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Kopu̅stas A, Ivanovaitė Š, Rakickas T, Pocevičiu̅tė E, Paksaitė J, Karvelis T, Zaremba M, Manakova E, Tutkus M. Oriented Soft DNA Curtains for Single-Molecule Imaging. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:3428-3437. [PMID: 33689355 PMCID: PMC8280724 DOI: 10.1021/acs.langmuir.1c00066] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Over the past 20 years, single-molecule methods have become extremely important for biophysical studies. These methods, in combination with new nanotechnological platforms, can significantly facilitate experimental design and enable faster data acquisition. A nanotechnological platform, which utilizes a flow-stretch of immobilized DNA molecules, called DNA Curtains, is one of the best examples of such combinations. Here, we employed new strategies to fabricate a flow-stretch assay of stably immobilized and oriented DNA molecules using a protein template-directed assembly. In our assay, a protein template patterned on a glass coverslip served for directional assembly of biotinylated DNA molecules. In these arrays, DNA molecules were oriented to one another and maintained extended by either single- or both-end immobilization to the protein templates. For oriented both-end DNA immobilization, we employed heterologous DNA labeling and protein template coverage with the antidigoxigenin antibody. In contrast to single-end immobilization, both-end immobilization does not require constant buffer flow for keeping DNAs in an extended configuration, allowing us to study protein-DNA interactions at more controllable reaction conditions. Additionally, we increased the immobilization stability of the biotinylated DNA molecules using protein templates fabricated from traptavidin. Finally, we demonstrated that double-tethered Soft DNA Curtains can be used in nucleic acid-interacting protein (e.g., CRISPR-Cas9) binding assay that monitors the binding location and position of individual fluorescently labeled proteins on DNA.
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Affiliation(s)
- Aurimas Kopu̅stas
- Departments
of Molecular Compound Physics, Nanoengineering, and Functional Materials and Electronics, Center for Physical Sciences and Technology, Savanoriu 231, Vilnius LT-02300, Lithuania
- Life
Sciences Center, Institute of Biotechnology, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania
| | - Šaru̅nė Ivanovaitė
- Departments
of Molecular Compound Physics, Nanoengineering, and Functional Materials and Electronics, Center for Physical Sciences and Technology, Savanoriu 231, Vilnius LT-02300, Lithuania
| | - Tomas Rakickas
- Departments
of Molecular Compound Physics, Nanoengineering, and Functional Materials and Electronics, Center for Physical Sciences and Technology, Savanoriu 231, Vilnius LT-02300, Lithuania
| | - Ernesta Pocevičiu̅tė
- Departments
of Molecular Compound Physics, Nanoengineering, and Functional Materials and Electronics, Center for Physical Sciences and Technology, Savanoriu 231, Vilnius LT-02300, Lithuania
- Life
Sciences Center, Institute of Biotechnology, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania
| | - Justė Paksaitė
- Life
Sciences Center, Institute of Biotechnology, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania
| | - Tautvydas Karvelis
- Life
Sciences Center, Institute of Biotechnology, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania
| | - Mindaugas Zaremba
- Life
Sciences Center, Institute of Biotechnology, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania
| | - Elena Manakova
- Life
Sciences Center, Institute of Biotechnology, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania
| | - Marijonas Tutkus
- Departments
of Molecular Compound Physics, Nanoengineering, and Functional Materials and Electronics, Center for Physical Sciences and Technology, Savanoriu 231, Vilnius LT-02300, Lithuania
- Life
Sciences Center, Institute of Biotechnology, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania
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2
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Li Y, Wan Z, Zuo L, Li S, Liu H, Ma Y, Zhou L, Jin X, Li Y, Zhang C. A Novel 2-dimensional Multiplex qPCR Assay for Single-Tube Detection of Nine Human Herpesviruses. Virol Sin 2021; 36:746-754. [PMID: 33635517 DOI: 10.1007/s12250-021-00354-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 12/28/2020] [Indexed: 11/28/2022] Open
Abstract
Human herpesviruses are double-stranded DNA viruses that are classified into nine species. More than 90% of adults are ever infected with one or more herpesviruses. The symptoms of infection with different herpesviruses are diverse ranging from mild or asymptomatic infections to deadly diseases such as aggressive lymphomas and sarcomas. Timely and accurate detection of herpesvirus infection is critical for clinical management and treatment. In this study, we established a single-tube nonuple qPCR assay for detection of all nine herpesviruses using a 2-D multiplex qPCR method with a house-keeping gene as the internal control. The novel assay can detect and distinguish different herpesviruses with 30 to 300 copies per 25 µL single-tube reaction, and does not cross-react with 20 other human viruses, including DNA and RNA viruses. The robustness of the novel assay was evaluated using 170 clinical samples. The novel assay showed a high consistency (100%) with the single qPCR assay for HHVs detection. The features of simple, rapid, high sensitivity, specificity, and low cost make this assay a high potential to be widely used in clinical diagnosis and patient treatment.
