant library generated. Draft genome sequence analysis showed that the mutants obtained possess not only single nucleotide variation (SNV) but also DNA fragment deletion, indicating that T4 DNA ligase in vivo may contribute to the repair of DNA double strand breaks. Conclusions Expression of T4 DNA ligase in vivo could notably enhance microbial survival to excess chromosomal damages caused by various mutagens. Potential application of T4 DNA ligase in microbial mutagenesis was explored by mutating and screening PHB producing E. coli XLPHB strain. When applied to atmospheric and room temperature plasma (ARTP) microbial mutagenesis, large survival pool was obtained. Mutants available for subsequent screening for desirable features. The use of T4 DNA ligase we were able to quickly improve the PHB production by generating a larger viable mutants pool. This method is a universal strategy can be employed in wide range of bacteria. It indicated that traditional random mutagenesis became more powerful in combine with modern genetic molecular biology and has exciting prospect. Electronic supplementary material The online version of this article (10.1186/s12934-019-1160-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Junshu Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, People's Republic of China
| | - Fapeng Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, People's Republic of China
| | - Tianyuan Su
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, People's Republic of China
| | - Yizhao Chang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, People's Republic of China
| | - Qi Guo
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, People's Republic of China
| | - Qian Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, People's Republic of China.,National Glycoengineering Center, Shandong University, Qingdao, 266237, China
| | - Quanfeng Liang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, People's Republic of China
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, People's Republic of China. .,CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 2566101, China.
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5
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Su T, Liu F, Chang Y, Guo Q, Wang J, Wang Q, Qi Q. The phage T4 DNA ligase mediates bacterial chromosome DSBs repair as single component non-homologous end joining. Synth Syst Biotechnol 2019; 4:107-112. [PMID: 31193309 PMCID: PMC6525309 DOI: 10.1016/j.synbio.2019.04.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 04/08/2019] [Accepted: 04/09/2019] [Indexed: 10/29/2022] Open
Abstract
DNA double-strand breaks (DSBs) are one of the most lethal forms of DNA damage that is not efficiently repaired in prokaryotes. Certain microorganisms can handle chromosomal DSBs using the error-prone non-homologous end joining (NHEJ) system and ultimately cause genome mutagenesis. Here, we demonstrated that Enterobacteria phage T4 DNA ligase alone is capable of mediating in vivo chromosome DSBs repair in Escherichia coli. The ligation efficiency of DSBs with T4 DNA ligase is one order of magnitude higher than the NHEJ system from Mycobacterium tuberculosis. This process introduces chromosome DNA excision with different sizes, which can be manipulated by regulating the activity of host-exonuclease RecBCD. The DNA deletion length reduced either by inactivating recB or expressing the RecBCD inhibitor Gam protein from λ phage. Furthermore, we also found single nucleotide substitutions at the DNA junction, suggesting that T4 DNA ligase, as a single component non-homologous end joining system, has great potential in genome mutagenesis, genome reduction and genome editing.
