The Experts below are selected from a list of 231 Experts worldwide ranked by ideXlab platform
Mel Silverman - One of the best experts on this subject based on the ideXlab platform.
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Description of a PCR-based technique for DNA Splicing and mutagenesis by producing 5' overhangs with run through stop DNA synthesis utilizing Ara-C
BMC Biotechnology, 2005Co-Authors: Menachem Ailenberg, Neil M. Goldenberg, Mel SilvermanAbstract:Background Splicing of DNA molecules is an important task in molecular biology that facilitates cloning, mutagenesis and creation of chimeric genes. Mutagenesis and DNA Splicing techniques exist, some requiring restriction enzymes, and others utilize staggered reannealing approaches. Results A method for DNA Splicing and mutagenesis without restriction enzymes is described. The method is based on mild template-dependent polymerization arrest with two molecules of cytosine arabinose (Ara-C) incorporated into PCR primers. Two rounds of PCR are employed: the first PCR produces 5' overhangs that are utilized for DNA Splicing. The second PCR is based on polymerization running through the Ara-C molecules to produce the desired final product. To illustrate application of the run through stop mutagenesis and DNA Splicing technique, we have carried out Splicing of two segments of the human cofilin 1 gene and introduced a mutational deletion into the product. Conclusion We have demonstrated the utility of a new PCR-based method for carrying out DNA Splicing and mutagenesis by incorporating Ara-C into the PCR primers.
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Description of a PCR-based technique for DNA Splicing and mutagenesis by producing 5' overhangs with run through stop DNA synthesis utilizing Ara-C
BMC biotechnology, 2005Co-Authors: Menachem Ailenberg, Neil M. Goldenberg, Mel SilvermanAbstract:Background Splicing of DNA molecules is an important task in molecular biology that facilitates cloning, mutagenesis and creation of chimeric genes. Mutagenesis and DNA Splicing techniques exist, some requiring restriction enzymes, and others utilize staggered reannealing approaches.
Menachem Ailenberg - One of the best experts on this subject based on the ideXlab platform.
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Description of a PCR-based technique for DNA Splicing and mutagenesis by producing 5' overhangs with run through stop DNA synthesis utilizing Ara-C
BMC Biotechnology, 2005Co-Authors: Menachem Ailenberg, Neil M. Goldenberg, Mel SilvermanAbstract:Background Splicing of DNA molecules is an important task in molecular biology that facilitates cloning, mutagenesis and creation of chimeric genes. Mutagenesis and DNA Splicing techniques exist, some requiring restriction enzymes, and others utilize staggered reannealing approaches. Results A method for DNA Splicing and mutagenesis without restriction enzymes is described. The method is based on mild template-dependent polymerization arrest with two molecules of cytosine arabinose (Ara-C) incorporated into PCR primers. Two rounds of PCR are employed: the first PCR produces 5' overhangs that are utilized for DNA Splicing. The second PCR is based on polymerization running through the Ara-C molecules to produce the desired final product. To illustrate application of the run through stop mutagenesis and DNA Splicing technique, we have carried out Splicing of two segments of the human cofilin 1 gene and introduced a mutational deletion into the product. Conclusion We have demonstrated the utility of a new PCR-based method for carrying out DNA Splicing and mutagenesis by incorporating Ara-C into the PCR primers.
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Description of a PCR-based technique for DNA Splicing and mutagenesis by producing 5' overhangs with run through stop DNA synthesis utilizing Ara-C
BMC biotechnology, 2005Co-Authors: Menachem Ailenberg, Neil M. Goldenberg, Mel SilvermanAbstract:Background Splicing of DNA molecules is an important task in molecular biology that facilitates cloning, mutagenesis and creation of chimeric genes. Mutagenesis and DNA Splicing techniques exist, some requiring restriction enzymes, and others utilize staggered reannealing approaches.
Neil M. Goldenberg - One of the best experts on this subject based on the ideXlab platform.
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Description of a PCR-based technique for DNA Splicing and mutagenesis by producing 5' overhangs with run through stop DNA synthesis utilizing Ara-C
BMC Biotechnology, 2005Co-Authors: Menachem Ailenberg, Neil M. Goldenberg, Mel SilvermanAbstract:Background Splicing of DNA molecules is an important task in molecular biology that facilitates cloning, mutagenesis and creation of chimeric genes. Mutagenesis and DNA Splicing techniques exist, some requiring restriction enzymes, and others utilize staggered reannealing approaches. Results A method for DNA Splicing and mutagenesis without restriction enzymes is described. The method is based on mild template-dependent polymerization arrest with two molecules of cytosine arabinose (Ara-C) incorporated into PCR primers. Two rounds of PCR are employed: the first PCR produces 5' overhangs that are utilized for DNA Splicing. The second PCR is based on polymerization running through the Ara-C molecules to produce the desired final product. To illustrate application of the run through stop mutagenesis and DNA Splicing technique, we have carried out Splicing of two segments of the human cofilin 1 gene and introduced a mutational deletion into the product. Conclusion We have demonstrated the utility of a new PCR-based method for carrying out DNA Splicing and mutagenesis by incorporating Ara-C into the PCR primers.
