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Calaça Serrão A, Wunnava S, Dass AV, Ufer L, Schwintek P, Mast CB, Braun D. High-Fidelity RNA Copying via 2',3'-Cyclic Phosphate Ligation. J Am Chem Soc 2024; 146:8887-8894. [PMID: 38503430 PMCID: PMC10995993 DOI: 10.1021/jacs.3c10813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 03/21/2024]
Abstract
Templated ligation offers an efficient approach to replicate long strands in an RNA world. The 2',3'-cyclic phosphate (>P) is a prebiotically available activation that also forms during RNA hydrolysis. Using gel electrophoresis and high-performance liquid chromatography, we found that the templated ligation of RNA with >P proceeds in simple low-salt aqueous solutions with 1 mM MgCl2 under alkaline pH ranging from 9 to 11 and temperatures from -20 to 25 °C. No additional catalysts were required. In contrast to previous reports, we found an increase in the number of canonical linkages to 50%. The reaction proceeds in a sequence-specific manner, with an experimentally determined ligation fidelity of 82% at the 3' end and 91% at the 5' end of the ligation site. With splinted oligomers, five ligations created a 96-mer strand, demonstrating a pathway for the ribozyme assembly. Due to the low salt requirements, the ligation conditions will be compatible with strand separation. Templated ligation mediated by 2',3'-cyclic phosphate in alkaline conditions therefore offers a performant replication and elongation reaction for RNA on early Earth.
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Affiliation(s)
- Adriana Calaça Serrão
- Department
of Physics, Center for Nanoscience, Ludwig-Maximilians-Universität
München, Amalienstraße 54, 80799 Munich, Germany
| | - Sreekar Wunnava
- Department
of Physics, Center for Nanoscience, Ludwig-Maximilians-Universität
München, Amalienstraße 54, 80799 Munich, Germany
| | - Avinash V. Dass
- Department
of Physics, Center for Nanoscience, Ludwig-Maximilians-Universität
München, Amalienstraße 54, 80799 Munich, Germany
- Department
of Physics and Astronomy, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S4M1, Canada
| | - Lennard Ufer
- Department
of Physics, Center for Nanoscience, Ludwig-Maximilians-Universität
München, Amalienstraße 54, 80799 Munich, Germany
| | - Philipp Schwintek
- Department
of Physics, Center for Nanoscience, Ludwig-Maximilians-Universität
München, Amalienstraße 54, 80799 Munich, Germany
| | - Christof B. Mast
- Department
of Physics, Center for Nanoscience, Ludwig-Maximilians-Universität
München, Amalienstraße 54, 80799 Munich, Germany
| | - Dieter Braun
- Department
of Physics, Center for Nanoscience, Ludwig-Maximilians-Universität
München, Amalienstraße 54, 80799 Munich, Germany
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2
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Shi J, Oger PM, Cao P, Zhang L. Thermostable DNA ligases from hyperthermophiles in biotechnology. Front Microbiol 2023; 14:1198784. [PMID: 37293226 PMCID: PMC10244674 DOI: 10.3389/fmicb.2023.1198784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 05/09/2023] [Indexed: 06/10/2023] Open
Abstract
DNA ligase is an important enzyme ubiquitous in all three kingdoms of life that can ligate DNA strands, thus playing essential roles in DNA replication, repair and recombination in vivo. In vitro, DNA ligase is also used in biotechnological applications requiring in DNA manipulation, including molecular cloning, mutation detection, DNA assembly, DNA sequencing, and other aspects. Thermophilic and thermostable enzymes from hyperthermophiles that thrive in the high-temperature (above 80°C) environments have provided an important pool of useful enzymes as biotechnological reagents. Similar to other organisms, each hyperthermophile harbors at least one DNA ligase. In this review, we summarize recent progress on structural and biochemical properties of thermostable DNA ligases from hyperthermophiles, focusing on similarities and differences between DNA ligases from hyperthermophilic bacteria and archaea, and between these thermostable DNA ligases and non-thermostable homologs. Additionally, altered thermostable DNA ligases are discussed. Possessing improved fidelity or thermostability compared to the wild-type enzymes, they could be potential DNA ligases for biotechnology in the future. Importantly, we also describe current applications of thermostable DNA ligases from hyperthermophiles in biotechnology.
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Affiliation(s)
- Jingru Shi
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, China
| | - Philippe M. Oger
- University of Lyon, INSA de Lyon, CNRS UMR, Villeurbanne, France
| | - Peng Cao
- Faculty of Environment and Life, Beijing University of Technology, Beijing, China
| | - Likui Zhang
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, China
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3
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Duckworth AT, Bilotti K, Potapov V, Lohman GJS. Profiling DNA Ligase Substrate Specificity with a Pacific Biosciences Single-Molecule Real-Time Sequencing Assay. Curr Protoc 2023; 3:e690. [PMID: 36880776 PMCID: PMC10494924 DOI: 10.1002/cpz1.690] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
DNA ligases catalyze the joining of breaks in nucleic acid backbones and are essential enzymes for in vivo genome replication and repair across all domains of life. These enzymes are also critically important to in vitro manipulation of DNA in applications such as cloning, sequencing, and molecular diagnostics. DNA ligases generally catalyze the formation of a phosphodiester bond between an adjacent 5'-phosphate and 3'-hydroxyl in DNA, but they exhibit different substrate structure preferences, sequence-dependent biases in reaction kinetics, and variable tolerance for mismatched base pairs. Information on substrate structure and sequence specificity can inform both biological roles and molecular biology applications of these enzymes. Given the high complexity of DNA sequence space, testing DNA ligase substrate specificity on individual nucleic acid sequences in parallel rapidly becomes impractical when a large sequence space is investigated. Here, we describe methods for investigating DNA ligase sequence bias and mismatch discrimination using Pacific Biosciences Single-Molecule Real-Time (PacBio SMRT) sequencing technology. Through its rolling-circle amplification methodology, SMRT sequencing can give multiple reads of the same insert. This feature permits high-quality top- and bottom-strand consensus sequences to be determined while preserving information on top-bottom strand mismatches that can be obfuscated or lost when using other sequencing methods. Thus, PacBio SMRT sequencing is uniquely suited to measuring substrate bias and enzyme fidelity through multiplexing a diverse set of sequences in a single reaction. The protocols describe substrate synthesis, library preparation, and data analysis methods suitable for measuring fidelity and bias of DNA ligases. The methods are easily adapted to different nucleic acid substrate structures and can be used to characterize many enzymes under a variety of reaction conditions and sequence contexts in a rapid and high-throughput manner. © 2023 New England Biolabs and The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Preparation of overhang DNA substrates for ligation Basic Protocol 2: Preparation of ligation fidelity libraries Support Protocol 1: Preparation of ligation libraries for PacBio Sequel II sequencing Support Protocol 2: Loading and sequencing of a prepared library on the Sequel II instrument Basic Protocol 3: Computational processing of ligase fidelity sequencing data.
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4
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Chen L, Eriksson A, Weström S, Pandzic T, Lehmann S, Cavelier L, Landegren U. Ultra-sensitive monitoring of leukemia patients using superRCA mutation detection assays. Nat Commun 2022; 13:4033. [PMID: 35821208 PMCID: PMC9276831 DOI: 10.1038/s41467-022-31397-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 06/16/2022] [Indexed: 11/09/2022] Open
Abstract
Rare tumor-specific mutations in patient samples serve as excellent markers to monitor the course of malignant disease and responses to therapy in clinical routine, and improved assay techniques are needed for broad adoption. We describe herein a highly sensitive and selective molecule amplification technology - superRCA assays - for rapid and highly specific detection of DNA sequence variants present at very low frequencies in DNA samples. Using a standard flow cytometer we demonstrate precise, ultra-sensitive detection of single-nucleotide mutant sequences from malignant cells against up to a 100,000-fold excess of DNA from normal cells in either bone marrow or peripheral blood, to follow the course of patients treated for acute myeloid leukemia (AML). We also demonstrate that sequence variants located in a high-GC region may be sensitively detected, and we illustrate the potential of the technology for early detection of disease recurrence as a basis for prompt change of therapy.
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Affiliation(s)
- Lei Chen
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, SE-752 37, Uppsala, Sweden. .,Rarity Bioscience AB, SE-752 37, Uppsala, Sweden.
| | - Anna Eriksson
- Department of Medical Sciences, Uppsala University, SE-751 05, Uppsala, Sweden
| | - Simone Weström
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, SE-752 37, Uppsala, Sweden
| | - Tatjana Pandzic
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, SE-752 37, Uppsala, Sweden
| | - Sören Lehmann
- Department of Medical Sciences, Uppsala University, SE-751 05, Uppsala, Sweden
| | - Lucia Cavelier
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, SE-752 37, Uppsala, Sweden
| | - Ulf Landegren
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, SE-752 37, Uppsala, Sweden.
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5
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Kimoto M, Soh SHG, Tan HP, Okamoto I, Hirao I. Cognate base-pair selectivity of hydrophobic unnatural bases in DNA ligation by T4 DNA ligase. Biopolymers 2020; 112:e23407. [PMID: 33156531 PMCID: PMC7900958 DOI: 10.1002/bip.23407] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 10/05/2020] [Accepted: 10/21/2020] [Indexed: 12/28/2022]
Abstract
We present cognate base pair selectivity in template-dependent ligation by T4 DNA ligase using a hydrophobic unnatural base pair (UBP), Ds-Pa. T4 DNA ligase efficiently recognizes the Ds-Pa pairing at the conjugation position, and Ds excludes the noncognate pairings with the natural bases. Our results indicate that the hydrophobic base pairing is allowed in enzymatic ligation with higher cognate base-pair selectivity, relative to the hydrogen-bond interactions between pairing bases. The efficient ligation using Ds-Pa can be employed in recombinant DNA technology using genetic alphabet expansion, toward the creation of semi-synthetic organisms containing UBPs.
