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Kalendar R, Shustov AV, Schulman AH. Palindromic Sequence-Targeted (PST) PCR, Version 2: An Advanced Method for High-Throughput Targeted Gene Characterization and Transposon Display. FRONTIERS IN PLANT SCIENCE 2021; 12:691940. [PMID: 34239528 PMCID: PMC8258406 DOI: 10.3389/fpls.2021.691940] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 05/20/2021] [Indexed: 05/28/2023]
Abstract
Genome walking (GW), a strategy for capturing previously unsequenced DNA fragments that are in proximity to a known sequence tag, is currently predominantly based on PCR. Recently developed PCR-based methods allow for combining of sequence-specific primers with designed capturing primers capable of annealing to unknown DNA targets, thereby offering the rapidity and effectiveness of PCR. This study presents a methodological improvement to the previously described GW technique known as palindromic sequence-targeted PCR (PST-PCR). Like PST-PCR, this new method (called PST-PCR v.2) relies on targeting of capturing primers to palindromic sequences arbitrarily present in natural DNA templates. PST-PCR v.2 consists of two rounds of PCR. The first round uses a combination of one sequence-specific primer with one capturing (PST) primer. The second round uses a combination of a single (preferred) or two universal primers; one anneals to a 5' tail attached to the sequence-specific primer and the other anneals to a different 5' tail attached to the PST primer. The key advantage of PST-PCR v.2 is the convenience of using a single universal primer with invariable sequences in GW processes involving various templates. The entire procedure takes approximately 2-3 h to produce the amplified PCR fragment, which contains a portion of a template flanked by the sequence-specific and capturing primers. PST-PCR v.2 is highly suitable for simultaneous work with multiple samples. For this reason, PST-PCR v.2 can be applied beyond the classical task of GW for studies in population genetics, in which PST-PCR v.2 is a preferred alternative to amplified fragment length polymorphism (AFLP) or next-generation sequencing. Furthermore, the conditions for PST-PCR v.2 are easier to optimize, as only one sequence-specific primer is used. This reduces non-specific random amplified polymorphic DNA (RAPD)-like amplification and formation of non-templated amplification. Importantly, akin to the previous version, PST-PCR v.2 is not sensitive to template DNA sequence complexity or quality. This study illustrates the utility of PST-PCR v.2 for transposon display (TD), which is a method to characterize inter- or intra-specific variability related to transposon integration sites. The Ac transposon sequence in the maize (Zea mays) genome was used as a sequence tag during the TD procedure to characterize the Ac integration sites.
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Affiliation(s)
- Ruslan Kalendar
- National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
- Viikki Plant Science Centre, HiLIFE Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | | | - Alan H. Schulman
- Viikki Plant Science Centre, HiLIFE Institute of Biotechnology, University of Helsinki, Helsinki, Finland
- Natural Resources Institute Finland (Luke), Helsinki, Finland
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Asif M, Siddiqui HA, Naqvi RZ, Amin I, Asad S, Mukhtar Z, Bashir A, Mansoor S. Development of event-specific detection method for identification of insect resistant NIBGE-1601 cotton harboring double gene Cry1Ac-Cry2Ab construct. Sci Rep 2021; 11:3479. [PMID: 33568702 PMCID: PMC7876094 DOI: 10.1038/s41598-021-82798-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Accepted: 01/07/2021] [Indexed: 11/09/2022] Open
Abstract
Bt cotton expressing Cry1Ac is being cultivated in Pakistan. It has been observed that pink bollworm may have developed resistance against single Bt gene (Cry1Ac). For durable resistance, insect resistant NIBGE-1601 cotton harboring double gene Cry1Ac-Cry2Ab construct was developed. There was a need to characterize NIBGE-1601 event for intellectual property rights protection. The Presence of NIBGE Cry1Ac and NIBGE Cry2Ab genes was checked in NIBGE-1601 cotton plants through PCR, while there was no amplification using primers specific for Monsanto events (MON531, MON15985, MON1445). Using genome walking technology, NIBGE-601 event has been characterized. Event-specific primers of NIBGE-1601 were designed and evaluated to differentiate it from other cotton events mentioned above. NIBGE-1601 event detection primers are highly specific, therefore, can detect NIBGE 1601 event at different conditions using single or multiplex PCR. In the qualitative PCR, using NIBGE-1601 event specific primers, 0.05 ng was the limit of detection for NIBGE-1601double gene cotton genomic DNA. Thus event characterization and development of event-specific diagnostics will help in breeding new cotton varieties resistant to cotton bollworms.
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Affiliation(s)
- Muhammad Asif
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic, Engineering, Faisalabad, Pakistan
| | - Hamid Anees Siddiqui
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic, Engineering, Faisalabad, Pakistan.,Pakistan Institute of Engineering and Applied Sciences, Nilore, Pakistan
| | - Rubab Zahra Naqvi
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic, Engineering, Faisalabad, Pakistan
| | - Imran Amin
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic, Engineering, Faisalabad, Pakistan
| | - Shaheen Asad
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic, Engineering, Faisalabad, Pakistan
| | - Zahid Mukhtar
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic, Engineering, Faisalabad, Pakistan
| | - Aftab Bashir
- Department of Biological Sciences, Forman Christian College, Lahore, Pakistan
| | - Shahid Mansoor
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic, Engineering, Faisalabad, Pakistan.
