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Yang H, Zhu L, Wang X, Song Y, Dong Y, Xu W. Extension characteristics of TdT and its application in biosensors. Crit Rev Biotechnol 2024; 44:981-995. [PMID: 37880088 DOI: 10.1080/07388551.2023.2270772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 08/18/2023] [Accepted: 09/14/2023] [Indexed: 10/27/2023]
Abstract
The advantages of rapid amplification of nucleic acid without a template based on terminal deoxyribonucleotidyl transferase (TdT) have been widely used in the field of biosensors. However, the catalytic efficiency of TdT is affected by extension conditions. The sensitivity of TdT- mediated biosensors can be improved only under appropriate conditions. Therefore, in this review, we provide a comprehensive overview of TdT extension characteristics and its applications in biosensors. We focus on the relationship between TdT extension conditions and extension efficiency. Furthermore, the construction strategy of TdT-mediated biosensors according to five different recognition types and their applications in targets are discussed and, finally, several current challenges and prospects in the field are taken into consideration.
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Affiliation(s)
- He Yang
- Department of Nutrition and Health, Ministry of Education, Key Laboratory of Precision Nutrition and Food Quality, Food Laboratory of Zhongyuan, China Agricultural University, Beijing, China
| | - Longjiao Zhu
- Department of Nutrition and Health, Ministry of Education, Key Laboratory of Precision Nutrition and Food Quality, Food Laboratory of Zhongyuan, China Agricultural University, Beijing, China
| | - Xinxin Wang
- Department of Nutrition and Health, Ministry of Education, Key Laboratory of Precision Nutrition and Food Quality, Food Laboratory of Zhongyuan, China Agricultural University, Beijing, China
| | - Yuhan Song
- Department of Nutrition and Health, Ministry of Education, Key Laboratory of Precision Nutrition and Food Quality, Food Laboratory of Zhongyuan, China Agricultural University, Beijing, China
- College of Food Science and Nutritional Engineering, Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), China Agricultural University, Beijing, China
| | - Yulan Dong
- Department of Nutrition and Health, Ministry of Education, Key Laboratory of Precision Nutrition and Food Quality, Food Laboratory of Zhongyuan, China Agricultural University, Beijing, China
- College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Wentao Xu
- Department of Nutrition and Health, Ministry of Education, Key Laboratory of Precision Nutrition and Food Quality, Food Laboratory of Zhongyuan, China Agricultural University, Beijing, China
- College of Food Science and Nutritional Engineering, Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), China Agricultural University, Beijing, China
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2
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Itsko M, Abu YB. Novel type of coagulation equation and its application to DNA repeat expansion process. J Theor Biol 2020; 511:110555. [PMID: 33346021 DOI: 10.1016/j.jtbi.2020.110555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 11/04/2020] [Accepted: 12/02/2020] [Indexed: 11/18/2022]
Abstract
DNA molecules containing repetitive motifs are prone to expand in their lengths. Once there appear a head to tail tandem of two identical DNA sequences in the system, they can propagate indefinitely by the mechanism involving cycles of staggered annealing of complementary DNA strands of variable lengths and polymerase mediated filling-in of the generated overhangs. Microgene Polymerization Reaction (MPR) is an experimental model for expansion of short repetitive DNA to longer lengths. The testable kinetic model of (MPR) was formulated and solved numerically by Itsko et al. in Kinetics of Repeat Propagation in the Microgene Polymerization Reaction (2009). Here, the simple cases of MPR were solved analytically using modified Smoluchowski coagulation equation. It was found that the repeats propagate according to Gumbel probability density function when the distribution of lengths of obtained polymers follows inverted Gumbel probability density function.
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Affiliation(s)
- Mark Itsko
- WDS Inc., Contractor to Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA 30033, USA.
| | - Yuval Ben Abu
- Department of Physics and Project Unit, Sapir Academic College, Sderot, Hof Ashkelon 79165, Israel; Clarendon Laboratory, Department of Physics, University of Oxford, UK.