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Affiliation(s)
- Michiko Kimoto
- Institute of Bioengineering and Nanotechnology, A*STAR, Singapore, Singapore
| | - Si Hui Gabriella Soh
- Institute of Bioengineering and Nanotechnology, A*STAR, Singapore, Singapore.,Raffles Institution, Singapore, Singapore
| | - Hui Pen Tan
- Institute of Bioengineering and Nanotechnology, A*STAR, Singapore, Singapore
| | - Itaru Okamoto
- Institute of Bioengineering and Nanotechnology, A*STAR, Singapore, Singapore
| | - Ichiro Hirao
- Institute of Bioengineering and Nanotechnology, A*STAR, Singapore, Singapore
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6
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Potapov V, Ong JL, Langhorst BW, Bilotti K, Cahoon D, Canton B, Knight TF, Evans TC, Lohman GJS. A single-molecule sequencing assay for the comprehensive profiling of T4 DNA ligase fidelity and bias during DNA end-joining. Nucleic Acids Res 2019; 46:e79. [PMID: 29741723 PMCID: PMC6061786 DOI: 10.1093/nar/gky303] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 04/12/2018] [Indexed: 12/14/2022] Open
Abstract
DNA ligases are key enzymes in molecular and synthetic biology that catalyze the joining of breaks in duplex DNA and the end-joining of DNA fragments. Ligation fidelity (discrimination against the ligation of substrates containing mismatched base pairs) and bias (preferential ligation of particular sequences over others) have been well-studied in the context of nick ligation. However, almost no data exist for fidelity and bias in end-joining ligation contexts. In this study, we applied Pacific Biosciences Single-Molecule Real-Time sequencing technology to directly sequence the products of a highly multiplexed ligation reaction. This method has been used to profile the ligation of all three-base 5′-overhangs by T4 DNA ligase under typical ligation conditions in a single experiment. We report the relative frequency of all ligation products with or without mismatches, the position-dependent frequency of each mismatch, and the surprising observation that 5′-TNA overhangs ligate extremely inefficiently compared to all other Watson–Crick pairings. The method can easily be extended to profile other ligases, end-types (e.g. blunt ends and overhangs of different lengths), and the effect of adjacent sequence on the ligation results. Further, the method has the potential to provide new insights into the thermodynamics of annealing and the kinetics of end-joining reactions.
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Affiliation(s)
- Vladimir Potapov
- Research Department, New England Biolabs, Ipswich, MA 01938, USA
| | - Jennifer L Ong
- Research Department, New England Biolabs, Ipswich, MA 01938, USA
| | - Bradley W Langhorst
- Applications and Product Development, New England Biolabs, Ipswich, MA 01938, USA
| | | | | | | | | | - Thomas C Evans
- Research Department, New England Biolabs, Ipswich, MA 01938, USA
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7
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A novel mutation tolerant padlock probe design for multiplexed detection of hypervariable RNA viruses. Sci Rep 2019; 9:2872. [PMID: 30814634 PMCID: PMC6393471 DOI: 10.1038/s41598-019-39854-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 01/31/2019] [Indexed: 12/13/2022] Open
Abstract
The establishment of a robust detection platform for RNA viruses still remains a challenge in molecular diagnostics due to their high mutation rates. Newcastle disease virus (NDV) is one such RNA avian virus with a hypervariable genome and multiple genotypes. Classical approaches like virus isolation, serology, immunoassays and RT-PCR are cumbersome, and limited in terms of specificity and sensitivity. Padlock probes (PLPs) are known for allowing the detection of multiple nucleic acid targets with high specificity, and in combination with Rolling circle amplification (RCA) have permitted the development of versatile pathogen detection assays. In this work, we aimed to detect hypervariable viruses by developing a novel PLP design strategy capable of tolerating mutations while preserving high specificity by targeting several moderately conserved regions and using degenerate bases. For this, we designed nine padlock probes based on the alignment of 335 sequences covering both Class I and II NDV. Our PLP design showed high coverage and specificity for the detection of eight out of ten reported genotypes of Class II NDV field isolated strains, yielding a detection limit of less than ten copies of viral RNA. Further taking advantage of the multiplex capability of PLPs, we successfully extended the assay for the simultaneous detection of three poultry RNA viruses (NDV, IBV and AIV) and combined it with a paper based microfluidic enrichment read-out for digital quantification. In summary, our novel PLP design addresses the current issue of tolerating mutations of highly emerging virus strains with high sensitivity and specificity.
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8
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Cui Y, Han X, An R, Zhang Y, Cheng K, Liang X, Komiyama M. Terminal hairpin in oligonucleotide dominantly prioritizes intramolecular cyclization by T4 ligase over intermolecular polymerization: an exclusive methodology for producing ssDNA rings. Nucleic Acids Res 2018; 46:e132. [PMID: 30169701 PMCID: PMC6294566 DOI: 10.1093/nar/gky769] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 08/02/2018] [Accepted: 08/22/2018] [Indexed: 12/22/2022] Open
Abstract
When oligonucleotide bearing a hairpin near either its 3'- or 5'-end was treated with T4 DNA ligase, the intramolecular cyclization dominantly proceeded and its monomeric cyclic ring was obtained in extremely high selectivity. The selectivity was hardly dependent on the concentration of the oligonucleotide, and thus it could be added in one portion to the mixture at the beginning of the reaction. Without the hairpin, however, the formation of polymeric byproducts was dominant under the same conditions. Hairpin-bearing oligonucleotides primarily take the folded form, and the enzymatically reactive species (its open form) is minimal. As the result, the intermolecular reactions are efficiently suppressed due to both thermodynamic and kinetic factors. The 'terminal hairpin strategy' was applicable to large-scale preparation of a variety of DNA rings. The combination of this methodology with 'diluted buffer strategy', developed previously, is still more effective for the purpose. When large amount of l-DNA bearing a terminal hairpin (e.g. 40 μM) was treated in a diluted ligase buffer (0.1× buffer) with T4 DNA ligase, the DNA ring was prepared in 100% selectivity. Even at [l-DNA]0 = 100 μM in 0.1× buffer, the DNA ring was also obtained in pure form, simply by removing tiny quantity of linear byproducts by Exonuclease I.
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Affiliation(s)
- Yixiao Cui
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Xutiange Han
- 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 266003, China
| | - Yaping Zhang
- 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
| | - 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 266003, China
| | - Makoto Komiyama
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
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9
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Severins I, Szczepaniak M, Joo C. Multiplex Single-Molecule DNA Barcoding Using an Oligonucleotide Ligation Assay. Biophys J 2018; 115:957-967. [PMID: 30195940 DOI: 10.1016/j.bpj.2018.08.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 07/10/2018] [Accepted: 08/06/2018] [Indexed: 12/16/2022] Open
Abstract
Detection of specific nucleic acid sequences is invaluable in biological studies such as genetic disease diagnostics and genome profiling. Here, we developed a highly sensitive and specific detection method that combines an advanced oligonucleotide ligation assay with multicolor single-molecule fluorescence. We demonstrated that under our experimental conditions, 7-nucleotide long DNA barcodes have the optimal short length to ascertain specificity while being long enough for sufficient ligation. Using four spectrally separated fluorophores to label DNA barcodes, we simultaneously distinguished four DNA target sequences differing by only a single nucleotide. Our single-molecule approach will allow for accurate identification of low-abundance molecules without the need for target DNA preamplification.
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Affiliation(s)
- Ivo Severins
- Kavli Institute of NanoScience, Department of BioNanoScience, Delft University of Technology, Delft, The Netherlands
| | - Malwina Szczepaniak
- Kavli Institute of NanoScience, Department of BioNanoScience, Delft University of Technology, Delft, The Netherlands.
| | - Chirlmin Joo
- Kavli Institute of NanoScience, Department of BioNanoScience, Delft University of Technology, Delft, The Netherlands.
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10
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Azuara-Liceaga E, Betanzos A, Cardona-Felix CS, Castañeda-Ortiz EJ, Cárdenas H, Cárdenas-Guerra RE, Pastor-Palacios G, García-Rivera G, Hernández-Álvarez D, Trasviña-Arenas CH, Diaz-Quezada C, Orozco E, Brieba LG. The Sole DNA Ligase in Entamoeba histolytica Is a High-Fidelity DNA Ligase Involved in DNA Damage Repair. Front Cell Infect Microbiol 2018; 8:214. [PMID: 30050869 PMCID: PMC6052137 DOI: 10.3389/fcimb.2018.00214] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 06/07/2018] [Indexed: 01/03/2023] Open
Abstract
The protozoan parasite Entamoeba histolytica is exposed to reactive oxygen and nitric oxide species that have the potential to damage its genome. E. histolytica harbors enzymes involved in DNA repair pathways like Base and Nucleotide Excision Repair. The majority of DNA repairs pathways converge in their final step in which a DNA ligase seals the DNA nicks. In contrast to other eukaryotes, the genome of E. histolytica encodes only one DNA ligase (EhDNAligI), suggesting that this ligase is involved in both DNA replication and DNA repair. Therefore, the aim of this work was to characterize EhDNAligI, its ligation fidelity and its ability to ligate opposite DNA mismatches and oxidative DNA lesions, and to study its expression changes and localization during and after recovery from UV and H2O2 treatment. We found that EhDNAligI is a high-fidelity DNA ligase on canonical substrates and is able to discriminate erroneous base-pairing opposite DNA lesions. EhDNAligI expression decreases after DNA damage induced by UV and H2O2 treatments, but it was upregulated during recovery time. Upon oxidative DNA damage, EhDNAligI relocates into the nucleus where it co-localizes with EhPCNA and the 8-oxoG adduct. The appearance and disappearance of 8-oxoG during and after both treatments suggest that DNA damaged was efficiently repaired because the mainly NER and BER components are expressed in this parasite and some of them were modulated after DNA insults. All these data disclose the relevance of EhDNAligI as a specialized and unique ligase in E. histolytica that may be involved in DNA repair of the 8-oxoG lesions.