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Sun X, Zhang J. Bacterial exopolysaccharides: Chemical structures, gene clusters and genetic engineering. Int J Biol Macromol 2021; 173:481-490. [PMID: 33493567 DOI: 10.1016/j.ijbiomac.2021.01.139] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 01/18/2021] [Accepted: 01/19/2021] [Indexed: 11/25/2022]
Abstract
In recent decades, the composition, structure, biosynthesis, and function of bacterial extracellular polysaccharides (EPS) have been extensively studied. EPS are synthesized through different biosynthetic pathways. The genes responsible for EPS synthesis are usually clustered on the genome or large plasmids of bacteria. Generally, different EPS synthesis gene clusters direct the synthesis of EPS with different chemical structures and biological activities. A better understanding of the gene functions involved in EPS biosynthesis is critical for the production of EPS with special biological activities. Genetic engineering methods are usually used to study EPS synthesis related genes. This review organizes the available information on EPS, including their structures, synthesis of related genes, and highlights the research progress of modifying EPS gene clusters through gene-editing methods.
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Affiliation(s)
- Xiaqing Sun
- Center for Molecular Metabolism, Nanjing University of Science & Technology, Nanjing, China
| | - Jianfa Zhang
- Center for Molecular Metabolism, Nanjing University of Science & Technology, Nanjing, China.
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Simple innovative adaptor to improve genome walking with convenient PCR. J Genet Eng Biotechnol 2020; 18:64. [PMID: 33083895 PMCID: PMC7575660 DOI: 10.1186/s43141-020-00082-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 09/30/2020] [Indexed: 11/10/2022]
Abstract
BACKGROUND Various polymerase chain reaction (PCR)-based methods have been applied for the development of genome walking (GW) technique. These methods which could be based on the application of restriction enzymes or primers have various efficiencies to identify the unknown nucleotide sequences. The present study was conducted to design a new innovative double-strand adaptor using MAP30 gene sequence of Momordica charantia plant as a model to improve genome walking with convenient PCR. RESULTS The adaptor was designed using multiple restriction sites of Hind III, BamH I, EcoR I, and Bgl II enzymes with no restriction site in a known sequence of the MAP30 gene. In addition, no modification was required to add phosphate, amine, or other groups to the adaptor, since restriction enzyme digestion of double-strand adaptor provided the 5' phosphate group. Here, preparation of the phosphate group in the genomic DNA of the plant digestion with restriction enzymes was performed followed by ligation with digested adaptor containing 5' phosphate group. CONCLUSION PCR was done to amplify the unknown sequence using MAP30 gene-specific primer and adaptor primer. Results confirmed the ability of the technique for successful identification of the sequence. Consequently, a newly designed adaptor in the developed technique reduced the time and cost of the method compared to the conventional genome walking; also, cloning and culturing of bacterial steps could be eliminated.
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Palindromic sequence-targeted (PST) PCR: a rapid and efficient method for high-throughput gene characterization and genome walking. Sci Rep 2019; 9:17707. [PMID: 31776407 PMCID: PMC6881309 DOI: 10.1038/s41598-019-54168-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 11/07/2019] [Indexed: 11/23/2022] Open
Abstract
Genome walking (GW) refers to the capture and sequencing of unknown regions in a long DNA molecule that are adjacent to a region with a known sequence. A novel PCR-based method, palindromic sequence-targeted PCR (PST-PCR), was developed. PST-PCR is based on a distinctive design of walking primers and special thermal cycling conditions. The walking primers (PST primers) match palindromic sequences (PST sites) that are randomly distributed in natural DNA. The PST primers have palindromic sequences at their 3′-ends. Upstream of the palindromes there is a degenerate sequence (8–12 nucleotides long); defined adapters are present at the 5′-termini. The thermal cycling profile has a linear amplification phase and an exponential amplification phase differing in annealing temperature. Changing the annealing temperature to switch the amplification phases at a defined cycle controls the balance between sensitivity and specificity. In contrast to traditional genome walking methods, PST-PCR is rapid (two to three hours to produce GW fragments) as it uses only one or two PCR rounds. Using PST-PCR, previously unknown regions (the promoter and intron 1) of the VRN1 gene of Timothy-grass (Phleum pratense L.) were captured for sequencing. In our experience, PST-PCR had higher throughput and greater convenience in comparison to other GW methods.