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Affiliation(s)
- Yingxue Li
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China.,CAS Key Laboratory of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China.,School of Biomedical Engineering, University of Science and Technology of China, Hefei, 260026, China
| | - Zhenzhou Wan
- Medical Laboratory of Taizhou Fourth People's Hospital, Taizhou, 225300, China
| | - Lulu Zuo
- Viral Hemorrhagic Fevers Research Unit, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Shenwei Li
- Shanghai International Travel Healthcare Center, Shanghai, 200335, China
| | - Honglian Liu
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Yingying Ma
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Lianqun Zhou
- CAS Key Laboratory of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China.,School of Biomedical Engineering, University of Science and Technology of China, Hefei, 260026, China
| | - Xia Jin
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Yuye Li
- Department of Dermatology and Venereology, First Affiliated Hospital of Kunming Medical University, Kunming, 650032, China.
| | - Chiyu Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China.
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3
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Achary PGR. Applications of Quantitative Structure-Activity Relationships (QSAR) based Virtual Screening in Drug Design: A Review. Mini Rev Med Chem 2020; 20:1375-1388. [DOI: 10.2174/1389557520666200429102334] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 11/07/2019] [Accepted: 11/08/2019] [Indexed: 12/18/2022]
Abstract
The scientists, and the researchers around the globe generate tremendous amount of information
everyday; for instance, so far more than 74 million molecules are registered in Chemical
Abstract Services. According to a recent study, at present we have around 1060 molecules, which are
classified as new drug-like molecules. The library of such molecules is now considered as ‘dark chemical
space’ or ‘dark chemistry.’ Now, in order to explore such hidden molecules scientifically, a good
number of live and updated databases (protein, cell, tissues, structure, drugs, etc.) are available today.
The synchronization of the three different sciences: ‘genomics’, proteomics and ‘in-silico simulation’
will revolutionize the process of drug discovery. The screening of a sizable number of drugs like molecules
is a challenge and it must be treated in an efficient manner. Virtual screening (VS) is an important
computational tool in the drug discovery process; however, experimental verification of the
drugs also equally important for the drug development process. The quantitative structure-activity relationship
(QSAR) analysis is one of the machine learning technique, which is extensively used in VS
techniques. QSAR is well-known for its high and fast throughput screening with a satisfactory hit rate.
The QSAR model building involves (i) chemo-genomics data collection from a database or literature
(ii) Calculation of right descriptors from molecular representation (iii) establishing a relationship
(model) between biological activity and the selected descriptors (iv) application of QSAR model to
predict the biological property for the molecules. All the hits obtained by the VS technique needs to be
experimentally verified. The present mini-review highlights: the web-based machine learning tools, the
role of QSAR in VS techniques, successful applications of QSAR based VS leading to the drug discovery
and advantages and challenges of QSAR.
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Affiliation(s)
- Patnala Ganga Raju Achary
- Department of Chemistry, Faculty of Engineering & Technology (ITER), Siksha ‘O’ Anusandhan, Deemed to be University, Khandagiri Square, Bhubaneswar- 751030, India
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4
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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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5
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Loukanov A, Nikolova S, Filipov C, Nakabayashi S. Metabolic labeling of Escherichia coli
genomic DNA with erythrosine-11-dUTP for functional imaging via correlative microscopy. Microsc Res Tech 2020; 83:937-944. [DOI: 10.1002/jemt.23487] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 03/02/2020] [Accepted: 03/18/2020] [Indexed: 12/19/2022]
Affiliation(s)
- Alexandre Loukanov
- Division of Strategic Research and Development, Graduate School of Science and Engineering; Saitama University; Saitama Japan
- Laboratory of Engineering NanoBiotechnology, Department of Engineering Geoecology; University of Mining and Geology “St. Ivan Rilski”; Sofia Bulgaria
| | - Svetla Nikolova
- Medical University-Sofia; University Hospital “Maichin Dom”, National Genetic Laboratory; Sofia Bulgaria
| | - Chavdar Filipov
- Faculty of Veterinary Medicine; University of Forestry, Sofia; Sofia Bulgaria
| | - Seiichiro Nakabayashi
- Division of Strategic Research and Development, Graduate School of Science and Engineering; Saitama University; Saitama Japan
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6
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Springall L, Hughes CD, Simons M, Azinas S, Van Houten B, Kad NM. Recruitment of UvrBC complexes to UV-induced damage in the absence of UvrA increases cell survival. Nucleic Acids Res 2019; 46:1256-1265. [PMID: 29240933 PMCID: PMC5814901 DOI: 10.1093/nar/gkx1244] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 12/01/2017] [Indexed: 02/05/2023] Open
Abstract
Nucleotide excision repair (NER) is the primary mechanism for removal of ultraviolet light (UV)-induced DNA photoproducts and is mechanistically conserved across all kingdoms of life. Bacterial NER involves damage recognition by UvrA2 and UvrB, followed by UvrC-mediated incision either side of the lesion. Here, using a combination of in vitro and in vivo single-molecule studies we show that a UvrBC complex is capable of lesion identification in the absence of UvrA. Single-molecule analysis of eGFP-labelled UvrB and UvrC in living cells showed that UV damage caused these proteins to switch from cytoplasmic diffusion to stable complexes on DNA. Surprisingly, ectopic expression of UvrC in a uvrA deleted strain increased UV survival. These data provide evidence for a previously unrealized mechanism of survival that can occur through direct lesion recognition by a UvrBC complex.