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Affiliation(s)
- Elisa Azuara-Liceaga
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Mexico City, Mexico,*Correspondence: Elisa Azuara-Liceaga
| | - Abigail Betanzos
- Consejo Nacional de Ciencia y Tecnología, Mexico City, Mexico,Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico City, Mexico
| | - Cesar S. Cardona-Felix
- Consejo Nacional de Ciencia y Tecnología, Mexico City, Mexico,Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados, Irapuato, Mexico
| | | | - Helios Cárdenas
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Mexico City, Mexico
| | - Rosa E. Cárdenas-Guerra
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Mexico City, Mexico
| | - Guillermo Pastor-Palacios
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados, Irapuato, Mexico
| | - Guillermina García-Rivera
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico City, Mexico
| | - David Hernández-Álvarez
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Mexico City, Mexico
| | - Carlos H. Trasviña-Arenas
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados, Irapuato, Mexico
| | - Corina Diaz-Quezada
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados, Irapuato, Mexico
| | - Esther Orozco
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico City, Mexico
| | - Luis G. Brieba
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados, Irapuato, Mexico,Luis G. Brieba
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11
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Krzywkowski T, Hauling T, Nilsson M. In Situ Single-Molecule RNA Genotyping Using Padlock Probes and Rolling Circle Amplification. Methods Mol Biol 2017; 1492:59-76. [PMID: 27822856 DOI: 10.1007/978-1-4939-6442-0_4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Present-day techniques allow for massively parallel and high-throughput characterization of the somatic mutation status of samples. Most of these assays rely on whole specimen extracts, where heterogeneous spatial context of the specimen is lost. This chapter describes an up-to-date protocol for multiplexed, in situ genotyping of RNA in preserved tissue and cell lines, using padlock probes and rolling circle amplification. The presented approach allows for automated quantification of mRNA expression and mutation status, in single cells or in designated specimen areas. Briefly, mRNA is first reverse-transcribed to cDNA. Padlock probes specifically hybridize to the cDNA copy of the allele and become circularized and thereby physically linked to their targets. Following this conversion, padlock probes are copied in situ by rolling circle amplification and labeled with flourophore-conjugated probes, allowing for their detection with conventional fluorescence microscopy.
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Affiliation(s)
- Tomasz Krzywkowski
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Tomtebodavägem 23A, 17165, Solna, Sweden
| | - Thomas Hauling
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Tomtebodavägem 23A, 17165, Solna, Sweden
| | - Mats Nilsson
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Tomtebodavägem 23A, 17165, Solna, Sweden.
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12
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Shore S, Henderson JM, Lebedev A, Salcedo MP, Zon G, McCaffrey AP, Paul N, Hogrefe RI. Small RNA Library Preparation Method for Next-Generation Sequencing Using Chemical Modifications to Prevent Adapter Dimer Formation. PLoS One 2016; 11:e0167009. [PMID: 27875576 PMCID: PMC5119831 DOI: 10.1371/journal.pone.0167009] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 11/07/2016] [Indexed: 12/14/2022] Open
Abstract
For most sample types, the automation of RNA and DNA sample preparation workflows enables high throughput next-generation sequencing (NGS) library preparation. Greater adoption of small RNA (sRNA) sequencing has been hindered by high sample input requirements and inherent ligation side products formed during library preparation. These side products, known as adapter dimer, are very similar in size to the tagged library. Most sRNA library preparation strategies thus employ a gel purification step to isolate tagged library from adapter dimer contaminants. At very low sample inputs, adapter dimer side products dominate the reaction and limit the sensitivity of this technique. Here we address the need for improved specificity of sRNA library preparation workflows with a novel library preparation approach that uses modified adapters to suppress adapter dimer formation. This workflow allows for lower sample inputs and elimination of the gel purification step, which in turn allows for an automatable sRNA library preparation protocol.
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Affiliation(s)
- Sabrina Shore
- Research and Development, Cell and Molecular Biology, TriLink BioTechnologies LLC., San Diego, California, United States of America
| | - Jordana M. Henderson
- Research and Development, Cell and Molecular Biology, TriLink BioTechnologies LLC., San Diego, California, United States of America
| | - Alexandre Lebedev
- Research and Development, Cell and Molecular Biology, TriLink BioTechnologies LLC., San Diego, California, United States of America
| | - Michelle P. Salcedo
- Research and Development, Cell and Molecular Biology, TriLink BioTechnologies LLC., San Diego, California, United States of America
| | - Gerald Zon
- Research and Development, Cell and Molecular Biology, TriLink BioTechnologies LLC., San Diego, California, United States of America
| | - Anton P. McCaffrey
- Research and Development, Cell and Molecular Biology, TriLink BioTechnologies LLC., San Diego, California, United States of America
| | - Natasha Paul
- Engineering and Instrumentation, Synthetic Genomics, Inc., La Jolla, California, United States of America
| | - Richard I. Hogrefe
- Research and Development, Cell and Molecular Biology, TriLink BioTechnologies LLC., San Diego, California, United States of America
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13
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Chauleau M, Shuman S. Kinetic mechanism and fidelity of nick sealing by Escherichia coli NAD+-dependent DNA ligase (LigA). Nucleic Acids Res 2016; 44:2298-309. [PMID: 26857547 PMCID: PMC4797296 DOI: 10.1093/nar/gkw049] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Accepted: 01/18/2016] [Indexed: 11/15/2022] Open
Abstract
Escherichia coli DNA ligase (EcoLigA) repairs 3′-OH/5′-PO4 nicks in duplex DNA via reaction of LigA with NAD+ to form a covalent LigA-(lysyl-Nζ)–AMP intermediate (step 1); transfer of AMP to the nick 5′-PO4 to form an AppDNA intermediate (step 2); and attack of the nick 3′-OH on AppDNA to form a 3′-5′ phosphodiester (step 3). A distinctive feature of EcoLigA is its stimulation by ammonium ion. Here we used rapid mix-quench methods to analyze the kinetic mechanism of single-turnover nick sealing by EcoLigA–AMP. For substrates with correctly base-paired 3′-OH/5′-PO4 nicks, kstep2 was fast (6.8–27 s−1) and similar to kstep3 (8.3–42 s−1). Absent ammonium, kstep2 and kstep3 were 48-fold and 16-fold slower, respectively. EcoLigA was exquisitely sensitive to 3′-OH base mispairs and 3′ N:abasic lesions, which elicited 1000- to >20000-fold decrements in kstep2. The exception was the non-canonical 3′ A:oxoG configuration, which EcoLigA accepted as correctly paired for rapid sealing. These results underscore: (i) how EcoLigA requires proper positioning of the nick 3′ nucleoside for catalysis of 5′ adenylylation; and (ii) EcoLigA's potential to embed mutations during the repair of oxidative damage. EcoLigA was relatively tolerant of 5′-phosphate base mispairs and 5′ N:abasic lesions.
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Affiliation(s)
- Mathieu Chauleau
- Molecular Biology Program, Sloan-Kettering Institute, New York, NY 10065, USA
| | - Stewart Shuman
- Molecular Biology Program, Sloan-Kettering Institute, New York, NY 10065, USA
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14
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Abstract
With the advent of nanotechnology, a variety of nanoarchitectures with varied physicochemical properties have been designed. Owing to the unique characteristics, DNAs have been used as a functional building block for novel nanoarchitecture. In particular, a self-assembly of long DNA molecules via a piece DNA staple has been utilized to attain such constructs. However, it needs many talented prerequisites (e.g., complicated computer program) with fewer yields of products. In addition, it has many limitations to overcome: for instance, (i) thermal instability under moderate environments and (ii) restraint in size caused by the restricted length of scaffold strands. Alternatively, the enzymatic sewing linkage of short DNA blocks is simply designed into long DNA assemblies but it is more error-prone due to the undeveloped sequence data. Here, we present, for the first time, a comprehensive study for directly combining DNA structures into higher DNA sewing constructs through the 5′-end cohesive ligation of T4 enzyme. Inspired by these achievements, the synthesized DNA nanomaterials were also utilized for effective detection and real-time diagnosis of cancer-specific and cytosolic RNA markers. This generalized protocol for generic DNA sewing is expected to be useful in several DNA nanotechnology as well as any nucleic acid-related fields.