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Tan J, Gong Q, Yu S, Hou Y, Zeng D, Zhu Q, Liu YG. A modified high-efficiency thermal asymmetric interlaced PCR method for amplifying long unknown flanking sequences. J Genet Genomics 2019; 46:363-366. [PMID: 31281029 DOI: 10.1016/j.jgg.2019.05.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 05/27/2019] [Accepted: 05/29/2019] [Indexed: 11/16/2022]
Affiliation(s)
- Jiantao Tan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China; Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Provincial Higher Education Institutions, South China Agricultural University, Guangzhou, 510642, China; College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Qi Gong
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China; Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Provincial Higher Education Institutions, South China Agricultural University, Guangzhou, 510642, China; College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Suize Yu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China; Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Provincial Higher Education Institutions, South China Agricultural University, Guangzhou, 510642, China; College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Yuke Hou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China; Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Provincial Higher Education Institutions, South China Agricultural University, Guangzhou, 510642, China; College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Dongchang Zeng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China; Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Provincial Higher Education Institutions, South China Agricultural University, Guangzhou, 510642, China; College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Qinlong Zhu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China; Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Provincial Higher Education Institutions, South China Agricultural University, Guangzhou, 510642, China; College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China.
| | - Yao-Guang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China; Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Provincial Higher Education Institutions, South China Agricultural University, Guangzhou, 510642, China; College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China.
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Kikkawa E, Tanaka M, Naruse TK, Tsuda TT, Tsuda M, Murata K, Kimura A. Diversity of MHC class I alleles in Spheniscus humboldti. Immunogenetics 2016; 69:113-124. [PMID: 27654451 DOI: 10.1007/s00251-016-0951-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 09/10/2016] [Indexed: 10/21/2022]
Abstract
The major histocompatibility complex locus (MHC) is a gene region related to immune response and exhibits a remarkably great diversity. We deduced that polymorphisms in MHC genes would help to solve several issues on penguins, including classification, phylogenetic relationship, and conservation. This study aimed to elucidate the structure and diversity of the so far unknown MHC class I gene in a penguin species. The structure of an MHC class I gene from the Humboldt penguin (Spheniscus humboldti) was determined by using an inverse PCR method. We designed PCR primers to directly determine nucleotide sequences of PCR products from the MHC class I gene and to obtain recombinant clones for investigating the diversity of the MHC class I gene in Humboldt penguins. A total of 24 MHC class I allele sequences were obtained from 40 individuals. Polymorphisms were mainly found in exons 2 and 3, as expected from the nature of MHC class I genes in vertebrate species including birds and mammals. Phylogenetic analyses of MHC class I alleles have revealed that the Humboldt penguin is closely related to the Red Knot (Calidris canutus) belonging to Charadriiformes.
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Affiliation(s)
- Eri Kikkawa
- College of Bioresource Sciences, Nihon University, Tokyo, Japan.,Department of Molecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Masafumi Tanaka
- Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara, Japan
| | - Taeko K Naruse
- Department of Molecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, Japan.
| | - Tomi T Tsuda
- Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara, Japan.,Human Life Science, Tokushima Bunri University, Tokushima, Japan
| | - Michio Tsuda
- Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara, Japan
| | - Koichi Murata
- College of Bioresource Sciences, Nihon University, Tokyo, Japan
| | - Akinori Kimura
- Department of Molecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, Japan.
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8
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Pradhan B, Sarvilinna N, Matilainen J, Aska E, Sjöberg J, Kauppi L. Detection and screening of chromosomal rearrangements in uterine leiomyomas by long-distance inverse PCR. Genes Chromosomes Cancer 2015; 55:215-26. [PMID: 26608380 DOI: 10.1002/gcc.22317] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2015] [Revised: 09/10/2015] [Accepted: 09/14/2015] [Indexed: 01/08/2023] Open
Abstract
Genome instability is a hallmark of many tumors and recently, next-generation sequencing methods have enabled analyses of tumor genomes at an unprecedented level. Studying rearrangement-prone chromosomal regions (putative "breakpoint hotspots") in detail, however, necessitates molecular assays that can detect de novo DNA fusions arising from these hotspots. Here we demonstrate the utility of a long-distance inverse PCR-based method for the detection and screening of de novo DNA rearrangements in uterine leiomyomas, one of the most common types of human neoplasm. This assay allows in principle any genomic region suspected of instability to be queried for DNA rearrangements originating there. No prior knowledge of the identity of the fusion partner chromosome is needed. We used this method to screen uterine leiomyomas for rearrangements at genomic locations known to be rearrangement-prone in this tumor type: upstream HMGA2 and within RAD51B. We identified a novel DNA rearrangement upstream of HMGA2 that had gone undetected in an earlier whole-genome sequencing study. In more than 30 additional uterine leiomyoma samples, not analyzed by whole-genome sequencing previously, no rearrangements were observed within the 1,107 bp and 1,996 bp assayed in the RAD51B and HMGA2 rearrangement hotspots. Our findings show that long-distance inverse PCR is a robust, sensitive, and cost-effective method for the detection and screening of DNA rearrangements from solid tumors that should be useful for many diagnostic applications.