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Affiliation(s)
- Tianyuan Su
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, People's Republic of China
| | - Fapeng Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, People's Republic of China
| | - Yizhao Chang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, People's Republic of China
| | - Qi Guo
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, People's Republic of China
| | - Junshu Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, People's Republic of China
| | - Qian Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, People's Republic of China.,National Glycoengineering Center, Shandong University, Qingdao, 266237, People's Republic of China
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, People's Republic of China.,CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, People's Republic of China
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6
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Gong J, Li Y, Lin T, Feng X, Chu L. Multiplex real-time PCR assay combined with rolling circle amplification (MPRP) using universal primers for non-invasive detection of tumor-related mutations. RSC Adv 2018; 8:27375-27381. [PMID: 35540013 PMCID: PMC9083282 DOI: 10.1039/c8ra05259j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 07/23/2018] [Indexed: 12/01/2022] Open
Abstract
With the continuous development and application of targeted drugs, it is particularly desirable to find a non-invasive diagnostic approach to screen patients for precision treatment. Specifically, detection of multiple cancer-related mutations is very important for targeted therapy and prediction of drug resistance. Although numerous advanced PCR methods have been developed to discriminate single nucleotide polymorphisms, their drawbacks significantly limit their application, such as low sensitivity and throughput, complicated operations, and expensive costs. In order to overcome these challenges, in this study, we developed a method combining multiplex and sensitive real-time PCR assay with rolling circle amplification. This allows specific and sensitive discrimination of the single nucleotide mutation and provides convenient multiplex detection by real-time PCR assay. The clinical potential of the MPRP assay was further demonstrated by comparing samples from 8 patients with a digital PCR assay. The coincident results between these two methods indicated that the MPRP assay can provide a specific, sensitive, and convenient method for multiplex detection of cancer-related mutations. The MPRP system for SNP discrimination was developed, which showed high specificity and sensitivity for multiplex detection of tumor-related mutations.![]()
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Affiliation(s)
| | - Yishuai Li
- Department of Thoracic Surgery
- Hebei Chest Hospital
- China
| | - Ting Lin
- Apexbio Biotech Co., LTD
- Beijing 100176
- China
| | | | - Li Chu
- Hebei Medical University
- China
- Department of Pharmacology
- Hebei University of Chinese Medicine
- China
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7
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An R, Li Q, Fan Y, Li J, Pan X, Komiyama M, Liang X. Highly efficient preparation of single-stranded DNA rings by T4 ligase at abnormally low Mg(II) concentration. Nucleic Acids Res 2017; 45:e139. [PMID: 28655200 PMCID: PMC5587803 DOI: 10.1093/nar/gkx553] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2017] [Revised: 05/27/2017] [Accepted: 06/15/2017] [Indexed: 12/04/2022] Open
Abstract
Preparation of large amount of single-stranded circular DNA in high selectivity is crucial for further developments of nanotechnology and other DNA sciences. Herein, a simple but practically useful methodology to prepare DNA rings has been presented. One of the essential factors is to use highly diluted T4 ligase buffer for ligase reactions. This strategy is based on our unexpected finding that, in diluted T4 buffers, intermolecular polymerization of DNA fragments is greatly suppressed with respect to their intramolecular cyclization. This promotion of cyclization is attributable to abnormally low concentration of Mg2+ ion (0.5-1.0 mM) but not ATP in the media for T4 ligase reactions. The second essential factor is to add DNA substrate intermittently to the mixture and maintain its temporal concentration low. By combining these two factors, single-stranded DNA rings of various sizes (31-74 nt) were obtained in high selectivity (89 mol% for 66-nt DNA) and in satisfactorily high productivity (∼0.2 mg/ml). A linear 72-nt DNA was converted to the corresponding DNA ring in nearly 100% selectivity. The superiority of this new method was further substantiated by the fact that small-sized DNA rings (31-42 nt), which were otherwise hardly obtainable, were successfully prepared in reasonable yields.
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Affiliation(s)
- Ran An
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Qi Li
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Yiqiao Fan
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Jing Li
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Xiaoming Pan
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Makoto Komiyama
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
- National Institute for Materials Science (NIMS), Namiki, Tsukuba 305-0044, Japan
| | - Xingguo Liang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
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8
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Kim C, Lee OC, Kim JY, Sung W, Lee NK. Dynamic Release of Bending Stress in Short dsDNA by Formation of a Kink and Forks. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201502055] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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9
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Kim C, Lee OC, Kim JY, Sung W, Lee NK. Dynamic Release of Bending Stress in Short dsDNA by Formation of a Kink and Forks. Angew Chem Int Ed Engl 2015; 54:8943-7. [PMID: 26046547 PMCID: PMC4744731 DOI: 10.1002/anie.201502055] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Indexed: 11/21/2022]
Abstract
Bending with high curvature is one of the major mechanical properties of double-stranded DNA (dsDNA) that is essential for its biological functions. The emergence of a kink arising from local melting in the middle of dsDNA has been suggested as a mechanism of releasing the energy cost of bending. Herein, we report that strong bending induces two types of short dsDNA deformations, induced by two types of local melting, namely, a kink in the middle and forks at the ends, which we demonstrate using D-shaped DNA nanostructures. The two types of deformed dsDNA structures dynamically interconvert on a millisecond timescale. The transition from a fork to a kink is dominated by entropic contribution (anti-Arrhenius behavior), while the transition from a kink to a fork is dominated by enthalpic contributions. The presence of mismatches in dsDNA accelerates kink formation, and the transition from a kink to a fork is removed when the mismatch size is three base pairs.