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Affiliation(s)
- Luke Springall
- School of Biological Sciences, University of Kent, Canterbury CT2 7NH, UK
| | - Craig D Hughes
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
| | - Michelle Simons
- School of Biological Sciences, University of Essex, Colchester CO4 3SQ, UK
| | - Stavros Azinas
- School of Biological Sciences, University of Essex, Colchester CO4 3SQ, UK
| | | | - Neil M Kad
- School of Biological Sciences, University of Kent, Canterbury CT2 7NH, UK
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7
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Electrochemiluminescent determination of the activity of uracil-DNA glycosylase: Combining nicking enzyme assisted signal amplification and catalyzed hairpin assembly. Mikrochim Acta 2019; 186:179. [DOI: 10.1007/s00604-019-3280-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 01/23/2019] [Indexed: 12/31/2022]
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8
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Kim Y, de la Torre A, Leal AA, Finkelstein IJ. Efficient modification of λ-DNA substrates for single-molecule studies. Sci Rep 2017; 7:2071. [PMID: 28522818 PMCID: PMC5437064 DOI: 10.1038/s41598-017-01984-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 04/05/2017] [Indexed: 01/15/2023] Open
Abstract
Single-molecule studies of protein-nucleic acid interactions frequently require site-specific modification of long DNA substrates. The bacteriophage λ is a convenient source of high quality long (48.5 kb) DNA. However, introducing specific sequences, tertiary structures, and chemical modifications into λ-DNA remains technically challenging. Most current approaches rely on multi-step ligations with low yields and incomplete products. Here, we describe a molecular toolkit for rapid preparation of modified λ-DNA. A set of PCR cassettes facilitates the introduction of recombinant DNA sequences into the λ-phage genome with 90-100% yield. Extrahelical structures and chemical modifications can be inserted at user-defined sites via an improved nicking enzyme-based strategy. As a proof-of-principle, we explore the interactions of S. cerevisiae Proliferating Cell Nuclear Antigen (yPCNA) with modified DNA sequences and structures incorporated within λ-DNA. Our results demonstrate that S. cerevisiae Replication Factor C (yRFC) can load yPCNA onto 5'-ssDNA flaps, (CAG)13 triplet repeats, and homoduplex DNA. However, yPCNA remains trapped on the (CAG)13 structure, confirming a proposed mechanism for triplet repeat expansion. We anticipate that this molecular toolbox will be broadly useful for other studies that require site-specific modification of long DNA substrates.
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Affiliation(s)
- Yoori Kim
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, 78712, USA
| | - Armando de la Torre
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, 78712, USA
| | - Andrew A Leal
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, 78712, USA
| | - Ilya J Finkelstein
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, 78712, USA.
- Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas, 78712, USA.
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9
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Wei H, Zhao G, Hu T, Tang S, Jiang J, Hu B, Guan Y. Mapping the nicking efficiencies of nickase R.BbvCI for side-specific LNA-substituted substrates using rolling circle amplification. Sci Rep 2016; 6:32560. [PMID: 27582033 PMCID: PMC5007493 DOI: 10.1038/srep32560] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 08/09/2016] [Indexed: 11/29/2022] Open
Abstract
We used a novel asymmetric cleavage analysis method based on rolling circle amplification (RCA) to determine the effects of LNA modification of substrate on the two subunits of R.BbvCI cleavage. We designed two sets of cleavage circular substrates by using two different ligation strategies and analyzed the single strand cleavage efficiency affected by different modification positions both from the cleaved strands and the uncleaved strands. Results showed that the effects of LNA on cleavage rates of modified strands and unmodified strands were both site-dependent. The Nb.BbvCI and Nt.BbvCI were affected by LNA modification in different way. Most of the modification positions showed strong inhibition of both of these two nickases cleavage. However, the modification in T3 position of bottom strand hardly affected both of the two nickases activities. The results suggested an intimated interaction between the two subunits of R.BbvCI, and the T3 position in bottom strand might be a less tight position which was hard to be disturbed.
