1
|
Park H, Gibbs JM. Selectivity and efficiency in the ligation of the pyrene:abasic base pair by T4 and PBCV-1 DNA ligases. Chem Commun (Camb) 2022; 58:9072-9075. [PMID: 35876431 DOI: 10.1039/d2cc03079a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Remarkable selectivity was observed in the ligation of 5'-phosphate 1-pyrene nucleotide terminated strands across from an abasic lesion in a DNA-templated ligation reaction by two different ligases suggesting that pyrene-terminated strands could be used in abasic site detection. Increasing ATP concentration was critical to enhancing the selectivity for this base pair with T4 DNA ligase.
Collapse
Affiliation(s)
- Hansol Park
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada.
| | - Julianne M Gibbs
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada.
| |
Collapse
|
2
|
Ren L, Ming Z, Zhang W, Liao Y, Tang X, Yan B, Lv H, Xiao X. Shared-probe system: An accurate, low-cost and general enzyme-assisted DNA probe system for detection of genetic mutation. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2021.09.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
3
|
Osman EA, Alladin-Mustan BS, Hales SC, Matharu GK, Gibbs JM. Enhanced mismatch selectivity of T4 DNA ligase far above the probe: Target duplex dissociation temperature. Biopolymers 2020; 112:e23393. [PMID: 32896905 DOI: 10.1002/bip.23393] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 07/11/2020] [Accepted: 07/13/2020] [Indexed: 11/06/2022]
Abstract
T4 DNA ligase is a widely used ligase in many applications; yet in single nucleotide polymorphism analysis, it has been found generally lacking owing to its tendency to ligate mismatches quite efficiently. To address this lack of selectivity, we explored the effect of temperature on the selectivity of the ligase in discriminating single base pair mismatches at the 3'-terminus of the ligating strand using short ligation probes (9-mers). Remarkably, we observe outstanding selectivities when the assay temperature is increased to 7 °C to 13 °C above the dissociation temperature of the matched probe:target duplexes using commercially available enzyme at low concentration. Higher enzyme concentration shifts the temperature range to 13 °C to 19 °C above the probe:target dissociation temperatures. Finally, substituting the 5'-phosphate terminus with an abasic nucleotide decreases the optimal temperature range to 7 °C to 10 °C above the matched probe:target duplex. We compare the temperature dependence of the T4 DNA ligase catalyzed ligation and a nonenzymatic ligation system to contrast the origin of their modes of selectivity. For the latter, temperatures above the probe:target duplex dissociation lead to lower ligation conversions even for the perfect matched system. This difference between the two ligation systems reveals the uniqueness of the T4 DNA ligase's ability to maintain excellent ligation yields for the matched system at elevated temperatures. Although our observations are consistent with previous mechanistic work on T4 DNA ligase, by mapping out the temperature dependence for different ligase concentrations and probe modifications, we identify simple strategies for introducing greater selectivity into SNP discrimination based on ligation yields.
Collapse
Affiliation(s)
- Eiman A Osman
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | | | - Sarah C Hales
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Gunwant K Matharu
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Julianne M Gibbs
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| |
Collapse
|
4
|
Zhu J, Wang J, Cheng K, Chen H, An R, Zhang Y, Komiyama M, Liang X. Effective Characterization of DNA Ligation Kinetics by High-Resolution Melting Analysis. Chembiochem 2019; 21:785-788. [PMID: 31592561 DOI: 10.1002/cbic.201900489] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 10/07/2019] [Indexed: 12/31/2022]
Abstract
High-resolution melting (HRM) analysis has been improved and applied for the first time to quantitative analysis of enzymatic reactions. By using the relative ratios of peak intensities of substrates and products, the quantitativity of conventional HRM analysis has been improved to allow detailed kinetic analysis. As an example, the ligation of sticky ends through the action of T4 DNA ligase has been kinetically analyzed, with comprehensive data on substrate specificity and other properties having been obtained. For the first time, the kinetic parameters (kobs and apparent Km ) of sticky-end ligation were obtained for both fully matched and mismatched sticky ends. The effect of ATP concentration on sticky-end ligation was also investigated. The improved HRM method should also be applicable to versatile DNA-transforming enzymes, because the only requirement is that the products have Tm values different enough from the substrates.