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3
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Giebel K, Green LE, Purdy KJ. A Pilot Study to Investigate the Feasibility of a Multiple Locus Variable Number Tandem Repeat Analysis to Understand the Epidemiology of Dichelobacter nodosus in Ovine Footrot. Front Vet Sci 2020; 7:581342. [PMID: 33344526 PMCID: PMC7738329 DOI: 10.3389/fvets.2020.581342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 11/09/2020] [Indexed: 11/13/2022] Open
Abstract
Dichelobacter nodosus is the essential pathogen in ovine footrot, an important cause of lameness in sheep that reduces productivity and welfare. The aim of this study was to investigate the feasibility of using multiple locus variable number tandem repeat analysis (MLVA) developed to investigate isolates to understand the molecular epidemiology of Dichelobacter nodosus in ovine footrot by investigation of communities of strains. MLVA sensitivity was improved by optimizing PCR conditions to 100% specificity for D. nodosus. The improved MLVA scheme was used to investigate non-cultured DNA purified from swabs (swab DNA) and cultured DNA from isolates (isolate DNA) from 152 foot and 38 gingival swab samples from 10 sheep sampled on four occasions in a longitudinal study. Isolate DNA was obtained from 6/152 (3.9%) feet and 5/6 yielded complete MLVA profiles, three strains were detected. Two of the three isolate strains were also detected in isolate DNA from 2 gingival crevice cultures. Complete MLVA profiles were obtained from swab DNA from 39 (25.7%) feet. There were 22 D. nodosus community types that were comprised of 7 single strain and 15 multi-strain communities. Six community types were detected more than once and three of these were detected on the same four sheep and the same two feet over time. There were a minimum of 17 and a maximum of 25 strain types of D. nodosus in the study. The three isolate strain types were also the most frequently detected strain types in swab DNA. We conclude that the MLVA from swab DNA detects the same strains as culture, is much more sensitive and can be used to describe and differentiate communities and strains on sheep, feet and over time. It is therefore a sensitive molecular tool to study D. nodosus strains directly from DNA without culture.
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Affiliation(s)
- Katharina Giebel
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
- School of Agriculture, Food and the Environment, Royal Agricultural University, Gloucestershire, United Kingdom
| | - Laura E. Green
- College of Life and Environmental Sciences, Institute for Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Kevin J. Purdy
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
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4
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Amos W, Filipe LN. Microsatellite frequencies vary with body mass and body temperature in mammals, suggesting correlated variation in mutation rate. PeerJ 2014; 2:e663. [PMID: 25392761 PMCID: PMC4226647 DOI: 10.7717/peerj.663] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2014] [Accepted: 10/21/2014] [Indexed: 11/20/2022] Open
Abstract
Substitution rate is often found to correlate with life history traits such as body mass, a predictor of population size and longevity, and body temperature. The underlying mechanism is unclear but most models invoke either natural selection or factors such as generation length that change the number of mutation opportunities per unit time. Here we use published genome sequences from 69 mammals to ask whether life history traits impact another form of genetic mutation, the high rates of predominantly neutral slippage in microsatellites. We find that the length-frequency distributions of three common dinucleotide motifs differ greatly between even closely related species. These frequency differences correlate with body mass and body temperature and can be used to predict the phenotype of an unknown species. Importantly, different length microsatellites show complicated patterns of excess and deficit that cannot be explained by a simple model where species with short generation lengths have experienced more mutations. Instead, the patterns probably require changes in mutation rate that impact alleles of different length to different extents. Body temperature plausibly influences mutation rate by modulating the propensity for slippage. Existing hypotheses struggle to account for a link between body mass and mutation rate. However, body mass correlates inversely with population size, which in turn predicts heterozygosity. We suggest that heterozygote instability, HI, the idea that heterozygous sites show increased mutability, could provide a plausible link between body mass and mutation rate.