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Affiliation(s)
- Hua Wei
- Department of Biochemistry and Molecular Biology, China Medical University, #77 Puhe Road, Shenyang, Liaoning, 110122, China.,Animal Science and Veterinary Medicine College, Shenyang Agricultural University, Shenyang, Liaoning, 110866, China
| | - Guojie Zhao
- Department of Biochemistry and Molecular Biology, China Medical University, #77 Puhe Road, Shenyang, Liaoning, 110122, China
| | - Tianyu Hu
- Department of Biochemistry and Molecular Biology, China Medical University, #77 Puhe Road, Shenyang, Liaoning, 110122, China
| | - Suming Tang
- Department of Biochemistry and Molecular Biology, China Medical University, #77 Puhe Road, Shenyang, Liaoning, 110122, China
| | - Jiquan Jiang
- Department of Biochemistry and Molecular Biology, China Medical University, #77 Puhe Road, Shenyang, Liaoning, 110122, China
| | - Bo Hu
- Department of Biochemistry and Molecular Biology, China Medical University, #77 Puhe Road, Shenyang, Liaoning, 110122, China
| | - Yifu Guan
- Department of Biochemistry and Molecular Biology, China Medical University, #77 Puhe Road, Shenyang, Liaoning, 110122, China
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10
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Lee J, Park IS, Jung E, Lee Y, Min DH. Direct, sequence-specific detection of dsDNA based on peptide nucleic acid and graphene oxide without requiring denaturation. Biosens Bioelectron 2014; 62:140-4. [PMID: 24997367 DOI: 10.1016/j.bios.2014.06.028] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 06/06/2014] [Accepted: 06/15/2014] [Indexed: 11/18/2022]
Abstract
Sequence-specific detection of double stranded DNA (dsDNA) is important in various research fields. In general, denaturation of dsDNA into single strands is necessary for the sequence-specific recognition of probes to target DNA, posing several drawbacks which decrease the efficiency as a DNA sensor. Herein, we report a direct, sequence-specific dsDNA detection system without requiring any thermal denaturing step. Our strategy utilizes peptide nucleic acid (PNA) and graphene oxide (GO) as a probe and as a fluorescence quencher, respectively. The PNA first binds to the end of dsDNA strand due to the relatively easily dissociable terminal base pairs of DNA duplex. Next, superior binding affinity of PNA towards complementary DNA induces branch migration for gradual strand replacement, resulting in the formation of PNA/DNA duplex. Unlike other dsDNA sensors based on complementary DNA probes, PNA in combination with GO enabled hybridization with the target sequence hidden as a duplex form without denaturing step and thus, the formation of PNA/DNA duplex was translated into selective fluorescence signal. Moreover, it provided tighter turn-on signal control with very low background signal and high sensitivity and sequence selectivity even in the presence of serum proteins.
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Affiliation(s)
- Jieon Lee
- Center for RNA Research, Institute for Basic Science, Seoul National University, Seoul 151-747, Republic of Korea; Department of Chemistry, Seoul National University, Seoul 151-747, Republic of Korea
| | - Il-Soo Park
- Center for RNA Research, Institute for Basic Science, Seoul National University, Seoul 151-747, Republic of Korea; Department of Chemistry, Seoul National University, Seoul 151-747, Republic of Korea
| | - Euihan Jung
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Republic of Korea
| | - Younghoon Lee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Republic of Korea
| | - Dal-Hee Min
- Center for RNA Research, Institute for Basic Science, Seoul National University, Seoul 151-747, Republic of Korea; Department of Chemistry, Seoul National University, Seoul 151-747, Republic of Korea.
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11
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KOBORI T, TAKAHASHI H. Expanding Possibilities of Rolling Circle Amplification as a Biosensing Platform. ANAL SCI 2014; 30:59-64. [DOI: 10.2116/analsci.30.59] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Toshiro KOBORI
- National Food Research Institute, National Agriculture and Food Research Organization
| | - Hirokazu TAKAHASHI
- National Food Research Institute, National Agriculture and Food Research Organization
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12
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De Novo DNA Synthesis and Its Biosensor Detection. ACTA ACUST UNITED AC 2013. [DOI: 10.1201/b15589-10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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13
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Sekerina SA, Grishin AV, Riazanova AI, Artiukh RI, Rogulin EA, Iunusova AK, Oretskaia TS, Zheleznaia LA, Kubareva EA. [Oligomerization of site-specific nicking endonuclease BspD6I at high protein concentrations]. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2013. [PMID: 23189557 DOI: 10.1134/s1068162012040127] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Ability of site-specific nickase BspD6I (Nt.BspD6I) to oligomerize at concentrations > or = 0.5 microM (> or = 0.035 mg/mL) is studied. Three states of Nt.BspD6I are registered via electrophoretic studies both in the presence and in the absence of DNA. Estimation of their molecular mass allows assigning them as a monomer, a dimer and a trimer. Both dimeric and monomeric Nt.BspD6I are shown to hydrolyze its DNA substrate with the identical specificity. Calculation of the electrostatic potential distribution on the Nt.BspD6I globule surface shows that the protein molecule is a dipole. The Nt. BspD6I oligomeric forms are likely to be the result of ionic protein interactions.
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14
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Abstract
Replicative DNA helicases generally unwind DNA as a single hexamer that encircles and translocates along one strand of the duplex while excluding the complementary strand (“steric exclusion”). In contrast, large T antigen (T-ag), the replicative DNA helicase of the Simian Virus 40 (SV40), is reported to function as a pair of stacked hexamers that pumps double-stranded DNA through its central channel while laterally extruding single-stranded DNA. Here, we use single-molecule and ensemble assays to show that T-ag assembled on the SV40 origin unwinds DNA efficiently as a single hexamer that translocates on single-stranded DNA in the 3′ to 5′ direction. Unexpectedly, T-ag unwinds DNA past a DNA-protein crosslink on the translocation strand, suggesting that the T-ag ring can open to bypass bulky adducts. Together, our data underscore the profound conservation among replicative helicase mechanisms while revealing a new level of plasticity in their interactions with DNA damage.