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Affiliation(s)
- Cheolhee Kim
- Department of Physics, Pohang University of Science and Technology, Pohang 790-784 (Republic of Korea)
| | - O-chul Lee
- Department of Physics, Pohang University of Science and Technology, Pohang 790-784 (Republic of Korea)
| | - Jae-Yeol Kim
- Department of Physics, Pohang University of Science and Technology, Pohang 790-784 (Republic of Korea)
| | - Wokyung Sung
- Department of Physics, Pohang University of Science and Technology, Pohang 790-784 (Republic of Korea)
- IBS Center for Self-assembly and Complexity, Pohang 790-784 (Republic of Korea)
| | - Nam Ki Lee
- Department of Physics, Pohang University of Science and Technology, Pohang 790-784 (Republic of Korea).
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10
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Rosanio G, Widom J, Uhlenbeck OC. In vitro selection of DNAs with an increased propensity to form small circles. Biopolymers 2015; 103:303-20. [DOI: 10.1002/bip.22608] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 01/07/2015] [Accepted: 01/08/2015] [Indexed: 11/07/2022]
Affiliation(s)
- Gabriel Rosanio
- Department of Molecular Biosciences; Northwestern University; Evanston IL 60208
- Department of Chemistry; Northwestern University; Evanston IL 60208
| | - Jonathan Widom
- Department of Molecular Biosciences; Northwestern University; Evanston IL 60208
- Department of Chemistry; Northwestern University; Evanston IL 60208
| | - Olke C. Uhlenbeck
- Department of Molecular Biosciences; Northwestern University; Evanston IL 60208
- Department of Chemistry; Northwestern University; Evanston IL 60208
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11
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Abstract
Sharp bending of double-stranded DNA (dsDNA) plays an essential role in genome structure and function. However, the elastic limit of dsDNA bending remains controversial. Here, we measured the opening rates of small dsDNA loops with contour lengths ranging between 40 and 200 bp using single-molecule Fluorescence Resonance Energy Transfer. The relationship of loop lifetime to loop size revealed a critical transition in bending stress. Above the critical loop size, the loop lifetime changed with loop size in a manner consistent with elastic bending stress, but below it, became less sensitive to loop size, indicative of softened dsDNA. The critical loop size increased from ∼60 bp to ∼100 bp with the addition of 5 mM magnesium. We show that our result is in quantitative agreement with the kinkable worm-like chain model, and furthermore, can reproduce previously reported looping probabilities of dsDNA over the range between 50 and 200 bp. Our findings shed new light on the energetics of sharply bent dsDNA.