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15
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Zhang Z, Liu Y, Ji X, Xiang X, He Z. A graphene oxide-based enzyme-free signal amplification platform for homogeneous DNA detection. Analyst 2015; 139:4806-9. [PMID: 25058563 DOI: 10.1039/c4an00933a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A graphene oxide (GO) based enzyme-free signal amplification platform for homogeneous DNA sensing is developed with simplicity and high sensitivity. In the absence of the target DNA, labeled hairpin probe 1 (H1) and probe 2 (H2) were adsorbed on the surface of GO, resulting in the fluorescence quenching of the dyes and minimizing the background fluorescence. The addition of the target DNA facilitated the formation of double-stranded DNA (dsDNA) between H1 and H2, causing the probes to separate from GO and release the target DNA through a strand displacement reaction. Meanwhile, the whole reaction started anew. This is an excellent isothermal signal amplification technique without the involvement of enzymes. By monitoring the change of the fluorescence intensity, the target DNA not only can be determined in buffer solution, but also can be detected in 1% serum solution spiked with a series of concentrations of the target DNA. In addition, the consumption amount of the probes in this method is lower than that in traditional molecular beacon methods.
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Affiliation(s)
- Zhen Zhang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China.
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16
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From Structure-Function Analyses to Protein Engineering for Practical Applications of DNA Ligase. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2015; 2015:267570. [PMID: 26508902 PMCID: PMC4609770 DOI: 10.1155/2015/267570] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 05/18/2015] [Indexed: 01/03/2023]
Abstract
DNA ligases are indispensable in all living cells and ubiquitous in all organs. DNA ligases are broadly utilized in molecular biology research fields, such as genetic engineering and DNA sequencing technologies. Here we review the utilization of DNA ligases in a variety of in vitro gene manipulations, developed over the past several decades. During this period, fewer protein engineering attempts for DNA ligases have been made, as compared to those for DNA polymerases. We summarize the recent progress in the elucidation of the DNA ligation mechanisms obtained from the tertiary structures solved thus far, in each step of the ligation reaction scheme. We also present some examples of engineered DNA ligases, developed from the viewpoint of their three-dimensional structures.
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Lohman GJS, Bauer RJ, Nichols NM, Mazzola L, Bybee J, Rivizzigno D, Cantin E, Evans TC. A high-throughput assay for the comprehensive profiling of DNA ligase fidelity. Nucleic Acids Res 2015; 44:e14. [PMID: 26365241 PMCID: PMC4737175 DOI: 10.1093/nar/gkv898] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 08/28/2015] [Indexed: 11/24/2022] Open
Abstract
DNA ligases have broad application in molecular biology, from traditional cloning methods to modern synthetic biology and molecular diagnostics protocols. Ligation-based detection of polynucleotide sequences can be achieved by the ligation of probe oligonucleotides when annealed to a complementary target sequence. In order to achieve a high sensitivity and low background, the ligase must efficiently join correctly base-paired substrates, while discriminating against the ligation of substrates containing even one mismatched base pair. In the current study, we report the use of capillary electrophoresis to rapidly generate mismatch fidelity profiles that interrogate all 256 possible base-pair combinations at a ligation junction in a single experiment. Rapid screening of ligase fidelity in a 96-well plate format has allowed the study of ligase fidelity in unprecedented depth. As an example of this new method, herein we report the ligation fidelity of Thermus thermophilus DNA ligase at a range of temperatures, buffer pH and monovalent cation strength. This screen allows the selection of reaction conditions that maximize fidelity without sacrificing activity, while generating a profile of specific mismatches that ligate detectably under each set of conditions.
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Affiliation(s)
| | | | | | | | - Joanna Bybee
- New England BioLabs, Inc., Ipswich, MA 01938-2723, USA
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18
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Mignardi M, Mezger A, Qian X, La Fleur L, Botling J, Larsson C, Nilsson M. Oligonucleotide gap-fill ligation for mutation detection and sequencing in situ. Nucleic Acids Res 2015; 43:e151. [PMID: 26240388 PMCID: PMC4678841 DOI: 10.1093/nar/gkv772] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 07/19/2015] [Indexed: 11/12/2022] Open
Abstract
In clinical diagnostics a great need exists for targeted in situ multiplex nucleic acid analysis as the mutational status can offer guidance for effective treatment. One well-established method uses padlock probes for mutation detection and multiplex expression analysis directly in cells and tissues. Here, we use oligonucleotide gap-fill ligation to further increase specificity and to capture molecular substrates for in situ sequencing. Short oligonucleotides are joined at both ends of a padlock gap probe by two ligation events and are then locally amplified by target-primed rolling circle amplification (RCA) preserving spatial information. We demonstrate the specific detection of the A3243G mutation of mitochondrial DNA and we successfully characterize a single nucleotide variant in the ACTB mRNA in cells by in situ sequencing of RCA products generated by padlock gap-fill ligation. To demonstrate the clinical applicability of our assay, we show specific detection of a point mutation in the EGFR gene in fresh frozen and formalin-fixed, paraffin-embedded (FFPE) lung cancer samples and confirm the detected mutation by in situ sequencing. This approach presents several advantages over conventional padlock probes allowing simpler assay design for multiplexed mutation detection to screen for the presence of mutations in clinically relevant mutational hotspots directly in situ.
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Affiliation(s)
- Marco Mignardi
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, SE-17121 Sweden
| | - Anja Mezger
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, SE-17121 Sweden
| | - Xiaoyan Qian
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, SE-17121 Sweden
| | - Linnea La Fleur
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, SE-75185, Sweden
| | - Johan Botling
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, SE-75185, Sweden
| | - Chatarina Larsson
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, SE-75185, Sweden
| | - Mats Nilsson
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, SE-17121 Sweden
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Shi D, Huang J, Chuai Z, Chen D, Zhu X, Wang H, Peng J, Wu H, Huang Q, Fu W. Isothermal and rapid detection of pathogenic microorganisms using a nano-rolling circle amplification-surface plasmon resonance biosensor. Biosens Bioelectron 2014; 62:280-7. [DOI: 10.1016/j.bios.2014.06.066] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Revised: 06/25/2014] [Accepted: 06/25/2014] [Indexed: 10/25/2022]
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20
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In situ mutation detection and visualization of intratumor heterogeneity for cancer research and diagnostics. Oncotarget 2014; 4:2407-18. [PMID: 24280411 PMCID: PMC3926836 DOI: 10.18632/oncotarget.1527] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Current assays for somatic mutation analysis are based on extracts from tissue sections that often contain morphologically heterogeneous neoplastic regions with variable contents of normal stromal and inflammatory cells, obscuring the results of the assays. We have developed an RNA-based in situ mutation assay that targets oncogenic mutations in a multiplex fashion that resolves the heterogeneity of the tissue sample. Activating oncogenic mutations are targets for a new generation of cancer drugs. For anti-EGFR therapy prediction, we demonstrate reliable in situ detection of KRAS mutations in codon 12 and 13 in colon and lung cancers in three different types of routinely processed tissue materials. High-throughput screening of KRAS mutation status was successfully performed on a tissue microarray. Moreover, we show how the patterns of expressed mutated and wild-type alleles can be studied in situ in tumors with complex combinations of mutated EGFR, KRAS and TP53. This in situ method holds great promise as a tool to investigate the role of somatic mutations during tumor progression and for prediction of response to targeted therapy.
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21
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Zuo B, Qian H, Wang Z, Wang X, Nisa N, Bayier A, Ying S, Hu X, Gong C, Guo Z, Wang F. A Study on BMPR-IB Genes of Bayanbulak Sheep. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2014; 26:36-42. [PMID: 25049703 PMCID: PMC4093051 DOI: 10.5713/ajas.2012.12238] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Revised: 09/24/2012] [Accepted: 09/05/2012] [Indexed: 11/27/2022]
Abstract
The average twin lambing rate of Bayanbulak sheep is 2% to 3%. However, a flock of sheep with a close genetic relationship and an average of 2 to 3 lambs per birth has been found recently. To determine the major genes controlling the prolificacy of the flock in the present study, the flock was designated A while 100 normal Bayanbulak sheep were randomly selected to comprise the control flock B. Ligase detection reaction method was applied to detect and analyze the 10 mutational loci of the 3 candidate prolificacy genes including bone morphogenetic protein type I receptors, bone morphogenetic protein 15, and growth differentiation factor 9. The 10 mutational loci are as follows: FecB locus of the BMPR-IB gene; FecXI, FecXB, FecXL, FecXH, FecXG, and FecXR of the BMP15 gene; and G1, G8, and FecTT of the GDF9 gene. Two mutations including BMPR-IB/FecB and GDF9/G1 were found in Bayanbulak sheep. Independence test results of the two flocks demonstrate that the FecB locus has a significant effect on the lambing number of Bayanbulak sheep. However, the mutation frequency of the G1 locus in GDF9 is very low. Independence test results demonstrate that the GDF9 locus does not have a significant impact on the lambing performance of Bayanbulak sheep. Among the 10 detected loci, BMPR-IB/FecB is the major gene that influences the high lambing rate of Bayanbulak sheep.