Collapse
Affiliation(s)
- Jianming Zhu
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, P. R. China
| | - Jing Wang
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, P. R. China.,CAS Key laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, P. R. China
| | - Kai Cheng
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, P. R. China
| | - Hui Chen
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, P. R. China
| | - Ran An
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, P. R. China
| | - Yaping Zhang
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, P. R. China
| | - Makoto Komiyama
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, P. R. China
| | - Xingguo Liang
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, P. R. China.,Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266003, P. R. China
| |
Collapse
|
5
|
Oda Y, Chiba J, Kurosaki F, Yamade Y, Inouye M. Additive‐Free Enzymatic Phosphorylation and Ligation of Artificial Oligonucleotides with C‐Nucleosides at the Reaction Points. Chembiochem 2019; 20:1945-1952. [DOI: 10.1002/cbic.201900217] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Indexed: 11/06/2022]
Affiliation(s)
- Yutaro Oda
- Graduate School of Pharmaceutical SciencesUniversity of Toyama 2630 Sugitani Toyama 930-0194 Japan
| | - Junya Chiba
- Graduate School of Pharmaceutical SciencesUniversity of Toyama 2630 Sugitani Toyama 930-0194 Japan
| | - Fumihiro Kurosaki
- Graduate School of Pharmaceutical SciencesUniversity of Toyama 2630 Sugitani Toyama 930-0194 Japan
| | - Yusuke Yamade
- Graduate School of Pharmaceutical SciencesUniversity of Toyama 2630 Sugitani Toyama 930-0194 Japan
| | - Masahiko Inouye
- Graduate School of Pharmaceutical SciencesUniversity of Toyama 2630 Sugitani Toyama 930-0194 Japan
| |
Collapse
|
6
|
Ming Z, Chen Q, Chen N, Lin M, Liu N, Hu J, Xiao X. Eliminating the secondary structure of targeting strands for enhancement of DNA probe based low-abundance point mutation detection. Anal Chim Acta 2019; 1075:137-143. [PMID: 31196419 DOI: 10.1016/j.aca.2019.05.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Revised: 04/25/2019] [Accepted: 05/05/2019] [Indexed: 10/26/2022]
Abstract
Nucleic acid probes are very useful tools in biological and medical science. However, the essential sensing mechanism of nucleic acid probes was prone to the interference of surrounding sequences. Especially when the target sequences formed secondary structures such as hairpin or quadruplex, the nucleic acid probes were hindered from hybridizing with target strands, greatly disabled the function of probes. Herein, we have established an Open strand based strategy for eliminating the influence of secondary structures on the performance of nucleic acid probes. The strategy was general toward different lengths, secondary structures and sequences of the targeting strand, and we found that the improvement was higher when the secondary structure of the targeting strand was more complicated. Experiments on synthetic single stranded DNA and real clinical genomic DNA samples were conducted for low abundance mutation detection, and the limit of detection for TERT-C228T and BRCA2 rs80359065 mutations could be 0.02% and 0.05% respectively, demonstrating the clinical practicability of our proposed strategy in low abundance mutation detection.
Collapse
Affiliation(s)
- Zhihao Ming
- Family Planning Research Institute/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, PR China
| | - Qianzhi Chen
- Cancer Research Institute, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, 430030, PR China
| | - Na Chen
- Family Planning Research Institute/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, PR China
| | - Meng Lin
- Family Planning Research Institute/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, PR China
| | - Na Liu
- Family Planning Research Institute/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, PR China
| | - Junbo Hu
- Cancer Research Institute, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, 430030, PR China
| | - Xianjin Xiao
- Family Planning Research Institute/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, PR China.
| |
Collapse
|
7
|
Xu J, Li L, Chen N, She Y, Wang S, Liu N, Xiao X. Endonuclease IV based competitive DNA probe assay for differentiation of low-abundance point mutations by discriminating stable single-base mismatches. Chem Commun (Camb) 2017; 53:9422-9425. [PMID: 28792020 DOI: 10.1039/c7cc04816e] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We disclosed the unique discrimination property of Endo IV toward stable single-base mismatches located at the second nucleotide 3' to the AP site. Coupled with thermodynamic differentiation and competitive blocker strands, a highly sensitive and specific detection system was established with discrimination factors of 510-1079 for G:X mismatches and LODs of 0.003-0.005% for KRAS G12A, KRAS G12V and KRAS G12S mutations.