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Kato T, Liang X, Asanuma H. Model of elongation of short DNA sequence by thermophilic DNA polymerase under isothermal conditions. Biochemistry 2012; 51:7846-53. [PMID: 22992125 DOI: 10.1021/bi3010413] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Short DNA sequences, especially those that are repetitive or palindromic, can be used as the seeds for synthesis of long DNA by some DNA polymerases in an unusual manner. Although several elongation mechanisms have been proposed, there is no well-established model that explains highly efficient elongation under isothermal conditions. In the present study, we analyzed the elongation of nonrepetitive sequences with distinct hairpins at each end. These DNAs were elongated efficiently under isothermal conditions by thermophilic Vent (exo(-)) DNA polymerase, and the products were longer than 10 kb within 10 min of the reaction. A 20-nucleotide DNA with only one hairpin was also elongated. Sequence analysis revealed that the long products are mainly tandem repeats of the short seed sequences. The thermal melting temperatures of the products were much higher than the reaction temperature, indicating that most DNAs form duplexes during the reaction. Accordingly, a terminal hairpin formation and self-priming extension model was proposed in detail, and the efficient elongation was explained. Formation of the hairpin at the 5' end plays an important role during the elongation.
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Affiliation(s)
- Tomohiro Kato
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa, Nagoya 464-8603, Japan
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6
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Yang S, Herdewijn P. Polymerase-dependent DNA synthesis from phosphoramidate-activated nucleotides. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2011; 30:597-608. [PMID: 21888550 DOI: 10.1080/15257770.2011.598491] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Nucleoside triphosphate mimetics, which are substrates for polymerases, can be used in the enzymatic synthesis of nucleic acids. Alternatively, they might also become reversible or irreversible enzyme inhibitors. In order to analyze the effects of 5'-phosphoramidate modification of deoxynucleotide in DNA synthesis, 3-phosphono-L-Ala-dNMP (N = A, T, or G) were evaluated as substrates of HIV-1 RT, Vent (exo(-)), and Therminator polymerase, respectively. The DNA-dependent DNA polymerase activity is significantly higher for Vent exo(-) polymerase than for HIV-1 RT, which is reflected by the capacity of Vent exo(-) polymerase to efficiently synthesize DNA without stalling effects. In addition, Vent (exo(-)) polymerase proved to be more accurate than Therminator polymerase, based on Watson-Crick base-pairing. The optimal yield (88%-97%) of full-length elongation can be obtained in 60 minutes by Vent (exo(-)) polymerase at 0.025 U/μL, with the phosphoramidate analogues as substrates. These data led us to conclude that the optimal pyrophosphate mimetic for the enzyme-catalyzed synthesis of DNA is polymerase dependent.
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Affiliation(s)
- Shiqiong Yang
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
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7
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Kahlisch L, Henne K, Draheim J, Brettar I, Höfle MG. High-resolution in situ genotyping of Legionella pneumophila populations in drinking water by multiple-locus variable-number tandem-repeat analysis using environmental DNA. Appl Environ Microbiol 2010; 76:6186-95. [PMID: 20656879 PMCID: PMC2937494 DOI: 10.1128/aem.00416-10] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2010] [Accepted: 07/02/2010] [Indexed: 11/20/2022] Open
Abstract
Central to the understanding of infections by the waterborne pathogen Legionella pneumophila is its detection at the clonal level. Currently, multiple-locus variable-number tandem-repeat (VNTR) analysis (MLVA) of L. pneumophila isolates can be used as a tool for high-resolution genotyping. Since L. pneumophila is difficult to isolate, the isolation of outbreak strains often fails due to a viable but nonculturable (VBNC) state of the respective environmental population. Therefore, we developed a cultivation-independent approach to detect single clones in drinking water. This approach is based on the extraction of DNA from drinking water followed by PCR using a set of eight VNTR primer pairs necessary for MLVA genotyping of L. pneumophila. The PCR amplicons were analyzed by single-strand conformation polymorphism (SSCP) and capillary electrophoresis to obtain the respective MLVA profiles. Parallel to the high-resolution analysis, we used the same environmental DNA to quantify the number of L. pneumophila cells in drinking water using real-time PCR with 16S rRNA gene-targeted primers. We used a set of drinking water samples from a small-scale drinking water network to test our approach. With these samples we demonstrated that the developed approach was directly applicable to DNA obtained from drinking water. We were able to detect more L. pneumophila MLVA genotypes in drinking water than we could detect by isolation. Our approach could be a valuable tool to identify outbreak strains even after the outbreak has occurred and has the potential to be applied directly to clinical material.