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Affiliation(s)
- Beiyao Zuo
- Animal Embryo Engineering Center of Nanjing Agricultural University, Nanjing, China
| | - Hongguang Qian
- Animal Embryo Engineering Center of Nanjing Agricultural University, Nanjing, China
| | - Ziyu Wang
- Animal Embryo Engineering Center of Nanjing Agricultural University, Nanjing, China
| | - Xu Wang
- Animal Embryo Engineering Center of Nanjing Agricultural University, Nanjing, China
| | - Noor Nisa
- Animal Embryo Engineering Center of Nanjing Agricultural University, Nanjing, China
| | - Aierdin Bayier
- Animal Embryo Engineering Center of Nanjing Agricultural University, Nanjing, China
| | - Shijia Ying
- Animal Embryo Engineering Center of Nanjing Agricultural University, Nanjing, China
| | - Xiaolong Hu
- Animal Embryo Engineering Center of Nanjing Agricultural University, Nanjing, China
| | - Changhai Gong
- Animal Embryo Engineering Center of Nanjing Agricultural University, Nanjing, China
| | - Zhiqin Guo
- Animal Embryo Engineering Center of Nanjing Agricultural University, Nanjing, China
| | - Feng Wang
- Animal Embryo Engineering Center of Nanjing Agricultural University, Nanjing, China
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22
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Universal fluorescent tri-probe ligation equipped with capillary electrophoresis for targeting SMN1 and SMN2 genes in diagnosis of spinal muscular atrophy. Anal Chim Acta 2014; 833:40-7. [PMID: 24909772 DOI: 10.1016/j.aca.2014.05.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 05/02/2014] [Accepted: 05/05/2014] [Indexed: 01/02/2023]
Abstract
This is the first ligase chain reaction used for diagnosis of spinal muscular atrophy (SMA). Universal fluorescent tri-probe ligation (UFTPL), a novel strategy used for distinguishing the multi-nucleotide alternations at single base, is developed to quantitatively analyze the SMN1/SMN2 genes in diagnosis of SMA. Ligase chain reaction was performed by adding three probes including universal fluorescent probe, connecting probe and recognizing probe to differentiate single nucleotide polymorphisms in UFTPL. Our approach was based on the two UFTPL products of survival motor neuron 1 (SMN1) and SMN2 genes (the difference of 9 mer) and analyzed by capillary electrophoresis (CE). We successfully determined various gene dosages of SMN1 and SMN2 genes in homologous or heterologous subjects. By using the UFTPL-CE method, the SMN1 and SMN2 genes were fully resolved with the resolution of 2.16±0.37 (n=3). The r values of SMN1 and SMN2 regression curves over a range of 1-4 copies were above 0.9944. Of the 48 DNA samples, the data of gene dosages were corresponding to that analyzed by conformation sensitive CE and denatured high-performance liquid chromatography (DHPLC). This technique was found to be a good methodology for quantification or determination of the relative genes having multi-nucleotide variants at single base.
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23
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GNAS sequencing identifies IPMN-specific mutations in a subgroup of diminutive pancreatic cysts referred to as "incipient IPMNs". Am J Surg Pathol 2014; 38:360-3. [PMID: 24525507 DOI: 10.1097/pas.0000000000000117] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Incipient intraductal papillary mucinous neoplasms (IPMNs) are poorly described subcentimeter pancreatic cysts with papillae and mucin similar to IPMNs. They are larger than pancreatic intraepithelial neoplasia but do not meet the cutoff size for IPMNs (≥ 1 cm). GNAS codon 201 mutations are hallmark genetic alterations of IPMNs. Hence, we sought to determine the GNAS status of incipient IPMNs to better classify these lesions. Incipient IPMNs from 3 institutions were histologically reassessed, manually microdissected, and the genomic DNA was extracted. Using a sensitive digital ligation technique, the mutational status of KRAS at codon 12 and GNAS at codon 201 was determined. We included 21 incipient IPMNs from 7 male and 12 female patients with a median age of 63 years (range, 40 to 76 y). Most patients underwent surgery for pancreatic ductal adenocarcinoma (N = 8) or ampullary adenocarcinoma (N = 3). The median incipient IPMN size was 4 mm (range, 2 to 7 mm), and a majority had gastric-foveolar (N = 11) or intestinal (N = 5) differentiation. The maximum dysplasia observed was intermediate, and most of the lesions had intermediate-grade dysplasia. Mutational analysis revealed KRAS codon 12 mutations in all 21 incipient IPMNs, whereas 7 lesions (33%) in 7 individual patients harbored GNAS codon 201 mutations. The presence of GNAS 201 mutations in incipient IPMNs suggests that a fraction of these cysts are in fact small IPMNs. Morphologically, incipient IPMNs do not appear to be high-risk lesions. Additional studies in a larger cohort are needed to define the relationship of incipient IPMNs to larger IPMNs and, more importantly, to determine their clinical significance.
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24
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Zou Z, Qing Z, He X, Wang K, He D, Shi H, Yang X, Qing T, Yang X. Ligation-rolling circle amplification combined with γ-cyclodextrin mediated stemless molecular beacon for sensitive and specific genotyping of single-nucleotide polymorphism. Talanta 2014; 125:306-12. [PMID: 24840448 DOI: 10.1016/j.talanta.2014.03.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Revised: 02/26/2014] [Accepted: 03/10/2014] [Indexed: 10/25/2022]
Abstract
A novel approach for highly sensitive and selective genotyping of single-nucleotide polymorphism (SNP) has been developed based on ligation-rolling circle amplification (L-RCA) and stemless molecular beacon. In this approach, two tailored DNA probes were involved. The stemless molecular beacon, formed through the inclusion interactions of γ-cyclodextrin (γ-CD) and bis-pyrene labeled DNA fragment, was served as signal probe. In the absence of mutant target, the two pyrene molecules were bound in the γ-CD cavity to form an excimer and showed a strong fluorescence at 475 nm. It was here named γ-CD-P-MB. The padlock DNA probe was designed as recognition probe. Upon the recognition of a point mutation DNA targets, the padlock probe was ligated to generate a circular template. An RCA amplification was then initiated using the circular template in the presence of Phi29 polymerase and dNTPs. The L-RCA products, containing repetitive sequence units, subsequently hybridized with the γ-CD-P-MB. This made pyrene molecules away from γ-CD cavity and caused a decrease of excimer fluorescence. As a proof-of-concept, SNP typing of β-thalassemia gene at position -28 was investigated using this approach. The detection limit of mutated target was determined to be 40 fM. In addition, DNA ligase offered high fidelity in distinguishing the mismatched bases at the ligation site, resulting in positive detection of mutant target even when the ratio of the wildtype to the mutant is 999:1. Given these attractive characteristics, the developed approach might provide a great genotyping platform for pathogenic diagnosis and genetic analysis.
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Affiliation(s)
- Zhen Zou
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Changsha 410082, PR China; College of Biology, Hunan University, Changsha 410082, PR China; Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Changsha 410082, PR China
| | - Zhihe Qing
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Changsha 410082, PR China; College of Biology, Hunan University, Changsha 410082, PR China; Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Changsha 410082, PR China
| | - Xiaoxiao He
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Changsha 410082, PR China; College of Biology, Hunan University, Changsha 410082, PR China; Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Changsha 410082, PR China.
| | - Kemin Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Changsha 410082, PR China; College of Biology, Hunan University, Changsha 410082, PR China; Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Changsha 410082, PR China.
| | - Dinggeng He
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Changsha 410082, PR China; College of Biology, Hunan University, Changsha 410082, PR China; Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Changsha 410082, PR China
| | - Hui Shi
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Changsha 410082, PR China; College of Biology, Hunan University, Changsha 410082, PR China; Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Changsha 410082, PR China
| | - Xue Yang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Changsha 410082, PR China; College of Biology, Hunan University, Changsha 410082, PR China; Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Changsha 410082, PR China
| | - Taiping Qing
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Changsha 410082, PR China; College of Biology, Hunan University, Changsha 410082, PR China; Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Changsha 410082, PR China
| | - Xiaoxiao Yang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Changsha 410082, PR China; College of Biology, Hunan University, Changsha 410082, PR China; Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Changsha 410082, PR China
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25
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Effects of 3'-OH and 5'-PO4 base mispairs and damaged base lesions on the fidelity of nick sealing by Deinococcus radiodurans RNA ligase. J Bacteriol 2014; 196:1704-12. [PMID: 24532777 DOI: 10.1128/jb.00020-14] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Deinococcus radiodurans RNA ligase (DraRnl) is the founding member of a family of end-joining enzymes encoded by diverse microbes and viruses. DraRnl ligates 3'-OH, 5'-PO4 nicks in double-stranded nucleic acids in which the nick 3'-OH end is RNA. Here we gauge the effects of 3'-OH and 5'-PO4 base mispairs and damaged base lesions on the rate of nick sealing. DraRnl is indifferent to the identity of the 3'-OH nucleobase, provided that it is correctly paired. With 3'-OH mispairs, the DraRnl sealing rate varies widely, with G-T and A-C mispairs being the best substrates and G-G, G-A, and A-A mispairs being the worst. DraRnl accepts 3' A-8-oxoguanine (oxoG) to be correctly paired, while it discriminates against U-oxoG and G-oxoG mispairs. DraRnl displays high activity and low fidelity in sealing 3'-OH ends opposite an 8-oxoadenine lesion. It prefers 3'-OH adenosine when sealing opposite an abasic template site. With 5'-PO4 mispairs, DraRnl seals a 5' T-G mispair as well as it does a 5' C-G pair; in most other respects, the ligation fidelity at 5' mispairs is similar to that at 3' mispairs. DraRnl accepts a 5' A-oxoG end to be correctly paired, yet it is more tolerant of 5' T-oxoG and 5' G-oxoG mispairs than the equivalent configurations on the 3' side of the nick. At 5' nucleobase-abasic site nicks, DraRnl prefers to ligate when the nucleobase is a purine. The biochemical properties of DraRnl are compatible with its participation in the templated repair of RNA damage or in the sealing of filled DNA gaps that have a 3' ribopatch.