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15
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Zyrina NV, Artyukh RI, Svad’bina IV, Zheleznaya LA, Matvienko NI. The effect of single-stranded DNA binding proteins on template/primer-independent DNA synthesis in the presence of nicking endonuclease Nt.BspD6I. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2012; 38:199-205. [DOI: 10.1134/s1068162012020161] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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16
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Luzzietti N, Knappe S, Richter I, Seidel R. Nicking enzyme-based internal labeling of DNA at multiple loci. Nat Protoc 2012; 7:643-53. [PMID: 22402634 DOI: 10.1038/nprot.2012.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The labeling of biomolecules has become standard practice in molecular biosciences. Modifications are used for detection, sorting and isolation of small molecules, complexes and entire cells. We have recently reported a method for introducing internal chemical and structural modifications into kbp-sized DNA target substrates that are frequently used in single-molecule experiments. It makes use of nicking enzymes that create single-stranded DNA gaps, which can be subsequently filled with labeled oligonucleotides. Here we provide a detailed protocol and further expand this method. We show that modifications can be introduced at distant loci within one molecule in a simple one-pot reaction. In addition, we achieve labeling on both strands at a specific locus, as demonstrated by Förster resonance energy transfer (FRET) experiments. The protocol requires an initial cloning of the target substrate (3-5 d), whereas the labeling itself takes 4-6 h. More elaborate purification and verification of label incorporation requires 2 h for each method.
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Affiliation(s)
- Nicholas Luzzietti
- Biotechnology Center, Dresden University of Technology, Dresden, Germany
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17
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Gupta R, Capalash N, Sharma P. Restriction endonucleases: natural and directed evolution. Appl Microbiol Biotechnol 2012; 94:583-99. [PMID: 22398859 DOI: 10.1007/s00253-012-3961-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2011] [Revised: 02/08/2012] [Accepted: 02/09/2012] [Indexed: 10/28/2022]
Abstract
Type II restriction endonucleases (REs) are highly sequence-specific compared with other classes of nucleases. PD-(D/E)XK nucleases, initially represented by only type II REs, now comprise a large and extremely diverse superfamily of proteins and, although sharing a structurally conserved core, typically display little or no detectable sequence similarity except for the active site motifs. Sequence similarity can only be observed in methylases and few isoschizomers. As a consequence, REs are classified according to combinations of functional properties rather than on the basis of genetic relatedness. New alignment matrices and classification systems based on structural core connectivity and cleavage mechanisms have been developed to characterize new REs and related proteins. REs recognizing more than 300 distinct specificities have been identified in RE database (REBASE: http://rebase.neb.com/cgi-bin/statlist ) but still the need for newer specificities is increasing due to the advancement in molecular biology and applications. The enzymes have undergone constant evolution through structural changes in protein scaffolds which include random mutations, homologous recombinations, insertions, and deletions of coding DNA sequences but rational mutagenesis or directed evolution delivers protein variants with new functions in accordance with defined biochemical or environmental pressures. Redesigning through random mutation, addition or deletion of amino acids, methylation-based selection, synthetic molecules, combining recognition and cleavage domains from different enzymes, or combination with domains of additional functions change the cleavage specificity or substrate preference and stability. There is a growing number of patents awarded for the creation of engineered REs with new and enhanced properties.
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Affiliation(s)
- Richa Gupta
- Department of Biotechnology, Panjab University, Chandigarh, India 160014
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18
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Fu YV, Yardimci H, Long DT, Ho TV, Guainazzi A, Bermudez VP, Hurwitz J, van Oijen A, Schärer OD, Walter JC. Selective bypass of a lagging strand roadblock by the eukaryotic replicative DNA helicase. Cell 2011; 146:931-41. [PMID: 21925316 DOI: 10.1016/j.cell.2011.07.045] [Citation(s) in RCA: 285] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Revised: 05/17/2011] [Accepted: 07/29/2011] [Indexed: 12/13/2022]
Abstract
The eukaryotic replicative DNA helicase, CMG, unwinds DNA by an unknown mechanism. In some models, CMG encircles and translocates along one strand of DNA while excluding the other strand. In others, CMG encircles and translocates along duplex DNA. To distinguish between these models, replisomes were confronted with strand-specific DNA roadblocks in Xenopus egg extracts. An ssDNA translocase should stall at an obstruction on the translocation strand but not the excluded strand, whereas a dsDNA translocase should stall at obstructions on either strand. We found that replisomes bypass large roadblocks on the lagging strand template much more readily than on the leading strand template. Our results indicate that CMG is a 3' to 5' ssDNA translocase, consistent with unwinding via "steric exclusion." Given that MCM2-7 encircles dsDNA in G1, the data imply that formation of CMG in S phase involves remodeling of MCM2-7 from a dsDNA to a ssDNA binding mode.
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Affiliation(s)
- Yu V Fu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
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19
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Zohar H, Muller SJ. Labeling DNA for single-molecule experiments: methods of labeling internal specific sequences on double-stranded DNA. NANOSCALE 2011; 3:3027-39. [PMID: 21734993 PMCID: PMC3322637 DOI: 10.1039/c1nr10280j] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
This review is a practical guide for experimentalists interested in specifically labeling internal sequences on double-stranded (ds) DNA molecules for single-molecule experiments. We describe six labeling approaches demonstrated in a single-molecule context and discuss the merits and drawbacks of each approach with particular attention to the amount of specialized training and reagents required. By evaluating each approach according to criteria relevant to single-molecule experiments, including labeling yield and compatibility with cofactors such as Mg(2+), we provide a simple reference for selecting a labeling method for given experimental constraints. Intended for non-specialists seeking accessible solutions to DNA labeling challenges, the approaches outlined emphasize simplicity, robustness, suitability for use by non-biologists, and utility in diverse single-molecule experiments.