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Affiliation(s)
- Leila Kahlisch
- Department of Vaccinology and Applied Microbiology, Helmholtz Centre for Infection Research (HZI), Inhoffenstrasse 7, D-38124 Braunschweig, Germany
| | - Karsten Henne
- Department of Vaccinology and Applied Microbiology, Helmholtz Centre for Infection Research (HZI), Inhoffenstrasse 7, D-38124 Braunschweig, Germany
| | - Josefin Draheim
- Department of Vaccinology and Applied Microbiology, Helmholtz Centre for Infection Research (HZI), Inhoffenstrasse 7, D-38124 Braunschweig, Germany
| | - Ingrid Brettar
- Department of Vaccinology and Applied Microbiology, Helmholtz Centre for Infection Research (HZI), Inhoffenstrasse 7, D-38124 Braunschweig, Germany
| | - Manfred G. Höfle
- Department of Vaccinology and Applied Microbiology, Helmholtz Centre for Infection Research (HZI), Inhoffenstrasse 7, D-38124 Braunschweig, Germany
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8
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Itsko M, Rabinovitch A, Zaritsky A. Kinetics of repeat propagation in the microgene polymerization reaction. Biophys J 2009; 96:1866-74. [PMID: 19254545 DOI: 10.1016/j.bpj.2008.10.061] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2008] [Accepted: 10/29/2008] [Indexed: 11/25/2022] Open
Abstract
Repetitive DNA is a periodic copolymer with the intrinsic property of exponential propagation to longer repeats. Microgene polymerization reaction (MPR) is a model system in which a short nonrepetitive homo-duplex DNA evolves to multiple repetitive products during heat-cool cycles. The mechanism underlying this process involves staggered annealing of complementary DNA strands of variable lengths and polymerase-mediated filling-in of the generated overhangs. MPR is considered here as a process sharing common features with two polymerization types, chain-growth and step-growth, and significant distinctions from both types were highlighted. The involved reaction stages were formulated and a kinetic model was derived and tested experimentally. The model can quantitatively explain MPR propagation and be used as a good approximation for this phenomenon.
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Affiliation(s)
- Mark Itsko
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er-Sheva 84105, Israel.
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9
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Multiple-locus variable-number tandem-repeat analysis for clonal identification of Vibrio parahaemolyticus isolates by using capillary electrophoresis. Appl Environ Microbiol 2009; 75:4079-88. [PMID: 19376898 DOI: 10.1128/aem.02729-08] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Epidemics of Vibrio parahaemolyticus in Chile have occurred since 1998. Direct genome restriction enzyme analysis (DGREA) using conventional gel electrophoresis permitted discrimination of different V. parahaemolyticus isolates obtained from these outbreaks and showed that this species consists of a highly diverse population. A multiple-locus variable-number tandem-repeat (VNTR) analysis (MLVA) approach was developed and applied to 22 clinical and 91 environmental V. parahaemolyticus isolates from Chile to understand their clonal structures. To this end, an advanced molecular technique was developed by applying multiplex PCR, fluorescent primers, and capillary electrophoresis, resulting in a high-resolution and high-throughput (HRHT) genotyping method. The genomic basis of this HRHT method was eight VNTR loci described previously by Kimura et al. (J. Microbiol. Methods 72:313-320, 2008) and two new loci which were identified by a detailed molecular study of 24 potential VNTR loci on both chromosomes. The isolates of V. parahaemolyticus belonging to the same DGREA pattern were distinguishable by the size variations in the indicative 10 VNTRs. This assay showed that these 10 VNTR loci were useful for distinguishing isolates of V. parahaemolyticus that had different DGREA patterns and also isolates that belong to the same group. Isolates that differed in their DGREA patterns showed polymorphism in their VNTR profiles. A total of 81 isolates was associated with 59 MLVA groups, providing fine-scale differentiation, even among very closely related isolates. The developed approach enables rapid and high-resolution analysis of V. parahaemolyticus with pandemic potential and provides a new surveillance tool for food-borne pathogens.