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26
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Chauleau M, Shuman S. Kinetic mechanism of nick sealing by T4 RNA ligase 2 and effects of 3'-OH base mispairs and damaged base lesions. RNA (NEW YORK, N.Y.) 2013; 19:1840-7. [PMID: 24158792 PMCID: PMC3884662 DOI: 10.1261/rna.041731.113] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
T4 RNA ligase 2 (Rnl2) repairs 3'-OH/5'-PO4 nicks in duplex nucleic acids in which the broken 3'-OH strand is RNA. Ligation entails three chemical steps: reaction of Rnl2 with ATP to form a covalent Rnl2-(lysyl-Nζ)-AMP intermediate (step 1); transfer of AMP to the 5'-PO4 of the nick to form an activated AppN- intermediate (step 2); and attack by the nick 3'-OH on the AppN- strand to form a 3'-5' phosphodiester (step 3). Here we used rapid mix-quench methods to analyze the kinetic mechanism and fidelity of single-turnover nick sealing by Rnl2-AMP. For substrates with correctly base-paired 3'-OH nick termini, kstep2 was fast (9.5 to 17.9 sec(-1)) and similar in magnitude to kstep3 (7.9 to 32 sec(-1)). Rnl2 fidelity was enforced mainly at the level of step 2 catalysis, whereby 3'-OH base mispairs and oxoguanine, oxoadenine, or abasic lesions opposite the nick 3'-OH elicited severe decrements in the rate of 5'-adenylylation and relatively modest slowing of the rate of phosphodiester synthesis. The exception was the noncanonical A:oxoG base pair, which Rnl2 accepted as a correctly paired end for rapid sealing. These results underscore (1) how Rnl2 requires proper positioning of the 3'-terminal ribonucleoside at the nick for optimal 5'-adenylylation and (2) the potential for nick-sealing ligases to embed mutations during the repair of oxidative damage.
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27
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Xiang Y, Deng K, Xia H, Yao C, Chen Q, Zhang L, Liu Z, Fu W. Isothermal detection of multiple point mutations by a surface plasmon resonance biosensor with Au nanoparticles enhanced surface-anchored rolling circle amplification. Biosens Bioelectron 2013; 49:442-9. [DOI: 10.1016/j.bios.2013.04.044] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2013] [Revised: 04/23/2013] [Accepted: 04/23/2013] [Indexed: 10/26/2022]
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28
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Shin GW, Chung B, Jung GY, Jung GY. Multiplex ligase-based genotyping methods combined with CE. Electrophoresis 2013; 35:1004-16. [PMID: 24123070 DOI: 10.1002/elps.201300361] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 09/05/2013] [Accepted: 09/05/2013] [Indexed: 12/30/2022]
Abstract
In this genomic era, the ability to assay multiple genomic hot spots that have strong clinical implications is greatly desired. Conventional PCR-based methods suffer from frequent false-positive detections, particularly when a multiplex analysis is desirable. As an alternative to the error-prone conventional methods, multiplex ligase-based genotyping methods combined with CE have a strong potential. In this review, both previously developed methods and emerging methods are described to reveal the specificity, sensitivity, and simplicity of the ligase-based methods. For each step (ligation, amplification, and separation), the principles of several alternative methods are discussed along with their applications to explore the future development of ligase-based diagnostic methods.
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Affiliation(s)
- Gi Won Shin
- Institute of Environmental and Energy Technology, Pohang University of Sciences and Technology, Pohang, Gyeongbuk, Korea
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Smith JH, Beals TP. Detection of nucleic acid targets using ramified rolling circle DNA amplification: a single nucleotide polymorphism assay model. PLoS One 2013; 8:e65053. [PMID: 23724122 PMCID: PMC3664557 DOI: 10.1371/journal.pone.0065053] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Accepted: 04/21/2013] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Isothermal amplification methods provide alternatives to PCR that may be preferable for some nucleic acid target detection tasks. Among current isothermal target detection methods, ramified rolling circle amplification (RAM) of single-stranded DNA circles that are formed by ligation of linear DNA probes (C-probes or padlock probes) offers a unique target detection system by linked primers and a simple amplification system that is unconstrained by the target's sequence context. Earlier implementations of RAM-based target detection were reported to be limited by background noise, due in part to unligated C-probe in the amplification reaction. We show here that a target-detection system using a biotinylated target-capture probe together with automated bead-handling reduces or eliminates background amplification noise. We demonstrate the system's performance by detection of a single-nucleotide polymorphism in human genomic DNA. METHODOLOGY Target detection by RAM entails hybridization and ligation of a C-probe, followed by amplification and RAM signal detection. We evaluated RAM target detection in genomic DNA using recognition of a human Factor V gene single nucleotide polymorphism (G1691A) as a model. Locus-specific C-probes were annealed and ligated to genomic DNAs that represent the 3 possible genotypes at this locus, then ligated C-probes were amplified by real time RAM. The majority of the steps in the assay were performed with a magnetic bead-based chemistry on an automated platform. We show that the specificity of C-probe ligation permits accurate genotyping of this polymorphism. The assay as described here eliminates some of the background noise previously described for C-probe ligation, RAM amplification assays. CONCLUSION The methods and results presented here show that a combination of C-probe detection, automated sample processing, and isothermal RAM amplification provide a practical approach for detecting DNA targets in complex mixtures.
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Affiliation(s)
- James H Smith
- Assay Development Department, Thorne Diagnostics Inc, Beverly, Massachusetts, United States of America.
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Engström A, Zardán Gómez de la Torre T, Strømme M, Nilsson M, Herthnek D. Detection of rifampicin resistance in Mycobacterium tuberculosis by padlock probes and magnetic nanobead-based readout. PLoS One 2013; 8:e62015. [PMID: 23630621 PMCID: PMC3632517 DOI: 10.1371/journal.pone.0062015] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Accepted: 03/17/2013] [Indexed: 01/29/2023] Open
Abstract
Control of the global epidemic tuberculosis is severely hampered by the emergence of drug-resistant Mycobacterium tuberculosis strains. Molecular methods offer a more rapid means of characterizing resistant strains than phenotypic drug susceptibility testing. We have developed a molecular method for detection of rifampicin-resistant M. tuberculosis based on padlock probes and magnetic nanobeads. Padlock probes were designed to target the most common mutations associated with rifampicin resistance in M. tuberculosis, i.e. at codons 516, 526 and 531 in the gene rpoB. For detection of the wild type sequence at all three codons simultaneously, a padlock probe and two gap-fill oligonucleotides were used in a novel assay configuration, requiring three ligation events for circularization. The assay also includes a probe for identification of the M. tuberculosis complex. Circularized probes were amplified by rolling circle amplification. Amplification products were coupled to oligonucleotide-conjugated magnetic nanobeads and detected by measuring the frequency-dependent magnetic response of the beads using a portable AC susceptometer.
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Affiliation(s)
- Anna Engström
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Department of Preparedness, Swedish Institute for Communicable Disease Control, Solna, Sweden
| | - Teresa Zardán Gómez de la Torre
- Department of Engineering Sciences, Division of Nanotechnology and Functional Materials, Uppsala University, The Ångström Laboratory, Uppsala, Sweden
| | - Maria Strømme
- Department of Engineering Sciences, Division of Nanotechnology and Functional Materials, Uppsala University, The Ångström Laboratory, Uppsala, Sweden
| | - Mats Nilsson
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - David Herthnek
- Department of Immunology, Genetics and Pathology, Uppsala University, Science for Life Laboratory, Rudbeck Laboratory, Uppsala, Sweden
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Electrochemiluminescent assay for detection of extremely rare mutations based on ligase reaction and bead enrichment. Anal Biochem 2013; 434:34-8. [DOI: 10.1016/j.ab.2012.10.036] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Revised: 10/24/2012] [Accepted: 10/25/2012] [Indexed: 01/05/2023]
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32
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Liang F, Liu YZ, Zhang P. Universal base analogues and their applications in DNA sequencing technology. RSC Adv 2013. [DOI: 10.1039/c3ra41492b] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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Matthaei H, Wu J, Dal Molin M, Debeljak M, Lingohr P, Katabi N, Klimstra DS, Adsay NV, Eshleman JR, Schulick RD, Kinzler KW, Vogelstein B, Hruban RH, Maitra A. GNAS codon 201 mutations are uncommon in intraductal papillary neoplasms of the bile duct. HPB (Oxford) 2012; 14:677-83. [PMID: 22954004 PMCID: PMC3461374 DOI: 10.1111/j.1477-2574.2012.00504.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND Activating point mutations of GNAS at codon 201 have been detected in approximately two thirds of intraductal papillary mucinous neoplasms (IPMNs) of the pancreas. Intraductal papillary neoplasms of the bile ducts (IPNBs) morphologically resemble pancreatic IPMNs. This study sought to assess the mutational status of GNAS at codon 201 in IPNBs. METHODS Thirty-four patients were included. DNA from microdissected IPNBs was subjected to a polymerase chain reaction and ligation method for the detection of GNAS mutations at codon 201 and of KRAS mutations at codon 12. Mutational status was compared with clinical and pathologic data. RESULTS The IPNBs had a median diameter of 3.5 cm and were located intrahepatically (n= 6), extrahepatically (n= 13), both intra- and extrahepatically (n= 4) or in the gallbladder (intracystic papillary neoplasms, n= 11). Most exhibited pancreatobiliary differentiation (n= 20), high-grade dysplasia (n= 26) and an associated adenocarcinoma (n= 20). Analysis of GNAS codon 201 identified only one mutant sample in a multifocal intestinal subtype intrahepatic IPNB with high-grade dysplasia. Six lesions harboured a KRAS codon 12 mutation. CONCLUSIONS GNAS codon 201 mutations are uncommon in IPNBs, by contrast with pancreatic IPMNs. More comprehensive molecular profiling is needed to uncover the pathways involved in IPNB development.