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Affiliation(s)
- Tung T Le
- School of Physics, Georgia Institute of Technology, 837 State Street, Atlanta, GA 30332, USA
| | - Harold D Kim
- School of Physics, Georgia Institute of Technology, 837 State Street, Atlanta, GA 30332, USA
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12
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Abstract
Bending of double-stranded DNA (dsDNA) is associated with many important biological processes such as DNA-protein recognition and DNA packaging into nucleosomes. Thermodynamics of dsDNA bending has been studied by a method called cyclization which relies on DNA ligase to covalently join short sticky ends of a dsDNA. However, ligation efficiency can be affected by many factors that are not related to dsDNA looping such as the DNA structure surrounding the joined sticky ends, and ligase can also affect the apparent looping rate through mechanisms such as nonspecific binding. Here, we show how to measure dsDNA looping kinetics without ligase by detecting transient DNA loop formation by FRET (Fluorescence Resonance Energy Transfer). dsDNA molecules are constructed using a simple PCR-based protocol with a FRET pair and a biotin linker. The looping probability density known as the J factor is extracted from the looping rate and the annealing rate between two disconnected sticky ends. By testing two dsDNAs with different intrinsic curvatures, we show that the J factor is sensitive to the intrinsic shape of the dsDNA.
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Affiliation(s)
- Tung T Le
- School of Physics, Georgia Institute of Technology
| | - Harold D Kim
- School of Physics, Georgia Institute of Technology;
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13
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Roushan M, Kaur P, Karpusenko A, Countryman PJ, Ortiz CP, Fang Lim S, Wang H, Riehn R. Probing transient protein-mediated DNA linkages using nanoconfinement. BIOMICROFLUIDICS 2014; 8:034113. [PMID: 25379073 PMCID: PMC4162420 DOI: 10.1063/1.4882775] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Accepted: 05/30/2014] [Indexed: 05/16/2023]
Abstract
We present an analytic technique for probing protein-catalyzed transient DNA loops that is based on nanofluidic channels. In these nanochannels, DNA is forced in a linear configuration that makes loops appear as folds whose size can easily be quantified. Using this technique, we study the interaction between T4 DNA ligase and DNA. We find that T4 DNA ligase binding changes the physical characteristics of the DNApolymer, in particular persistence length and effective width. We find that the rate of DNA fold unrolling is significantly reduced when T4 DNA ligase and ATP are applied to bare DNA. Together with evidence of T4 DNA ligase bridging two different segments of DNA based on AFM imaging, we thus conclude that ligase can transiently stabilize folded DNA configurations by coordinating genetically distant DNA stretches.
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Affiliation(s)
- Maedeh Roushan
- Department of Physics, NC State University , Raleigh, North Carolina 27695, USA
| | - Parminder Kaur
- Department of Physics, NC State University , Raleigh, North Carolina 27695, USA
| | - Alena Karpusenko
- Department of Physics, NC State University , Raleigh, North Carolina 27695, USA
| | | | - Carlos P Ortiz
- Department of Physics, NC State University , Raleigh, North Carolina 27695, USA
| | - Shuang Fang Lim
- Department of Physics, NC State University , Raleigh, North Carolina 27695, USA
| | - Hong Wang
- Department of Physics, NC State University , Raleigh, North Carolina 27695, USA
| | - Robert Riehn
- Department of Physics, NC State University , Raleigh, North Carolina 27695, USA
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14
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Le TT, Kim HD. Measuring shape-dependent looping probability of DNA. Biophys J 2013; 104:2068-76. [PMID: 23663850 DOI: 10.1016/j.bpj.2013.03.029] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2013] [Revised: 03/14/2013] [Accepted: 03/18/2013] [Indexed: 01/06/2023] Open
Abstract
Recently, several studies have shown that short doubled-stranded DNA (dsDNA) loops more readily than the wormlike chain model predicts. In most of these experiments, the intrinsic bendedness of dsDNA, which in theory can dramatically influence looping dynamics, was either avoided or unaccounted for. To investigate the effect of the shape of dsDNA on looping dynamics, we characterized the shapes of several synthetic dsDNA molecules of equal length but different sequences using gel electrophoresis. We then measured their looping rates using a FRET (Förster resonance energy transfer)-based assay and extracted the looping probability density known as the J factor (jM). We also used, for comparison, several dinucleotide angular parameter sets derived from the observed electrophoretic mobility to compute the jM predicted by the wormlike chain model. Although we found a strong correlation between curvature and jM, the measured jM was higher than most dinucleotide model predictions. This result suggests that it is difficult to reconcile the looping probability with the observed gel mobility within the wormlike chain model and underscores the importance of determining the intrinsic shape of dsDNA for proper theoretical analysis.