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10
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Evidence for Nonindependent Evolution of Adjacent Microsatellites in the Human Genome. J Mol Evol 2009; 68:160-70. [DOI: 10.1007/s00239-008-9192-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2008] [Revised: 12/02/2008] [Accepted: 12/02/2008] [Indexed: 10/21/2022]
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11
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Amos W, Clarke A. Body temperature predicts maximum microsatellite length in mammals. Biol Lett 2008; 4:399-401. [PMID: 18522923 DOI: 10.1098/rsbl.2008.0209] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A long-standing mystery in genome evolution is why short tandem repeats vary so much in length and frequency. Here, we test the hypothesis that body temperature acts to influence the rate and nature of slippage-based mutations. Using the data from both 28 species where genome sequencing is advanced and 76 species from which marker loci have been published, we show that in mammals, maximum repeat number is inversely correlated with body temperature, with warmer-blooded species having shorter 'long' microsatellites. Our results support a model of microsatellite evolution in which maximum length is limited by a temperature-dependent stability threshold.
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Affiliation(s)
- William Amos
- Department of Zoology, University of Cambridge, Cambridge, UK.
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12
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Itsko M, Zaritsky A, Rabinovitch A. Thermodynamics of unstable DNA structures from the kinetics of the microgene PCR. J Phys Chem B 2008; 112:13149-56. [PMID: 18795769 DOI: 10.1021/jp8045142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The microgene polymerization reaction (MPR) generates head-to-tail tandem repeats from homoduplexes (HDs). In MPR initiation, one HD putatively aligns two others in the proximity required to form a nucleation complex, thus allowing the DNA polymerase to skip the intertemplate gap and generate an initial doublet (ID) prone to repeat propagation. The current investigation refines this stage by additional thermodynamic considerations and elucidates the fundamental mechanism underlying propagation. Four different HD types were designed to extend the range of melting temperatures and to simultaneously modify the stabilities of their secondary structures. Following the propagation kinetics with these, using real-time PCR at different temperatures revealed a new stage in the MPR, amplification of an ID by an original HD, and enabled us to decipher the biphasic kinetics of the process. This amplification merges with the propagation stage if the lifetime of the staggered conformation of the ID is sufficiently long for DNA polymerase to fill in the overhangs. The observed increase with temperature of thermodynamically unfavorable conformations of singlet and doublet HDs that underlies, respectively, MPR initiation and propagation is well correlated with simulations by UNAFold.