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Affiliation(s)
- Hanno Matthaei
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of MedicineBaltimore, MD, USA,Department of Surgery, University of BonnBonn, Germany
| | - Jian Wu
- Ludwig Center for Cancer Genetics, Johns Hopkins University School of MedicineBaltimore, MD, USA,State Key Laboratory of Cancer Biology, Cell Engineering Research Center & Department of Cell Biology, The Fourth Military Medical UniversityXi'an, China
| | - Marco Dal Molin
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of MedicineBaltimore, MD, USA
| | - Marija Debeljak
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of MedicineBaltimore, MD, USA
| | | | - Nora Katabi
- Department of Pathology, Memorial Sloan–Kettering Cancer CenterNew York, NY, USA
| | - David S Klimstra
- Department of Pathology, Memorial Sloan–Kettering Cancer CenterNew York, NY, USA
| | - N Volkan Adsay
- Department of Pathology, Emory University School of MedicineAtlanta, GA, USA
| | - James R Eshleman
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of MedicineBaltimore, MD, USA,Department of Oncology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of MedicineBaltimore, MD, USA
| | - Richard D Schulick
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of MedicineBaltimore, MD, USA,Department of Surgery, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of MedicineBaltimore, MD, USA
| | - Kenneth W Kinzler
- Ludwig Center for Cancer Genetics, Johns Hopkins University School of MedicineBaltimore, MD, USA
| | - Bert Vogelstein
- Ludwig Center for Cancer Genetics, Johns Hopkins University School of MedicineBaltimore, MD, USA,Department of Oncology, Howard Hughes Medical Institute, Johns Hopkins University School of MedicineBaltimore, MD, USA
| | - Ralph H Hruban
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of MedicineBaltimore, MD, USA,Department of Oncology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of MedicineBaltimore, MD, USA
| | - Anirban Maitra
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of MedicineBaltimore, MD, USA,Department of Oncology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of MedicineBaltimore, MD, USA
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Wang H, Chen HW, Hupert ML, Chen PC, Datta P, Pittman TL, Goettert J, Murphy MC, Williams D, Barany F, Soper SA. Fully Integrated Thermoplastic Genosensor for the Highly Sensitive Detection and Identification of Multi-Drug-Resistant Tuberculosis. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201200732] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Wang H, Chen HW, Hupert ML, Chen PC, Datta P, Pittman TL, Goettert J, Murphy MC, Williams D, Barany F, Soper SA. Fully integrated thermoplastic genosensor for the highly sensitive detection and identification of multi-drug-resistant tuberculosis. Angew Chem Int Ed Engl 2012; 51:4349-53. [PMID: 22431490 DOI: 10.1002/anie.201200732] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2012] [Indexed: 11/08/2022]
Affiliation(s)
- Hong Wang
- Department of Chemistry and Mechanical Engineering, Louisiana State University, USA
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Study on the relationship between TagSNPs and haplotype of hCHK2 and esophageal cancer in Kazakh and Han in Xinjiang. Contemp Oncol (Pozn) 2012; 16:407-12. [PMID: 23788918 PMCID: PMC3687443 DOI: 10.5114/wo.2012.31769] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2011] [Revised: 04/23/2012] [Accepted: 06/13/2012] [Indexed: 11/21/2022] Open
Abstract
Aim of the study To determine the association of hCHK2 rs2278022, rs2602431, and rs2970077 polymorphisms and haplotypes with susceptibility to esophageal cancer in Kazakh and Han in Xinjiang Uygur Autonomous Region. Material and methods Molecular epidemiology was carried out on 239 cases of esophageal cancer (132 Kazakh, 107 Han) and 513 controls (309 Kazakh, 204 Han) of Xinjiang. Polymorphisms of hCHK2 at rs2278022, rs2602431 and rs2970077 were analyzed by polymerase chain reaction-ligase detection reaction (PCR-LDR). Haplotypes were estimated by the SHEsis software. Statistical differences in genotype/haplotype frequencies, and frequencies between the case group and the control group were estimated. Results 1) No significant difference was observed in the frequency of hCHK2 at rs2278022, rs2602431 and rs2970077 between the cases and controls in Kazakh and Han (P > 0.05); 2) In Kazakh and Han, the distribution of haplotypes was not significantly different between esophageal cancer cases and controls (P > 0.05). Conclusions Polymorphisms of hCHK2 at rs2278022, rs2602431 and rs2970077 and haplotypes are unlikely to be associated with the susceptibility to esophageal cancer in Kazakh and Han.
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Zou B, Ma Y, Wu H, Zhou G. Signal amplification by rolling circle amplification on universal flaps yielded from target-specific invasive reaction. Analyst 2012; 137:729-34. [DOI: 10.1039/c1an15886d] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Luo Y, Gao W, Liu F, Gao Y. Mitochondrial nt3010G-nt3970C haplotype is implicated in high-altitude adaptation of Tibetans. ACTA ACUST UNITED AC 2011; 22:181-90. [DOI: 10.3109/19401736.2011.632771] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Wu J, Matthaei H, Maitra A, Molin MD, Wood LD, Eshleman JR, Goggins M, Canto MI, Schulick RD, Edil BH, Wolfgang CL, Klein AP, Diaz LA, Allen PJ, Schmidt CM, Kinzler KW, Papadopoulos N, Hruban RH, Vogelstein B. Recurrent GNAS mutations define an unexpected pathway for pancreatic cyst development. Sci Transl Med 2011; 3:92ra66. [PMID: 21775669 PMCID: PMC3160649 DOI: 10.1126/scitranslmed.3002543] [Citation(s) in RCA: 573] [Impact Index Per Article: 44.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
More than 2% of the adult U.S. population harbors a pancreatic cyst. These often pose a difficult management problem because conventional criteria cannot always distinguish cysts with malignant potential from those that are innocuous. One of the most common cystic neoplasms of the pancreas, and a bona fide precursor to invasive adenocarcinoma, is called intraductal papillary mucinous neoplasm (IPMN). To help reveal the pathogenesis of these lesions, we purified the DNA from IPMN cyst fluids from 19 patients and searched for mutations in 169 genes commonly altered in human cancers. In addition to the expected KRAS mutations, we identified recurrent mutations at codon 201 of GNAS. A larger number (113) of additional IPMNs were then analyzed to determine the prevalence of KRAS and GNAS mutations. In total, we found that GNAS mutations were present in 66% of IPMNs and that either KRAS or GNAS mutations could be identified in 96%. In eight cases, we could investigate invasive adenocarcinomas that developed in association with IPMNs containing GNAS mutations. In seven of these eight cases, the GNAS mutations present in the IPMNs were also found in the invasive lesion. GNAS mutations were not found in other types of cystic neoplasms of the pancreas or in invasive adenocarcinomas not associated with IPMNs. In addition to defining a new pathway for pancreatic neoplasia, these data suggest that GNAS mutations can inform the diagnosis and management of patients with cystic pancreatic lesions.
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Affiliation(s)
- Jian Wu
- Ludwig Center for Cancer Genetics and Howard Hughes Medical Institutions, Johns Hopkins Kimmel Cancer Center, Baltimore, MD 21231, USA
| | - Hanno Matthaei
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, MD 21231, USA
| | - Anirban Maitra
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, MD 21231, USA
| | - Marco Dal Molin
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, MD 21231, USA
| | - Laura D. Wood
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, MD 21231, USA
| | - James R. Eshleman
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, MD 21231, USA
| | - Michael Goggins
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, MD 21231, USA
| | - Marcia I. Canto
- Department of Surgery, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, MD 21231, USA
| | - Richard D. Schulick
- Department of Surgery, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, MD 21231, USA
| | - Barish H. Edil
- Department of Surgery, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, MD 21231, USA
| | - Christopher L. Wolfgang
- Department of Surgery, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, MD 21231, USA
| | - Alison P. Klein
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, MD 21231, USA
| | - Luis A. Diaz
- Ludwig Center for Cancer Genetics and Howard Hughes Medical Institutions, Johns Hopkins Kimmel Cancer Center, Baltimore, MD 21231, USA
| | - Peter J. Allen
- Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - C. Max Schmidt
- Departments of Surgery, Biochemistry and Molecular Biology, Indiana University, Indianapolis, IN 46202, USA
| | - Kenneth W. Kinzler
- Ludwig Center for Cancer Genetics and Howard Hughes Medical Institutions, Johns Hopkins Kimmel Cancer Center, Baltimore, MD 21231, USA
| | - Nickolas Papadopoulos
- Ludwig Center for Cancer Genetics and Howard Hughes Medical Institutions, Johns Hopkins Kimmel Cancer Center, Baltimore, MD 21231, USA
| | - Ralph H. Hruban
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, MD 21231, USA
| | - Bert Vogelstein
- Ludwig Center for Cancer Genetics and Howard Hughes Medical Institutions, Johns Hopkins Kimmel Cancer Center, Baltimore, MD 21231, USA
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Vinogradova O, Pyshnyi D. Selectivity of Enzymatic Conversion of Oligonucleotide Probes during Nucleotide Polymorphism Analysis of DNA. Acta Naturae 2010; 2:36-53. [PMID: 22649627 PMCID: PMC3347538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The analysis of DNA nucleotide polymorphisms is one of the main goals of DNA diagnostics. DNA-dependent enzymes (DNA polymerases and DNA ligases) are widely used to enhance the sensitivity and reliability of systems intended for the detection of point mutations in genetic material. In this article, we have summarized the data on the selectiveness of DNA-dependent enzymes and on the structural factors in enzymes and DNA which influence the effectiveness of mismatch discrimination during enzymatic conversion of oligonucleotide probes on a DNA template. The data presented characterize the sensitivity of a series of DNA-dependent enzymes that are widely used in the detection of noncomplementary base pairs in nucleic acid substrate complexes. We have analyzed the spatial properties of the enzyme-substrate complexes. These properties are vital for the enzymatic reaction and the recognition of perfect DNA-substrates. We also discuss relevant approaches to increasing the selectivity of enzyme-dependent reactions. These approaches involve the use of modified oligonucleotide probes which "disturb" the native structure of the DNA-substrate complexes.