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Affiliation(s)
- Tung T Le
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia, USA
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15
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Peters JP, Yelgaonkar SP, Srivatsan SG, Tor Y, James Maher L. Mechanical properties of DNA-like polymers. Nucleic Acids Res 2013; 41:10593-604. [PMID: 24013560 PMCID: PMC3905893 DOI: 10.1093/nar/gkt808] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The molecular structure of the DNA double helix has been known for 60 years, but we remain surprisingly ignorant of the balance of forces that determine its mechanical properties. The DNA double helix is among the stiffest of all biopolymers, but neither theory nor experiment has provided a coherent understanding of the relative roles of attractive base stacking forces and repulsive electrostatic forces creating this stiffness. To gain insight, we have created a family of double-helical DNA-like polymers where one of the four normal bases is replaced with various cationic, anionic or neutral analogs. We apply DNA ligase-catalyzed cyclization kinetics experiments to measure the bending and twisting flexibilities of these polymers under low salt conditions. Interestingly, we show that these modifications alter DNA bending stiffness by only 20%, but have much stronger (5-fold) effects on twist flexibility. We suggest that rather than modifying DNA stiffness through a mechanism easily interpretable as electrostatic, the more dominant effect of neutral and charged base modifications is their ability to drive transitions to helical conformations different from canonical B-form DNA.
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Affiliation(s)
- Justin P Peters
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, 200 First St. SW, Rochester, MN 55905, USA, Indian Institute of Science Education and Research, 900, NCL Innovation Park, Dr. Homi Bhabha Road, Pune 411008, India and Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
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16
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Al-Manasra AM, Al-Razem F. Cloning and expression of a new bacteriophage (SHPh) DNA ligase isolated from sewage. J Genet Eng Biotechnol 2012. [DOI: 10.1016/j.jgeb.2012.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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17
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Vafabakhsh R, Ha T. Extreme bendability of DNA less than 100 base pairs long revealed by single-molecule cyclization. Science 2012; 337:1097-101. [PMID: 22936778 PMCID: PMC3565842 DOI: 10.1126/science.1224139] [Citation(s) in RCA: 223] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The classical view of DNA posits that DNA must be stiff below the persistence length [<150 base pairs (bp)], but recent studies addressing this have yielded contradictory results. We developed a fluorescence-based, protein-free assay for studying the cyclization of single DNA molecules in real time. The assay samples the equilibrium population of a sharply bent, transient species that is entirely suppressed in single-molecule mechanical measurements and is biologically more relevant than the annealed species sampled in the traditional ligase-based assay. The looping rate has a weak length dependence between 67 and 106 bp that cannot be described by the worm-like chain model. Many biologically important protein-DNA interactions that involve looping and bending of DNA below 100 bp likely use this intrinsic bendability of DNA.