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Affiliation(s)
- Mark Itsko
- Departments of Life Sciences and Physics, Ben-Gurion University of the Negev, Be'er-Sheva, Israel
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13
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Tan E, Erwin B, Dames S, Ferguson T, Buechel M, Irvine B, Voelkerding K, Niemz A. Specific versus nonspecific isothermal DNA amplification through thermophilic polymerase and nicking enzyme activities. Biochemistry 2008; 47:9987-99. [PMID: 18729381 DOI: 10.1021/bi800746p] [Citation(s) in RCA: 132] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Rapid isothermal nucleic acid amplification technologies can enable diagnosis of human pathogens and genetic variations in a simple, inexpensive, user-friendly format. The isothermal exponential amplification reaction (EXPAR) efficiently amplifies short oligonucleotides called triggers in less than 10 min by means of thermostable polymerase and nicking endonuclease activities. We recently demonstrated that this reaction can be coupled with upstream generation of trigger oligonucleotides from a genomic target sequence, and with downstream visual detection using DNA-functionalized gold nanospheres. The utility of EXPAR in clinical diagnostics is, however, limited by a nonspecific background amplification phenomenon, which is further investigated in this report. We found that nonspecific background amplification includes an early phase and a late phase. Observations related to late phase background amplification are in general agreement with literature reports of ab initio DNA synthesis. Early phase background amplification, which limits the sensitivity of EXPAR, differs however from previous reports of nonspecific DNA synthesis. It is observable in the presence of single-stranded oligonucleotides following the EXPAR template design rules and generates the trigger sequence expected for the EXPAR template present in the reaction. It appears to require interaction between the DNA polymerase and the single-stranded EXPAR template. Early phase background amplification can be suppressed or eliminated by physically separating the template and polymerase until the final reaction temperature has been reached, thereby enabling detection of attomolar starting trigger concentrations.
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Affiliation(s)
- Eric Tan
- Keck Graduate Institute of Applied Life Sciences, Claremont, California 91711, USA
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14
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Ouyang D, Yi L, Liu L, Mu HT, Xi Z. In vitro expansion of DNA triplet repeats with bulge binders and different DNA polymerases. FEBS J 2008; 275:4510-21. [DOI: 10.1111/j.1742-4658.2008.06593.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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15
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Initiation of the microgene polymerization reaction with non-repetitive homo-duplexes. Biochem Biophys Res Commun 2008; 368:606-13. [PMID: 18243133 DOI: 10.1016/j.bbrc.2008.01.108] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2008] [Accepted: 01/24/2008] [Indexed: 10/22/2022]
Abstract
Microgene Polymerization Reaction (MPR) is used as an experimental system to artificially simulate evolution of short, non-repetitive homo-duplex DNA into multiply-repetitive products that can code for functional proteins. Blunt-end ligation by DNA polymerase is crucial in expansion of homo-duplexes (HDs) into head-to-tail multiple repeats in MPR. The propagation mechanism is known, but formation of the initial doublet (ID) by juxtaposing two HDs and polymerization through the gap has been ambiguous. Initiation events with pairs of HDs using Real-Time PCR were more frequent at higher HD concentrations and slightly below the melting temperature. A process molecularity of about 3.1, calculated from the amplification efficiency and the difference in PCR cycles at which propagation was detected at varying HD concentrations, led to a simple mechanism for ID formation: the gap between two HDs is bridged by a third. Considering thermodynamic aspects of the presumed intermediate "nucleation complex" can predict relative propensity for the process with other HDs.
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16
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Vondrusková J, Parízková N, Kypr J. Factors influencing DNA expansion in the course of polymerase chain reaction. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2007; 26:65-82. [PMID: 17162588 DOI: 10.1080/15257770601052299] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
We performed more than 3,500 polymerase chain reactions (PCRs) under various conditions with more than 400 DNA fragments of 4-150 nucleotides in length. Some of the PCRs provided expanded DNA molecules of kilobase lengths whereas others led to no expansion. Repetitiveness of the primary structure was mostly found to be necessary but not sufficient for the expansion. (A+T)-rich fragments expand better than (G+C)-rich ones and pyrimidine-rich fragments expand better than purine-rich fragments. Terminal nucleotides and the fragment length also are important for the expansion. Examples are presented when relatively small alterations of the DNA primary structure caused a dramatic change in the expansion. For example, A8T8 expanded a lot whereas T8A8 did not expand at all. The present work has implications for pathological expansions of microsatellites in the human genome as well as regarding the genome evolution in general.