Collapse
Affiliation(s)
- Jiaju Xu
- Family Planning Research Institute/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, P. R. China.
| | | | | | | | | | | | | |
Collapse
|
8
|
Schneider N, Meier M. Efficient in situ detection of mRNAs using the Chlorella virus DNA ligase for padlock probe ligation. RNA (NEW YORK, N.Y.) 2017; 23:250-256. [PMID: 27879431 PMCID: PMC5238799 DOI: 10.1261/rna.057836.116] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 11/18/2016] [Indexed: 05/22/2023]
Abstract
Padlock probes are single-stranded DNA molecules that are circularized upon hybridization to their target sequence by a DNA ligase. In the following, the circulated padlock probes are amplified and detected with fluorescently labeled probes complementary to the amplification product. The hallmark of padlock probe assays is a high detection specificity gained by the ligation reaction. Concomitantly, the ligation reaction is the largest drawback for a quantitative in situ detection of mRNAs due to the low affinities of common DNA or RNA ligases to RNA-DNA duplex strands. Therefore, current protocols require that mRNAs be reverse transcribed to DNA before detection with padlock probes. Recently, it was found that the DNA ligase from Paramecium bursaria Chlorella virus 1 (PBCV-1) is able to efficiently ligate RNA-splinted DNA. Hence, we designed a padlock probe assay for direct in situ detection of mRNAs using the PBCV-1 DNA ligase. Experimental single-cell data were used to optimize and characterize the efficiency of mRNA detection with padlock probes. Our results demonstrate that the PBCV-1 DNA ligase overcomes the efficiency limitation of current protocols for direct in situ mRNA detection, making the PBCV-1 DNA ligase an attractive tool to simplify in situ ligation sequencing applications.
Collapse
Affiliation(s)
- Nils Schneider
- Microfluidic and Biological Engineering, Department of Microsystems Engineering-IMTEK, University of Freiburg, 79110 Freiburg, Germany
- Centre for Biological Signalling Studies-BIOSS, University of Freiburg, 79104 Freiburg, Germany
| | - Matthias Meier
- Microfluidic and Biological Engineering, Department of Microsystems Engineering-IMTEK, University of Freiburg, 79110 Freiburg, Germany
- Centre for Biological Signalling Studies-BIOSS, University of Freiburg, 79104 Freiburg, Germany
| |
Collapse
|
9
|
Selvaraj C, Krishnasamy G, Jagtap SS, Patel SK, Dhiman SS, Kim TS, Singh SK, Lee JK. Structural insights into the binding mode of d-sorbitol with sorbitol dehydrogenase using QM-polarized ligand docking and molecular dynamics simulations. Biochem Eng J 2016. [DOI: 10.1016/j.bej.2016.07.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
10
|
Kausar A, Osman EA, Gadzikwa T, Gibbs-Davis JM. The presence of a 5'-abasic lesion enhances discrimination of single nucleotide polymorphisms while inducing an isothermal ligase chain reaction. Analyst 2016; 141:4272-7. [PMID: 27326790 DOI: 10.1039/c6an00614k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Lesion-induced DNA amplification (LIDA) has been employed in the detection of single nucleotide polymorphisms (SNPs). Due to the presence of the proximal abasic lesion, T4 DNA ligase exhibits greater intolerance to basepair mismatches when compared with mismatch ligation in the absence of the abasic lesion. Moreover the presence of the abasic group also results in an isothermal ligase chain reaction enabling SNP detection with great discrimination and sensitivity. Specifically, at forty minutes, the ratio of amplified product from the matched and mismatched initiated reactions are 7-12 depending on the mismatch. The ease of implementation of our method is demonstrated by real-time analysis of DNA amplification using a fluorescent plate reader.
Collapse
Affiliation(s)
- Abu Kausar
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada.
| | | | | | | |
Collapse
|
11
|
He W, Mao J, Feng T, Wang L, Li Z, Zu W, Liang W, Zhang L. A novel system for forensic SNP analysis through PCR–ligase detection reaction. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2015. [DOI: 10.1016/j.fsigss.2015.09.092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|