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Affiliation(s)
- Barun Pradhan
- Genome-Scale Biology Research Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Nanna Sarvilinna
- Genome-Scale Biology Research Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Obstetrics and Gynecology, Helsinki University Hospital, Helsinki, Finland
| | - Juha Matilainen
- Genome-Scale Biology Research Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Elli Aska
- Genome-Scale Biology Research Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Jari Sjöberg
- Obstetrics and Gynecology, Helsinki University Hospital, Helsinki, Finland
| | - Liisa Kauppi
- Genome-Scale Biology Research Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
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Raman P, Grachtchouk V, Lyons RH, Koenig RJ. Identification of the Genomic Insertion Site of the Thyroid Peroxidase Promoter-Cre Recombinase Transgene Using a Novel, Efficient, Next-Generation DNA Sequencing Method. Thyroid 2015; 25:1162-6. [PMID: 26179797 PMCID: PMC4589305 DOI: 10.1089/thy.2015.0215] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
BACKGROUND It can be useful to know the transgene insertion site in transgenic mice for a variety of reasons, but determining the insertion site generally is a time consuming, expensive, and laborious task. METHODS A simple method is presented to determine transgene insertion sites that combines the enrichment of a sequencing library by polymerase chain reaction (PCR) for sequences containing the transgene, followed by next-generation sequencing of the enriched library. This method was applied to determine the site of integration of the thyroid peroxidase promoter-Cre recombinase mouse transgene that is commonly used to create thyroid-specific gene deletions. RESULTS The insertion site was found to be between bp 12,372,316 and 12,372,324 on mouse chromosome 9, with the nearest characterized genes being Cntn5 and Jrkl, ∼1.5 and 0.9 Mbp from the transgene, respectively. One advantage of knowing a transgene insertion site is that it facilitates distinguishing hemizygous from homozygous transgenic mice. Although this can be accomplished by real-time quantitative PCR, the expected Ct difference is only one cycle, which is challenging to assess accurately. Therefore, the transgene insertion site information was used to develop a 3-primer qualitative PCR assay that readily distinguishes wild type, hemizygous, and homozygous TPO-Cre mice based upon size differences of the wild type and transgenic allele PCR products. CONCLUSIONS Identification of the genomic insertion site of the thyroid peroxidase promoter-Cre mouse transgene should facilitate the use of these mice in studies of thyroid biology.
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Affiliation(s)
- Priyadarshini Raman
- 1 Department of Internal Medicine, Division of Metabolism, Endocrinology, and Diabetes, University of Michigan , Ann Arbor, Michigan
| | - Vladimir Grachtchouk
- 1 Department of Internal Medicine, Division of Metabolism, Endocrinology, and Diabetes, University of Michigan , Ann Arbor, Michigan
| | - Robert H Lyons
- 2 Department of Biological Chemistry, University of Michigan , Ann Arbor, Michigan
| | - Ronald J Koenig
- 1 Department of Internal Medicine, Division of Metabolism, Endocrinology, and Diabetes, University of Michigan , Ann Arbor, Michigan
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Jakobi ML, Stumpp SN, Stiesch M, Eberhard J, Heuer W. The Peri-Implant and Periodontal Microbiota in Patients with and without Clinical Signs of Inflammation. Dent J (Basel) 2015; 3:24-42. [PMID: 29567923 PMCID: PMC5851201 DOI: 10.3390/dj3020024] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 03/25/2015] [Indexed: 11/29/2022] Open
Abstract
Late implant failures, caused by the inflammation of surrounding tissues are a problem in implant dentistry. The path of bacterial transmission from teeth to implants is not completely understood. Therefore, the purpose of this study was to analyze intraindividual bacterial transmission characterizing subgingival microbiomes in teeth and implants, both in healthy subjects and in those with signs of periodontitis or peri-implantitis. Samples of peri-implant and dental sulcus fluid were collected. To identify the predominant microbiota, amplified fragments of bacterial 16S rRNA gene were separated by single strand conformation polymorphism analysis, sequenced and taxonomically classified. A total of 25 different predominant genera were found in the diseased group and 14 genera in the healthy group. Species richness did not differ significantly between implants, neighboring teeth and teeth with largest probing depth in the diseased group. Additionally, no differences between teeth and implants in the healthy group were detected. In contrast, microbial diversity varied between the different sampling points. Species richness is similar in healthy and diseased sites, but the composition of the bacterial community differed within the individual subjects. The underlying analyses strongly suggest that complete transmission from neighboring teeth to implants is unlikely.
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Affiliation(s)
| | - Sascha Nico Stumpp
- Department of Prosthetic Dentistry and Biomedical Materials Science, Hannover Medical School, Carl-Neuberg-Strasse 1, Hannover 30625, Germany.
| | - Meike Stiesch
- Department of Prosthetic Dentistry and Biomedical Materials Science, Hannover Medical School, Carl-Neuberg-Strasse 1, Hannover 30625, Germany.
| | - Jörg Eberhard
- Department of Prosthetic Dentistry and Biomedical Materials Science, Hannover Medical School, Carl-Neuberg-Strasse 1, Hannover 30625, Germany.
| | - Wieland Heuer
- Department of Prosthetic Dentistry and Biomedical Materials Science, Hannover Medical School, Carl-Neuberg-Strasse 1, Hannover 30625, Germany.