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Affiliation(s)
- Jitka Vondrusková
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
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17
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Itsko M, Zaritsky A. Exposing cryptic antibacterial activity in Cyt1Ca fromBacillus thuringiensis israelensisby genetic manipulations. FEBS Lett 2007; 581:1775-82. [DOI: 10.1016/j.febslet.2007.03.064] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2007] [Revised: 03/22/2007] [Accepted: 03/22/2007] [Indexed: 10/23/2022]
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18
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Lindstedt BA. Multiple-locus variable number tandem repeats analysis for genetic fingerprinting of pathogenic bacteria. Electrophoresis 2005; 26:2567-82. [PMID: 15937984 DOI: 10.1002/elps.200500096] [Citation(s) in RCA: 244] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
DNA fingerprinting has attracted considerable interest as means for identifying, tracing and preventing the dissemination of infectious agents. Various methods have been developed for typing of pathogenic bacteria, which differ in discriminative power, reproducibility and ease of interpretation. During recent years a typing method, which uses the information provided by whole genome sequencing of bacterial species, has gained increased attention. Short sequence repeat (SSR) motifs are known to undergo frequent variation in the number of repeated units through cellular mechanisms most commonly active during chromosome replication. A class of SSRs, named variable number of tandem repeats (VNTRs), has proven to be a suitable target for assessing genetic polymorphisms within bacterial species. This review attempts to give an overview of bacterial agents where VNTR-based typing, or multiple-locus variant-repeat analysis (MLVA) has been developed for typing purposes, together with addressing advantages and drawbacks associated with the use of tandem repeated DNA motifs as targets for bacterial typing and identification.
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Affiliation(s)
- Bjørn-Arne Lindstedt
- Norwegian Institute of Public Health, Division for Infectious Diseases Control, Oslo, Norway.
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19
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Zhelev Z, Bakalova R, Ewis A, Ohba H, Ishikawa M, Baba Y. Nonradioactive telomerase activity assay by microchip electrophoresis: Privileges to the classical gel electrophoresis assay. Electrophoresis 2005; 26:3021-4. [PMID: 16078194 DOI: 10.1002/elps.200410435] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The present study accents on the privileges of microchip-based electrophoresis to the conventional gel electrophoresis in separation of telomerase repeat amplification protocol/polymerase chain reaction (PCR) ladder products obtained in telomerase-catalyzed reaction in cancer cells. We try to clarify the interpretation of the results obtained by both electrophoretic procedures and to avoid misinterpretation as a result of PCR-dependent artefacts.
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Affiliation(s)
- Zhivko Zhelev
- Single-Molecule Bioanalysis Laboratory (SMBL), National Institute for Advanced Industrial Science and Technology, AIST-Shikoku, Takamatsu, Japan
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20
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Kikuchi-Maki A, Yusa SI, Catina TL, Campbell KS. KIR2DL4 is an IL-2-regulated NK cell receptor that exhibits limited expression in humans but triggers strong IFN-gamma production. THE JOURNAL OF IMMUNOLOGY 2004; 171:3415-25. [PMID: 14500636 DOI: 10.4049/jimmunol.171.7.3415] [Citation(s) in RCA: 146] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Killer cell Ig-like receptor (KIR)2DL4 (2DL4, CD158d) was previously described as the only KIR expressed by every human NK cell. It is also structurally atypical among KIRs because it possesses a basic transmembrane residue, which is characteristic of many activating receptors, but also contains a cytoplasmic immunoreceptor tyrosine-based inhibitory motif (ITIM). We expressed epitope-tagged 2DL4 in an NK-like cell line to study receptor function. Three distinct 2DL4 cDNA clones were analyzed: one encoding the "conventional" 2DL4 with the cytoplasmic ITIM (2DL4.1) and two encoding different cytoplasmic truncated forms lacking the ITIM (2DL4.2 and 2DL4(*)). Surprisingly, one truncated receptor (2DL4.2), which is the product of a prevalent human 2DL4 allele, was not expressed on the cell surface, indicating that some individuals may lack functional 2DL4 protein expression. Conversely, both 2DL4.1 and 2DL4(*) were expressed on the cell surface and up-regulated by IL-2. Analysis of primary NK cells with anti-2DL4 mAb confirmed the lack of surface expression in a donor with the 2DL4.2 genotype. Donors with the 2DL4.1 genotype occasionally expressed receptor only on CD56(high) NK cells, although their expression was up-regulated by IL-2. Interestingly, Ab engagement of epitope-tagged 2DL4 triggered rapid and robust IFN-gamma production, but weak redirected cytotoxicity in an NK-like cell line, which was the opposite pattern to that observed upon engagement of another NK cell activating receptor, NKp44. Importantly, both 2DL4.1 and 2DL4(*) exhibited similar activation potential, indicating that the ITIM does not influence 2DL4.1 activating function. The unique activation properties of 2DL4 suggest linkage to a distinct signaling pathway.