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Affiliation(s)
- Hagar Zohar
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA
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20
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Abstract
Sequence-specific DNA modification is of significance for applications in bio- and nano-technology, medical diagnostics and fundamental life sciences research. Preferentially, labelling should be performed covalently, which avoids doubts about label dissociation from the DNA under various conditions. Several methods to label native DNA have been developed in the last two decades. Triple-helix-forming oligodeoxynucleotides and hairpin polyamides that bind DNA sequences specifically in the major and minor groove respectively were used as targeting devices for subsequent covalent labelling. In addition, enzyme-directed labelling approaches utilizing nicking endonucleases in combination with DNA polymerases or DNA methyltransferases have been employed. This review summarizes various techniques useful for functionalization of long native DNA.
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21
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Schopf E, Liu Y, Deng JC, Yang S, Cheng G, Chen Y. tuberculosis detection via rolling circle amplification. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2011; 3:267-273. [PMID: 32938023 DOI: 10.1039/c0ay00529k] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Hybridization-based assays for DNA detection often use single-stranded DNA (ssDNA) probes to capture ssDNA targets in solution. Unfortunately, these assays are often not able to detect double-stranded DNA (dsDNA). Here, we achieve highly sensitive dsDNA target detection by including short oligonucleotide sequences during denaturing and cooling. After performing an isothermal nucleic acid amplification technique (Rolling Circle Amplification, RCA), these captured dsDNA targets are labeled, allowing single amplified molecules to be imaged and counted. This detection method was first applied to the detection of PCR-generated (polymerase chain reaction) dsDNA targets, yielding a limit of detection of 4.25 fM. As an application of the developed assay, the detection of extracted Mycobacterium tuberculosis (M. tb.) genomic DNA was attempted. A M. tb.-specific target was detected with high specificity compared to similar bacteria, and a detection limit of 10 000 colony forming units (cfu) ml-1 was achieved, close to the sensitivity required for clinical diagnosis.
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Affiliation(s)
- Eric Schopf
- Department of Mechanical and Aerospace Engineering, California NanoSystems Institute, University of California, Los Angeles, California 90095, USA.
| | - Yang Liu
- Department of Mechanical and Aerospace Engineering, California NanoSystems Institute, University of California, Los Angeles, California 90095, USA.
| | - Jane C Deng
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, California 90095, USA
| | - Siyin Yang
- Department of Mechanical and Aerospace Engineering, California NanoSystems Institute, University of California, Los Angeles, California 90095, USA.
| | - Genhong Cheng
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, California 90095, USA
| | - Yong Chen
- Department of Mechanical and Aerospace Engineering, California NanoSystems Institute, University of California, Los Angeles, California 90095, USA.
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22
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Simultaneous single-molecule measurements of phage T7 replisome composition and function reveal the mechanism of polymerase exchange. Proc Natl Acad Sci U S A 2011; 108:3584-9. [PMID: 21245349 DOI: 10.1073/pnas.1018824108] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A complete understanding of the molecular mechanisms underlying the functioning of large, multiprotein complexes requires experimental tools capable of simultaneously visualizing molecular architecture and enzymatic activity in real time. We developed a novel single-molecule assay that combines the flow-stretching of individual DNA molecules to measure the activity of the DNA-replication machinery with the visualization of fluorescently labeled DNA polymerases at the replication fork. By correlating polymerase stoichiometry with DNA synthesis of T7 bacteriophage replisomes, we are able to quantitatively describe the mechanism of polymerase exchange. We find that even at relatively modest polymerase concentration (∼2 nM), soluble polymerases are recruited to an actively synthesizing replisome, dramatically increasing local polymerase concentration. These excess polymerases remain passively associated with the replisome through electrostatic interactions with the T7 helicase for ∼50 s until a stochastic and transient dissociation of the synthesizing polymerase from the primer-template allows for a polymerase exchange event to occur.
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23
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Luzzietti N, Brutzer H, Klaue D, Schwarz FW, Staroske W, Clausing S, Seidel R. Efficient preparation of internally modified single-molecule constructs using nicking enzymes. Nucleic Acids Res 2010; 39:e15. [PMID: 21071409 PMCID: PMC3035433 DOI: 10.1093/nar/gkq1004] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Investigations of enzymes involved in DNA metabolism have strongly benefited from the establishment of single molecule techniques. These experiments frequently require elaborate DNA substrates, which carry chemical labels or nucleic acid tertiary structures. Preparing such constructs often represents a technical challenge: long modified DNA molecules are usually produced via multi-step processes, involving low efficiency intermolecular ligations of several fragments. Here, we show how long stretches of DNA (>50 bp) can be modified using nicking enzymes to produce complex DNA constructs. Multiple different chemical and structural modifications can be placed internally along DNA, in a specific and precise manner. Furthermore, the nicks created can be resealed efficiently yielding intact molecules, whose mechanical properties are preserved. Additionally, the same strategy is applied to obtain long single-strand overhangs subsequently used for efficient ligation of ss- to dsDNA molecules. This technique offers promise for a wide range of applications, in particular single-molecule experiments, where frequently multiple internal DNA modifications are required.