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Abstract
Identification of unknown sequences that flank known sequences of interest requires PCR amplification of DNA fragments that contain the junction between the known and unknown flanking sequences. Since amplified products often contain a mixture of specific and nonspecific products, the quick and clean (QC) cloning procedure was developed to clone specific products only. QC cloning is a ligation-independent cloning procedure that relies on the exonuclease activity of T4 DNA polymerase to generate single-stranded extensions at the ends of the vector and insert. A specific feature of QC cloning is the use of vectors that contain a sequence called catching sequence that allows cloning specific products only. QC cloning is performed by a one-pot incubation of insert and vector in the presence of T4 DNA polymerase at room temperature for 10 min followed by direct transformation of the incubation mix in chemo-competent Escherichia coli cells.
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12
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Lin J, Zhang Q, Zhu LQ, Yu QH, Yang Q. The copy number and integration site analysis of IGF-1 transgenic goat. Int J Mol Med 2014; 34:900-10. [PMID: 25018125 DOI: 10.3892/ijmm.2014.1841] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2014] [Accepted: 06/12/2014] [Indexed: 11/05/2022] Open
Abstract
Transgenic animals have been used previously to study gene function, produce important proteins, and generate models for the study of human diseases. As the number of transgenic species increases, reliable detection and molecular characterization of integration sites and copy number are crucial for confirming transgene expression and genetic stability, as well as for safety evaluation and to meet commercial demands. In this study, we generated four transgenic goats by somatic cell nuclear transfer (SCNT). After birth, the cloned goat contained transferred insulin-like growth factor I (IGF-1) gene was initially confirmed using a polymerase chain reaction (PCR)‑based method. The four cloned goats were identified as IGF-1 transgenic goats by southern blotting. The number of copies of the IGF-1 gene in each of the transgenic goats was determined. Additionally, four integration sites of the transgene in the transgenic goats with a modified thermal asymmetric interlaced (TAIL)-PCR method were identified. The four different integration sites were located on chromosomes 2, 11, 16 and 18. The present study identified the copy number and integration sites using quantitative PCR (qPCR) and TAIL-PCR, enabling the bio-safety evaluation of the transgenic goats.
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Affiliation(s)
- Jian Lin
- Key Laboratory of Animal Physiology and Biochemistry, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, P.R. China
| | - Qiang Zhang
- Key Laboratory of Animal Physiology and Biochemistry, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, P.R. China
| | - Li Q Zhu
- Key Laboratory of Animal Physiology and Biochemistry, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, P.R. China
| | - Qing H Yu
- Key Laboratory of Animal Physiology and Biochemistry, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, P.R. China
| | - Qian Yang
- Key Laboratory of Animal Physiology and Biochemistry, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, P.R. China
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Atanassov I, Stefanova K, Tomova I, Kamburova M. Seamless GFP and GFP-Amylase Cloning in Gateway Shuttle Vector, Expression of the Recombinant Proteins inE. ColiandBacillus Megateriumand Assessment of the GFP-Amylase Thermostability. BIOTECHNOL BIOTEC EQ 2014. [DOI: 10.5504/bbeq.2013.0079] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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14
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Liu T, Fang Y, Yao W, Guan Q, Bai G, Jing Z. A tailing genome walking method suitable for genomes with high local GC content. Anal Biochem 2013; 441:101-3. [PMID: 23831478 DOI: 10.1016/j.ab.2013.06.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Revised: 06/13/2013] [Accepted: 06/25/2013] [Indexed: 11/30/2022]
Abstract
The tailing genome walking strategies are simple and efficient. However, they sometimes can be restricted due to the low stringency of homo-oligomeric primers. Here we modified their conventional tailing step by adding polythymidine and polyguanine to the target single-stranded DNA (ssDNA). The tailed ssDNA was then amplified exponentially with a specific primer in the known region and a primer comprising 5' polycytosine and 3' polyadenosine. The successful application of this novel method for identifying integration sites mediated by φC31 integrase in goat genome indicates that the method is more suitable for genomes with high complexity and local GC content.
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Affiliation(s)
- Taian Liu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Public Health of Agricultural Ministry, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China
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15
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Vila M, Díaz-Santos E, de la Vega M, Rodríguez H, Vargas A, León R. Promoter trapping in microalgae using the antibiotic paromomycin as selective agent. Mar Drugs 2012; 10:2749-65. [PMID: 23211713 PMCID: PMC3528124 DOI: 10.3390/md10122749] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Revised: 10/12/2012] [Accepted: 11/15/2012] [Indexed: 11/16/2022] Open
Abstract
The lack of highly active endogenous promoters to drive the expression of transgenes is one of the main drawbacks to achieving efficient transformation of many microalgal species. Using the model chlorophyte Chlamydomonas reinhardtii and the paromomycin resistance APHVIII gene from Streptomyces rimosus as a marker, we have demonstrated that random insertion of the promoterless marker gene and subsequent isolation of the most robust transformants allows for the identification of novel strong promoter sequences in microalgae. Digestion of the genomic DNA with an enzyme that has a unique restriction site inside the marker gene and a high number of target sites in the genome of the microalga, followed by inverse PCR, allows for easy determination of the genomic region, which precedes the APHVIII marker gene. In most of the transformants analyzed, the marker gene is inserted in intragenic regions and its expression relies on its adequate insertion in frame with native genes. As an example, one of the new promoters identified was used to direct the expression of the APHVIII marker gene in C. reinhardtii, showing high transformation efficiencies.