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MESH Headings
- Adjuvants, Immunologic/biosynthesis
- Adjuvants, Immunologic/genetics
- Adjuvants, Immunologic/physiology
- Amino Acid Motifs/physiology
- Amino Acid Sequence
- Cell Line
- Cell Membrane/genetics
- Cell Membrane/immunology
- Cell Membrane/metabolism
- Cytoplasm/immunology
- Cytoplasm/metabolism
- DNA Fragmentation/immunology
- Down-Regulation/immunology
- Genotype
- Humans
- Interferon-gamma/biosynthesis
- Interleukin-2/pharmacology
- Interleukin-2/physiology
- Jurkat Cells
- Killer Cells, Natural/immunology
- Killer Cells, Natural/metabolism
- Lymphocyte Activation/immunology
- Molecular Sequence Data
- Natural Cytotoxicity Triggering Receptor 2
- Receptors, Immunologic/biosynthesis
- Receptors, Immunologic/genetics
- Receptors, Immunologic/physiology
- Receptors, KIR
- Receptors, KIR2DL4
- Retroviridae/genetics
- Retroviridae/immunology
- Transduction, Genetic
- Tyrosine/metabolism
- Up-Regulation/immunology
- fas Receptor/physiology
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Affiliation(s)
- Akiko Kikuchi-Maki
- Fox Chase Cancer Center, Division of Basic Science, Institute for Cancer Research, Philadelphia, PA 19111, USA
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Heidenfelder BL, Makhov AM, Topal MD. Hairpin formation in Friedreich's ataxia triplet repeat expansion. J Biol Chem 2003; 278:2425-31. [PMID: 12441336 DOI: 10.1074/jbc.m210643200] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Triplet repeat tracts occur throughout the human genome. Expansions of a (GAA)(n)/(TTC)(n) repeat tract during its transmission from parent to child are tightly associated with the occurrence of Friedreich's ataxia. Evidence supports DNA slippage during DNA replication as the cause of the expansions. DNA slippage results in single-stranded expansion intermediates. Evidence has accumulated that predicts that hairpin structures protect from DNA repair the expansion intermediates of all of the disease-associated repeats except for those of Friedreich's ataxia. How the latter repeat expansions avoid repair remains a mystery because (GAA)(n) and (TTC)(n) repeats are reported not to self-anneal. To characterize the Friedreich's ataxia intermediates, we generated massive expansions of (GAA)(n) and (TTC)(n) during DNA replication in vitro using human polymerase beta and the Klenow fragment of Escherichia coli polymerase I. Electron microscopy, endonuclease cleavage, and DNA sequencing of the expansion products demonstrate, for the first time, the occurrence of large and growing (GAA)(n) and (TTC)(n) hairpins during DNA synthesis. The results provide unifying evidence that predicts that hairpin formation during DNA synthesis mediates all of the disease-associated, triplet repeat expansions.
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Affiliation(s)
- Brooke L Heidenfelder
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, 27599-7295, USA
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