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Affiliation(s)
- Nicholas Luzzietti
- Biotechnology Center, Technische Universität Dresden, D-01062 Dresden, Germany
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24
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Zohar H, Hetherington CL, Bustamante C, Muller SJ. Peptide nucleic acids as tools for single-molecule sequence detection and manipulation. NANO LETTERS 2010; 10:4697-701. [PMID: 20923183 PMCID: PMC3322611 DOI: 10.1021/nl102986v] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The ability to strongly and sequence-specifically attach modifications such as fluorophores and haptens to individual double-stranded (ds) DNA molecules is critical to a variety of single-molecule experiments. We propose using modified peptide nucleic acids (PNAs) for this purpose and implement them in two model single-molecule experiments where individual DNA molecules are manipulated via microfluidic flow and optical tweezers, respectively. We demonstrate that PNAs are versatile and robust sequence-specific tethers.
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Affiliation(s)
- Hagar Zohar
- Department of Chemical Engineering, California Institute for Quantitative Biosciences, and Howard Hughes Medical InstituteUniversity of California, Berkeley, California 94720, United States
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Chan SH, Stoddard BL, Xu SY. Natural and engineered nicking endonucleases--from cleavage mechanism to engineering of strand-specificity. Nucleic Acids Res 2010; 39:1-18. [PMID: 20805246 PMCID: PMC3017599 DOI: 10.1093/nar/gkq742] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Restriction endonucleases (REases) are highly specific DNA scissors that have facilitated the development of modern molecular biology. Intensive studies of double strand (ds) cleavage activity of Type IIP REases, which recognize 4–8 bp palindromic sequences, have revealed a variety of mechanisms of molecular recognition and catalysis. Less well-studied are REases which cleave only one of the strands of dsDNA, creating a nick instead of a ds break. Naturally occurring nicking endonucleases (NEases) range from frequent cutters such as Nt.CviPII (^CCD; ^ denotes the cleavage site) to rare-cutting homing endonucleases (HEases) such as I-HmuI. In addition to these bona fida NEases, individual subunits of some heterodimeric Type IIS REases have recently been shown to be natural NEases. The discovery and characterization of more REases that recognize asymmetric sequences, particularly Types IIS and IIA REases, has revealed recognition and cleavage mechanisms drastically different from the canonical Type IIP mechanisms, and has allowed researchers to engineer highly strand-specific NEases. Monomeric LAGLIDADG HEases use two separate catalytic sites for cleavage. Exploitation of this characteristic has also resulted in useful nicking HEases. This review aims at providing an overview of the cleavage mechanisms of Types IIS and IIA REases and LAGLIDADG HEases, the engineering of their nicking variants, and the applications of NEases and nicking HEases.
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26
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Song Q, Wu H, Feng F, Zhou G, Kajiyama T, Kambara H. Pyrosequencing on nicked dsDNA generated by nicking endonucleases. Anal Chem 2010; 82:2074-81. [PMID: 20121068 DOI: 10.1021/ac902825r] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Although the pyrosequencing method is simple and fast, the step of ssDNA preparation increases the cost, labor, and cross-contamination risk. In this paper, we proposed a method enabling pyrosequencing directly on dsDNA digested by nicking endonucleases (NEases). Recognition sequence of NEases was introduced using artificially mismatched bases in a PCR primer (in the case of genotyping) or a reverse-transcription primer (in the case of gene expression analysis). PCR products were treated to remove excess amounts of primers, nucleotides, and pyrophosphate (PPi) prior to sequencing. After the nicking reaction, pyrosequencing starts at the nicked 3' end, and extension reaction occurs when the added dNTP is complementary to the non-nicked strand. Although the activity of strand displacement by Klenow is limited, approximately 10 bases are accurately sequenced; this length is long enough for genotyping and SRPP-based differential gene expression analysis. It was observed that the signals of two allele-specific bases in a pyrogram from nicked dsDNA are highly quantitative, enabling quantitative determination of allele-specific templates; thus, Down's Syndrome diagnosis as well as differential gene expression analysis was successfully executed. The results indicate that pyrosequencing using nicked dsDNA as templates is a simple, inexpensive, and reliable way in either quantitative genotyping or gene expression analysis.
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Affiliation(s)
- Qinxin Song
- China Pharmaceutical University, Nanjing 210009, China
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27
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Zheleznaya LA, Kachalova GS, Artyukh RI, Yunusova AK, Perevyazova TA, Matvienko NI. Nicking endonucleases. BIOCHEMISTRY (MOSCOW) 2010; 74:1457-66. [DOI: 10.1134/s0006297909130033] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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28
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Too PHM, Zhu Z, Chan SH, Xu SY. Engineering Nt.BtsCI and Nb.BtsCI nicking enzymes and applications in generating long overhangs. Nucleic Acids Res 2009; 38:1294-303. [PMID: 19955230 PMCID: PMC2831314 DOI: 10.1093/nar/gkp1092] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Type IIS restriction endonuclease BtsCI (GGATG 2/0) is a neoschizomer of FokI (GGATG 9/13) and cleaves closer to the recognition sequence. Although M.BtsCI shows 62% amino acid sequence identity to M.FokI, BtsCI and FokI restriction endonucleases do not share significant amino acid sequence similarity. BtsCI belongs to a group of Type IIS restriction endonucleases, BsmI, Mva1269I and BsrI, that carry two different catalytic sites in a single polypeptide. By inactivating one of the catalytic sites through mutagenesis, we have generated nicking variants of BtsCI that specifically nick the bottom-strand or the top-strand of the target site. By treating target DNA sequentially with the appropriate combinations of FokI and BtsCI nicking variants, we are able to generate long overhangs suitable for fluorescent labeling through end-filling or other techniques based on annealing of complementary DNA sequences.