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Affiliation(s)
- Marta Vila
- Biochemistry Laboratory, Experimental Sciences Faculty, University of Huelva, Huelva 27071, Spain
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16
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Abstract
As the number of transgenic livestock increases, reliable detection and molecular characterization of transgene integration sites and copy number are crucial not only for interpreting the relationship between the integration site and the specific phenotype but also for commercial and economic demands. However, the ability of conventional PCR techniques to detect incomplete and multiple integration events is limited, making it technically challenging to characterize transgenes. Next-generation sequencing has enabled cost-effective, routine and widespread high-throughput genomic analysis. Here, we demonstrate the use of next-generation sequencing to extensively characterize cattle harboring a 150-kb human lactoferrin transgene that was initially analyzed by chromosome walking without success. Using this approach, the sites upstream and downstream of the target gene integration site in the host genome were identified at the single nucleotide level. The sequencing result was verified by event-specific PCR for the integration sites and FISH for the chromosomal location. Sequencing depth analysis revealed that multiple copies of the incomplete target gene and the vector backbone were present in the host genome. Upon integration, complex recombination was also observed between the target gene and the vector backbone. These findings indicate that next-generation sequencing is a reliable and accurate approach for the molecular characterization of the transgene sequence, integration sites and copy number in transgenic species.
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17
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Genome walking by next generation sequencing approaches. BIOLOGY 2012; 1:495-507. [PMID: 24832505 PMCID: PMC4009806 DOI: 10.3390/biology1030495] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Revised: 08/31/2012] [Accepted: 09/25/2012] [Indexed: 01/07/2023]
Abstract
Genome Walking (GW) comprises a number of PCR-based methods for the identification of nucleotide sequences flanking known regions. The different methods have been used for several purposes: from de novo sequencing, useful for the identification of unknown regions, to the characterization of insertion sites for viruses and transposons. In the latter cases Genome Walking methods have been recently boosted by coupling to Next Generation Sequencing technologies. This review will focus on the development of several protocols for the application of Next Generation Sequencing (NGS) technologies to GW, which have been developed in the course of analysis of insertional libraries. These analyses find broad application in protocols for functional genomics and gene therapy. Thanks to the application of NGS technologies, the original vision of GW as a procedure for walking along an unknown genome is now changing into the possibility of observing the parallel marching of hundreds of thousands of primers across the borders of inserted DNA molecules in host genomes.
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Spalinskas R, Van den Bulcke M, Van den Eede G, Milcamps A. LT-RADE: An Efficient User-Friendly Genome Walking Method Applied to the Molecular Characterization of the Insertion Site of Genetically Modified Maize MON810 and Rice LLRICE62. FOOD ANAL METHOD 2012. [DOI: 10.1007/s12161-012-9438-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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19
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Wang Z, Ye S, Li J, Zheng B, Bao M, Ning G. Fusion primer and nested integrated PCR (FPNI-PCR): a new high-efficiency strategy for rapid chromosome walking or flanking sequence cloning. BMC Biotechnol 2011; 11:109. [PMID: 22093809 PMCID: PMC3239319 DOI: 10.1186/1472-6750-11-109] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2011] [Accepted: 11/17/2011] [Indexed: 11/27/2022] Open
Abstract
Background The advent of genomics-based technologies has revolutionized many fields of biological enquiry. However, chromosome walking or flanking sequence cloning is still a necessary and important procedure to determining gene structure. Such methods are used to identify T-DNA insertion sites and so are especially relevant for organisms where large T-DNA insertion libraries have been created, such as rice and Arabidopsis. The currently available methods for flanking sequence cloning, including the popular TAIL-PCR technique, are relatively laborious and slow. Results Here, we report a simple and effective fusion primer and nested integrated PCR method (FPNI-PCR) for the identification and cloning of unknown genomic regions flanked known sequences. In brief, a set of universal primers was designed that consisted of various 15-16 base arbitrary degenerate oligonucleotides. These arbitrary degenerate primers were fused to the 3' end of an adaptor oligonucleotide which provided a known sequence without degenerate nucleotides, thereby forming the fusion primers (FPs). These fusion primers are employed in the first step of an integrated nested PCR strategy which defines the overall FPNI-PCR protocol. In order to demonstrate the efficacy of this novel strategy, we have successfully used it to isolate multiple genomic sequences namely, 21 orthologs of genes in various species of Rosaceace, 4 MYB genes of Rosa rugosa, 3 promoters of transcription factors of Petunia hybrida, and 4 flanking sequences of T-DNA insertion sites in transgenic tobacco lines and 6 specific genes from sequenced genome of rice and Arabidopsis. Conclusions The successful amplification of target products through FPNI-PCR verified that this novel strategy is an effective, low cost and simple procedure. Furthermore, FPNI-PCR represents a more sensitive, rapid and accurate technique than the established TAIL-PCR and hiTAIL-PCR procedures.