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Affiliation(s)
- Reza Vafabakhsh
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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18
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Lohman GJS, Chen L, Evans TC. Kinetic characterization of single strand break ligation in duplex DNA by T4 DNA ligase. J Biol Chem 2011; 286:44187-44196. [PMID: 22027837 PMCID: PMC3243518 DOI: 10.1074/jbc.m111.284992] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2011] [Revised: 10/14/2011] [Indexed: 01/24/2023] Open
Abstract
T4 DNA ligase catalyzes phosphodiester bond formation between juxtaposed 5'-phosphate and 3'-hydroxyl termini in duplex DNA in three steps: 1) enzyme-adenylylate formation by reaction with ATP; 2) adenylyl transfer to a 5'-phosphorylated polynucleotide to generate adenylylated DNA; and 3) phosphodiester bond formation with release of AMP. This investigation used synthetic, nicked DNA substrates possessing either a 5'-phosphate or a 5'-adenylyl phosphate. Steady state experiments with a nicked substrate containing juxtaposed dC and 5'-phosphorylated dT deoxynucleotides (substrate 1) yielded kcat and kcat/Km values of 0.4±0.1 s(-1) and 150±50 μm(-1) s(-1), respectively. Under identical reaction conditions, turnover of an adenylylated version of this substrate (substrate 1A) yielded kcat and kcat/Km values of 0.64±0.08 s(-1) and 240±40 μm(-1) s(-1). Single turnover experiments utilizing substrate 1 gave fits for the forward rates of Step 2 (k2) and Step 3 (k3) of 5.3 and 38 s(-1), respectively, with the slowest step ∼10-fold faster than the rate of turnover seen under steady state conditions. Single turnover experiments with substrate 1A produced a Step 3 forward rate constant of 4.3 s(-1), also faster than the turnover rate of 1A. Enzyme self-adenylylation was confirmed to also occur on a fast time scale (∼6 s(-1)), indicating that the rate-limiting step for T4 DNA ligase nick sealing is not a chemical step but rather is most likely product release. Pre-steady state reactions displayed a clear burst phase, consistent with this conclusion.
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Affiliation(s)
| | - Lixin Chen
- New England Biolabs Inc., Ipswich, Massachusetts 01938-2723
| | - Thomas C Evans
- New England Biolabs Inc., Ipswich, Massachusetts 01938-2723.
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19
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Abstract
Fluorescent sensors that make use of DNA structures have become widely useful in monitoring enzymatic activities. Early studies focused primarily on enzymes that naturally use DNA or RNA as the substrate. However, recent advances in molecular design have enabled the development of nucleic acid sensors for a wider range of functions, including enzymes that do not normally bind DNA or RNA. Nucleic acid sensors present some potential advantages over classical small-molecule sensors, including water solubility and ease of synthesis. An overview of the multiple strategies under recent development is presented in this critical review, and expected future developments in microarrays, single molecule analysis, and in vivo sensing are discussed (160 references).
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Affiliation(s)
- Nan Dai
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Eric T. Kool
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
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20
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Cherstvy AG. DNA Cyclization: Suppression or Enhancement by Electrostatic Repulsions? J Phys Chem B 2011; 115:4286-94. [DOI: 10.1021/jp2003479] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- A. G. Cherstvy
- Institute of Complex Systems, ICS-2, Theoretical Soft Matter and Biophysics, Forschungszentrum Jülich, 52425 Jülich, Germany
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21
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Demurtas D, Amzallag A, Rawdon EJ, Maddocks JH, Dubochet J, Stasiak A. Bending modes of DNA directly addressed by cryo-electron microscopy of DNA minicircles. Nucleic Acids Res 2009; 37:2882-93. [PMID: 19282451 PMCID: PMC2685088 DOI: 10.1093/nar/gkp137] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
We use cryo-electron microscopy (cryo-EM) to study the 3D shapes of 94-bp-long DNA minicircles and address the question of whether cyclization of such short DNA molecules necessitates the formation of sharp, localized kinks in DNA or whether the necessary bending can be redistributed and accomplished within the limits of the elastic, standard model of DNA flexibility. By comparing the shapes of covalently closed, nicked and gapped DNA minicircles, we conclude that 94-bp-long covalently closed and nicked DNA minicircles do not show sharp kinks while gapped DNA molecules, containing very flexible single-stranded regions, do show sharp kinks. We corroborate the results of cryo-EM studies by using Bal31 nuclease to probe for the existence of kinks in 94-bp-long minicircles.
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Affiliation(s)
- Davide Demurtas
- Faculty of Biology and Medicine, Center for Integrative Genomics, University of Lausanne, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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