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Affiliation(s)
- O.A. Vinogradova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division, Russian Academy of Sciences
| | - D.V. Pyshnyi
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division, Russian Academy of Sciences
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Pack SP, Doi A, Choi YS, Kim HB, Makino K. Accurate guanine:cytosine discrimination in T4 DNA ligase-based single nucleotide polymorphism analysis using an oxanine-containing ligation fragment. Anal Biochem 2010; 398:257-9. [DOI: 10.1016/j.ab.2009.11.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2009] [Revised: 11/10/2009] [Accepted: 11/10/2009] [Indexed: 10/20/2022]
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Yi P, Chen Z, Yu L, Zheng Y, Liu G, Xie H, Zhou Y, Zheng X, Han J, Li L. Development of a PCR/LDR/capillary electrophoresis assay with potential for the detection of a beta-thalassemia fetal mutation in maternal plasma. J Matern Fetal Neonatal Med 2010; 23:920-7. [DOI: 10.3109/14767050903387060] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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43
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Ginya H, Matsushita R, Yohda M. Quantification and improvement of error rate during ligase detection reaction. J Biosci Bioeng 2010; 109:202-4. [DOI: 10.1016/j.jbiosc.2009.07.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2009] [Revised: 07/17/2009] [Accepted: 07/17/2009] [Indexed: 11/28/2022]
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Doi A, Pack SP, Makino K. Comparison of the molecular influences of NO-induced lesions in DNA strands on the reactivity of polynucleotide kinases, DNA ligases and DNA polymerases. J Biochem 2010; 147:697-703. [DOI: 10.1093/jb/mvq003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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45
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Association of TNF-A-863 and CGRP979 gene polymorphisms with susceptibility to severe chronic periodontitis in Chinese Han nationality. ACTA ACUST UNITED AC 2009. [DOI: 10.3724/sp.j.1008.2009.00541] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Sinville R, Coyne J, Meagher RJ, Cheng YW, Barany F, Barron A, Soper SA. Ligase detection reaction for the analysis of point mutations using free-solution conjugate electrophoresis in a polymer microfluidic device. Electrophoresis 2009; 29:4751-60. [PMID: 19053073 DOI: 10.1002/elps.200800197] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
We have developed a new method for the analysis of low abundant point mutations in genomic DNA using a combination of an allele-specific ligase detection reaction (LDR) with free-solution conjugate electrophoresis (FSCE) to generate and analyze the genetic products. FSCE eliminates the need for a polymer sieving matrix by conjugating chemically synthesized polyamide "drag-tags" onto the LDR primers. The additional drag of the charge-neutral drag-tag breaks the linear scaling of the charge-to-friction ratio of DNA and enables size-based separations of DNA in free solution using electrophoresis with no sieving matrix. We successfully demonstrate the conjugation of polyamide drag-tags onto a set of four LDR primers designed to probe the K-ras oncogene for mutations highly associated with colorectal cancer, the simultaneous generation of fluorescently labeled LDR/drag-tag conjugate (LDR-dt) products in a multiplexed, single-tube format with mutant:WT ratios as low as 1:100, respectively, and the single-base, high-resolution separation of all four LDR-dt products. Separations were conducted in free solution with no polymer network using both a commercial capillary array electrophoresis (CAE) system and a PMMA microchip replicated via hot-embossing with only a Tris-based running buffer containing additives to suppress the EOF. Typical analysis times for LDR-dt were 11 min using the CAE system and as low as 85 s for the PMMA microchips. With resolution comparable to traditional gel-based CAE, FSCE along with microchip electrophoresis decreased the separation time by more than a factor of 40.
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Affiliation(s)
- Rondedrick Sinville
- Center for BioModular Multi-Scale Microsystems, Department of Chemistry, Louisiana State University, Baton Rouge, LA 70803, USA
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Conze T, Shetye A, Tanaka Y, Gu J, Larsson C, Göransson J, Tavoosidana G, Söderberg O, Nilsson M, Landegren U. Analysis of genes, transcripts, and proteins via DNA ligation. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2009; 2:215-239. [PMID: 20636060 DOI: 10.1146/annurev-anchem-060908-155239] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Analytical reactions in which short DNA strands are used in combination with DNA ligases have proven useful for measuring, decoding, and locating most classes of macromolecules. Given the need to accumulate large amounts of precise molecular information from biological systems in research and in diagnostics, ligation reactions will continue to offer valuable strategies for advanced analytical reactions. Here, we provide a basis for further development of methods by reviewing the history of analytical ligation reactions, discussing the properties of ligation reactions that render them suitable for engineering novel assays, describing a wide range of successful ligase-based assays, and briefly considering future directions.
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Affiliation(s)
- Tim Conze
- Department of Genetics and Pathology, The Rudbeck Lab, Uppsala University, Uppsala, Sweden
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Xu C, Zhou YF, Deng JY, Deng X, Guo YC, Cui ZQ, Zhang ZP, Wei HP, Bi LJ, Zhang XE. On-chip ligation of multiplexing probe-pairs for identifying point mutations out of dense SNP loci. Biosens Bioelectron 2008; 24:818-24. [DOI: 10.1016/j.bios.2008.07.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2008] [Revised: 07/01/2008] [Accepted: 07/02/2008] [Indexed: 11/30/2022]
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Development of multiplex PCR-ligase detection reaction assay for detection of West Nile virus. J Clin Microbiol 2008; 46:2269-79. [PMID: 18495862 DOI: 10.1128/jcm.02335-07] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
We have developed a novel multiplex reverse transcription-PCR ligase detection reaction (RT-PCR/LDR) assay for the detection of West Nile virus (WNV) in both clinical and mosquito pool samples. The method relies on the amplification of three different genomic regions, one in the coding sequence of nonstructural protein NS2a and two in nonstructural protein NS5, to minimize the risk of detection failure due to genetic variation. The sensitivity of the PCR is complemented by the high specificity of the LDR step, and the detection of the LDR products can be achieved with capillary electrophoresis (CE) or a universal DNA microarray. We evaluated the limit of detection by both one-step and two-step multiplex RT-PCR/LDR/CE approaches, which reached, respectively, 0.005 and 0.017 PFU. The assay demonstrated 99% sensitivity when mosquito pool samples were tested and 100% sensitivity with clinical samples when the one-step approach was used. The broad strain coverage was confirmed by testing 34 WNV isolates belonging to lineages 1 and 2, and the high specificity of the assay was determined by testing other flaviviruses, as well as negative mosquito pool and clinical samples. In summary, the multiplex RT-PCR/LDR assay could represent a valuable complement to WNV serological diagnosis, especially in early symptomatic patients. In addition, the multiplexing capacity of the technique, which can be coupled to universal DNA microarray detection, makes it an amenable tool to develop a more comprehensive assay for viral pathogens.
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Socher E, Jarikote DV, Knoll A, Röglin L, Burmeister J, Seitz O. FIT probes: peptide nucleic acid probes with a fluorescent base surrogate enable real-time DNA quantification and single nucleotide polymorphism discovery. Anal Biochem 2008; 375:318-30. [PMID: 18249184 DOI: 10.1016/j.ab.2008.01.009] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2007] [Revised: 01/08/2008] [Accepted: 01/08/2008] [Indexed: 11/19/2022]
Abstract
The ability to accurately quantify specific nucleic acid molecules in complex biomolecule solutions in real time is important in diagnostic and basic research. Here we describe a DNA-PNA (peptide nucleic acid) hybridization assay that allows sensitive quantification of specific nucleic acids in solution and concomitant detection of select single base mutations in resulting DNA-PNA duplexes. The technique employs so-called FIT (forced intercalation) probes in which one base is replaced by a thiazole orange (TO) dye molecule. If a DNA molecule that is complementary to the FIT-PNA molecule (except at the site of the dye) hybridizes to the probe, the TO dye exhibits intense fluorescence because stacking in the duplexes enforces a coplanar arrangement even in the excited state. However, a base mismatch at either position immediately adjacent to the TO dye dramatically decreases fluorescence, presumably because the TO dye has room to undergo torsional motions that lead to rapid depletion of the excited state. Of note, we found that the use of d-ornithine rather than aminoethylglycine as the PNA backbone increases the intensity of fluorescence emitted by matched probe-target duplexes while specificity of fluorescence signaling under nonstringent conditions is also increased. The usefulness of the ornithine-containing FIT probes was demonstrated in the real-time PCR analysis providing a linear measurement range over at least seven orders of magnitude. The analysis of two important single nucleotide polymorphisms (SNPs) in the CFTR gene confirmed the ability of FIT probes to facilitate unambiguous SNP calls for genomic DNA by quantitative PCR.
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Affiliation(s)
- Elke Socher
- Institut für Chemie, Humboldt-Universität zu Berlin, D-12489 Berlin, Germany
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