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Affiliation(s)
- Zhen Wang
- Key laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, PR China
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20
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A novel method to perform genomic walks using a combination of single strand DNA circularization and rolling circle amplification. J Microbiol Methods 2011; 87:38-43. [DOI: 10.1016/j.mimet.2011.07.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2011] [Revised: 07/04/2011] [Accepted: 07/05/2011] [Indexed: 11/20/2022]
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21
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Abstract
Genome walking is a molecular procedure for the direct identification of nucleotide sequences from purified genomes. The only requirement is the availability of a known nucleotide sequence from which to start. Several genome walking methods have been developed in the last 20 years, with continuous improvements added to the first basic strategies, including the recent coupling with next generation sequencing technologies. This review focuses on the use of genome walking strategies in several aspects of the study of eukaryotic genomes. In a first part, the analysis of the numerous strategies available is reported. The technical aspects involved in genome walking are particularly intriguing, also because they represent the synthesis of the talent, the fantasy and the intelligence of several scientists. Applications in which genome walking can be employed are systematically examined in the second part of the review, showing the large potentiality of this technique, including not only the simple identification of nucleotide sequences but also the analysis of large collections of mutants obtained from the insertion of DNA of viral origin, transposons and transfer DNA (T-DNA) constructs. The enormous amount of data obtained indicates that genome walking, with its large range of applicability, multiplicity of strategies and recent developments, will continue to have much to offer for the rapid identification of unknown sequences in several fields of genomic research.
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Affiliation(s)
- Claudia Leoni
- Department of Biochemistry and Molecular Biology, University of Bari, Bari, Italy
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22
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Ménoret S, Tesson L, Remy S, Usal C, Iscache AL, Thynard R, Nguyen TH, Anegon I. Transgenesis and genome analysis, Nantes, France, June 6th 2011. Transgenic Res 2011. [PMCID: PMC7101805 DOI: 10.1007/s11248-011-9541-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Séverine Ménoret
- Platform Transgenic Rats Nantes IBiSA, Nantes, France
- CHU Nantes, Nantes, France
- Université de Nantes, Nantes, France
- CNRS, Nantes, France
| | - Laurent Tesson
- Platform Transgenic Rats Nantes IBiSA, Nantes, France
- CHU Nantes, Nantes, France
- Université de Nantes, Nantes, France
- INSERM UMR 643, 44093 Nantes, France
| | - Séverine Remy
- Platform Transgenic Rats Nantes IBiSA, Nantes, France
- CHU Nantes, Nantes, France
- Université de Nantes, Nantes, France
- INSERM UMR 643, 44093 Nantes, France
| | - Claire Usal
- Platform Transgenic Rats Nantes IBiSA, Nantes, France
- CHU Nantes, Nantes, France
- Université de Nantes, Nantes, France
- INSERM UMR 643, 44093 Nantes, France
| | - Anne-Laure Iscache
- Platform Transgenic Rats Nantes IBiSA, Nantes, France
- CHU Nantes, Nantes, France
- Université de Nantes, Nantes, France
- INSERM UMR 643, 44093 Nantes, France
| | - Reynald Thynard
- Platform Transgenic Rats Nantes IBiSA, Nantes, France
- CHU Nantes, Nantes, France
- Université de Nantes, Nantes, France
- INSERM UMR 643, 44093 Nantes, France
| | | | - Ignacio Anegon
- Platform Transgenic Rats Nantes IBiSA, Nantes, France
- CHU Nantes, Nantes, France
- Université de Nantes, Nantes, France
- CNRS, Nantes, France
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Park DJ. Lariat-dependent nested PCR for flanking sequence determination. Methods Mol Biol 2011; 687:43-55. [PMID: 20967600 DOI: 10.1007/978-1-60761-944-4_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
Methods detailed in this chapter relate to the use of Lariat-dependent Nested (LaNe) PCR to characterize unknown RNA or DNA sequence flanking known regions. A multitude of approaches designed to determine flanking sequences have been described in the literature. Variously, problems related to these approaches include lack of resolution or failure, depending on experimental context, and complex handling. LaNe-based methods are designed to harness "two-sided" gene-specific PCR with the option of nesting but without the requirement for inefficient and involved enzyme preprocessing steps.
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Affiliation(s)
- Daniel J Park
- Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Parkville, Victoria, Australia.