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29
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Prathipati P, Ma NL, Manjunatha UH, Bender A. Fishing the Target of Antitubercular Compounds: In Silico Target Deconvolution Model Development and Validation. J Proteome Res 2009; 8:2788-98. [DOI: 10.1021/pr8010843] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Philip Prathipati
- Novartis Institute for Tropical Diseases, 10 Biopolis Road, #05-01 Chromos, 138670, Singapore, and Lead Discovery Informatics, Center for Proteomic Chemistry, Novartis Institutes for BioMedical Research, Inc., 250 Massachusetts Avenue, Cambridge, Massachusetts 02139
| | - Ngai Ling Ma
- Novartis Institute for Tropical Diseases, 10 Biopolis Road, #05-01 Chromos, 138670, Singapore, and Lead Discovery Informatics, Center for Proteomic Chemistry, Novartis Institutes for BioMedical Research, Inc., 250 Massachusetts Avenue, Cambridge, Massachusetts 02139
| | - Ujjini H. Manjunatha
- Novartis Institute for Tropical Diseases, 10 Biopolis Road, #05-01 Chromos, 138670, Singapore, and Lead Discovery Informatics, Center for Proteomic Chemistry, Novartis Institutes for BioMedical Research, Inc., 250 Massachusetts Avenue, Cambridge, Massachusetts 02139
| | - Andreas Bender
- Novartis Institute for Tropical Diseases, 10 Biopolis Road, #05-01 Chromos, 138670, Singapore, and Lead Discovery Informatics, Center for Proteomic Chemistry, Novartis Institutes for BioMedical Research, Inc., 250 Massachusetts Avenue, Cambridge, Massachusetts 02139
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30
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Sanders KL, Catto LE, Bellamy SRW, Halford SE. Targeting individual subunits of the FokI restriction endonuclease to specific DNA strands. Nucleic Acids Res 2009; 37:2105-15. [PMID: 19223323 PMCID: PMC2673415 DOI: 10.1093/nar/gkp046] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Many restriction endonucleases are dimers that act symmetrically at palindromic DNA sequences, with each active site cutting one strand. In contrast, FokI acts asymmetrically at a non-palindromic sequence, cutting ‘top’ and ‘bottom’ strands 9 and 13 nucleotides downstream of the site. FokI is a monomeric protein with one active site and a single monomer covers the entire recognition sequence. To cut both strands, the monomer at the site recruits a second monomer from solution, but it is not yet known which DNA strand is cut by the monomer bound to the site and which by the recruited monomer. In this work, mutants of FokI were used to show that the monomer bound to the site made the distal cut in the bottom strand, whilst the recruited monomer made in parallel the proximal cut in the top strand. Procedures were also established to direct FokI activity, either preferentially to the bottom strand or exclusively to the top strand. The latter extends the range of enzymes for nicking specified strands at specific sequences, and may facilitate further applications of FokI in gene targeting.
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Affiliation(s)
- Kelly L Sanders
- Department of Biochemistry, School of Medical Sciences, University of Bristol, Bristol, UK
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31
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Structural analysis of the heterodimeric type IIS restriction endonuclease R.BspD6I acting as a complex between a monomeric site-specific nickase and a catalytic subunit. J Mol Biol 2008; 384:489-502. [PMID: 18835275 DOI: 10.1016/j.jmb.2008.09.033] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2008] [Revised: 09/10/2008] [Accepted: 09/16/2008] [Indexed: 11/20/2022]
Abstract
The heterodimeric restriction endonuclease R.BspD6I from Bacillus species D6 recognizes a pseudosymmetric sequence and cuts both DNA strands outside the recognition sequence. The large subunit, Nt.BspD6I, acts as a type IIS site-specific monomeric nicking endonuclease. The isolated small subunit, ss.BspD6I, does not bind DNA and is not catalytically active. We solved the crystal structures of Nt.BspD6I and ss.BspD6I at high resolution. Nt.BspD6I consists of three domains, two of which exhibit structural similarity to the recognition and cleavage domains of FokI. ss.BspD6I has a fold similar to that of the cleavage domain of Nt.BspD6I, each containing a PD-(D/E)XK motif and a histidine as an additional putative catalytic residue. In contrast to the DNA-bound FokI structure, in which the cleavage domain is rotated away from the DNA, the crystal structure of Nt.BspD6I shows the recognition and cleavage domains in favorable orientations for interactions with DNA. Docking models of complexes of Nt.BspD6I and R.BspD6I with cognate DNA were constructed on the basis of structural similarity to individual domains of FokI, R.BpuJI and HindIII. A three-helix bundle forming an interdomain linker in Nt.BspD6I acts as a rigid spacer adjusting the orientations of the spatially separated domains to match the distance between the recognition and cleavage sites accurately.
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