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Schneider B, Drexler HG, Macleod RAF. Molecular breakpoint analysis of chromosome translocations in cancer cell lines by Long Distance Inverse-PCR. Methods Mol Biol 2011; 731:321-332. [PMID: 21516418 DOI: 10.1007/978-1-61779-080-5_26] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
With conventional cytogenetic screening by fluorescence in situ hybridization (FISH) using genomic tilepath clones, identification of genes in oncogenic chromosome translocations is often laborious, notably if the region of interest is gene-dense. Conventional molecular methods for partner identification may also suffer severe limitations; for instance, genomic PCR screening requires prior knowledge of both sets of breakpoints, while rapid amplification of cDNA ends (RACE) is not only limited to translocations causing mRNA fusion, but also fails to provide potentially relevant breakpoint data. With Long Distance Inverse (LDI)-PCR, however, it is theoretically possible to identify unknown translocation partners and to map the breakpoints down to the base pair level. Implementing LDI-PCR only requires approximate sequence information on one partner, rendering it ideal for use in combination with frontline FISH analysis. The protocol described here has been tuned for use by those wishing to identify new cancer genes in tumor cell lines.
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Affiliation(s)
- Björn Schneider
- DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany.
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25
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Gröning JAD, Tischler D, Kaschabek SR, Schlömann M. Optimization of a genome-walking method to suit GC-rich template DNA from biotechnological relevant Actinobacteria. J Basic Microbiol 2010; 50:499-502. [PMID: 20806255 DOI: 10.1002/jobm.201000032] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
SiteFinding-PCR has been recently reported to be a useful technique in order to identify unknown DNA fragments located adjacent to available sequences. However, this method has so far only been applied to few DNA sources including plants, samples from bioleaching communities, and a Pseudomonas strain. In order to complete the sequence information of two gene clusters in Gram-positive rhodococci the original protocol was applied yielding amplicons of insufficient size. The binding site of the previously published SiteFinder-2 oligo proved to be unsuitable for Rhodococcus and other members of the Actinobacteria since the binding motif occurred too frequently. Available genome sequences of different Actinobacteria were analysed and the binding site of the SiteFinder oligo modified. Moreover, PCR conditions were adapted to the high GC content of the template DNA allowing the successful adaptation of this method to two members of the Actinobacteria.
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Two-color, 30 second microwave-accelerated Metal-Enhanced Fluorescence DNA assays: a new Rapid Catch and Signal (RCS) technology. J Immunol Methods 2010; 366:1-7. [PMID: 21147112 DOI: 10.1016/j.jim.2010.12.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2010] [Revised: 11/30/2010] [Accepted: 12/02/2010] [Indexed: 11/20/2022]
Abstract
For analyses of DNA fragment sequences in solution we introduce a 2-color DNA assay, utilizing a combination of the Metal-Enhanced Fluorescence (MEF) effect and microwave-accelerated DNA hybridization. The assay is based on a new "Catch and Signal" technology, i.e. the simultaneous specific recognition of two target DNA sequences in one well by complementary anchor-ssDNAs, attached to silver island films (SiFs). It is shown that fluorescent labels (Alexa 488 and Alexa 594), covalently attached to ssDNA fragments, play the role of biosensor recognition probes, demonstrating strong response upon DNA hybridization, locating fluorophores in close proximity to silver NPs, which is ideal for MEF. Subsequently the emission dramatically increases, while the excited state lifetime decreases. It is also shown that 30s microwave irradiation of wells, containing DNA molecules, considerably (~1000-fold) speeds up the highly selective hybridization of DNA fragments at ambient temperature. The 2-color "Catch and Signal" DNA assay platform can radically expedite quantitative analysis of genome DNA sequences, creating a simple and fast bio-medical platform for nucleic acid analysis.
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Bae JH, Sohn JH. Template-blocking PCR: an advanced PCR technique for genome walking. Anal Biochem 2009; 398:112-6. [PMID: 19903447 DOI: 10.1016/j.ab.2009.11.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2009] [Revised: 11/03/2009] [Accepted: 11/03/2009] [Indexed: 12/12/2022]
Abstract
This article describes the development of an improved method for the isolation of genomic fragments adjacent to a known DNA sequence based on a cassette ligation-mediated polymerase chain reaction (PCR) technique. To reduce the nonspecific amplification of PCR-based genome walking, the 3' ends of the restriction enzyme-digested genomic DNA fragments were blocked with dideoxynucleoside triphosphate (ddNTP) and ligated with properly designed cassettes. The modified genomic DNA fragments flanked with cassettes were used as a template for the amplification of a target gene with a gene-specific primer (GSP) and a cassette primer (CP). The ddNTP blocking of the genomic DNA ends significantly reduced the nonspecific amplification and resulted in a simple and rapid walking along the genome. The efficiency of the template-blocking PCR method was confirmed by a carefully designed control experiment. The method was successfully applied for the cloning of the PGK1 promoter from Pichia ciferrii and two novel cellulase genes from Penicillium sp.
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Affiliation(s)
- Jung-Hoon Bae
- Industrial Biotechnology and Bioenergy Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Yusong, Daejeon 305-333, Republic of Korea
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