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Description of a PCR-based technique for DNA Splicing and mutagenesis by producing 5' overhangs with run through stop DNA synthesis utilizing Ara-C
BMC biotechnology, 2005Co-Authors: Menachem Ailenberg, Neil M. Goldenberg, Mel SilvermanAbstract:Background Splicing of DNA molecules is an important task in molecular biology that facilitates cloning, mutagenesis and creation of chimeric genes. Mutagenesis and DNA Splicing techniques exist, some requiring restriction enzymes, and others utilize staggered reannealing approaches.
Yuhani Yusof - One of the best experts on this subject based on the ideXlab platform.
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Differentiating the Persistency and Permanency of Some Two Stages DNA Splicing Language via Yusof-Goode (Y-G) Approach
Journal of Physics: Conference Series, 2017Co-Authors: Mohammad Hassan Mudaber, Yuhani Yusof, Mohd Sham MohamadAbstract:Predicting the existence of restriction enzymes sequences on the recombinant DNA fragments, after accomplishing the manipulating reaction, via mathematical approach is considered as a convenient way in terms of DNA recombination. In terms of mathematics, for this characteristic of the recombinant DNA strands, which involve the recognition sites of restriction enzymes, is called persistent and permanent. Normally differentiating the persistency and permanency of two stages recombinant DNA strands using wet-lab experiment is expensive and time-consuming due to running the experiment at two stages as well as adding more restriction enzymes on the reaction. Therefore, in this research, by using Yusof-Goode (Y-G) model the difference between persistent and permanent Splicing language of some two stages is investigated. Two theorems were provided, which show the persistency and non-permanency of two stages DNA Splicing language.
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MODELLING OF TWO STAGES DNA Splicing LANGUAGES ON DE BRUIJN GRAPH
Jurnal Teknologi, 2015Co-Authors: Mohammad Hassan Mudaber, Yuhani Yusof, Mohd Sham Mohamad, Aizi Nor Mazila Ramli, Wen Li LimAbstract:Finding the sequence of the genome from its compositions as well as a mathematical graph is the most interesting topic in a field of DNA molecular. Since lack of technology is the big obstacle that biologists are facing to read a long sequence of the genome from beginning up to the end, therefore finding the compositions of the genome having very long sequence and also its description via de Bruijn graph is challenging or even impossible. In this paper, Yusof-Goode (Y-G) approach is used to generate the DNA Splicing languages based on cutting sites of initial strings (one or two cutting sites) and crossing and contexts factors of restriction enzymes. The two short sequences of DNA (8bp) and two restriction enzymes are considered to create a connection between mathematics and DNA molecular. This relation will be presented as de Bruijn graph so that every edge of the de Bruijn graph gives a k-mer composition of DNA molecule and also each path of the de Bruijn graph gives a DNA sequence and vice-versa. Besides, the persistency and permanency of two stages DNA Splicing languages can be predicted using this model.
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PERSISTENCY AND PERMANENCY OF TWO STAGES Splicing LANGUAGES VIA YUSOF-GOODE APPROACH: TWO INITIAL STRINGS AND TWO RULES
Jurnal Teknologi, 2015Co-Authors: Mohammad Hassan Mudaber, Yuhani Yusof, Mohd Sham Mohamad, Wen Li LimAbstract:The notation of representing restriction enzymes in the form of double-triple in order to formulate Yusof-Goode (Y-G) Splicing system was mathematically proposed by Yusof in 2012. The aim of introducing Y-G Splicing system was to study the process of recombinant deoxyribonucleic acid or DNA strand in a translucent way. In real situation, when the recombination action occurs, the recombinant DNA strands which will arise often contain the patterns of the restriction enzymes. Persistency and permanency are two properties of Splicing system, which show whether the recombinant DNA strands will be split by the existence of restrictions enzymes or not if the reaction goes to the second stage. In this research, the persistency and permanency of two stages Splicing languages according to the number of cutting sites of initial strings as well as crossing sites and context factors of Splicing rules are investigated. Therefore, a Y-G Splicing system consisting of two initial strings (with two cutting sites) and two rules is used to present the above properties of two stages DNA Splicing languages.
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Molecular aspects of DNA Splicing system
2015Co-Authors: Yuhani Yusof, Wen Li Lim, T. Elizabeth Goode, Nor Haniza Sarmin, Fong Wan Heng, Mohd Firdaus Abdul WahabAbstract:The pioneer model of deoxyribonucleic acid (DNA) Splicing system in a framework of Formal Language Theory was introduced by Head that led to the existence of other models of Splicing system, namely Paun, Pixton and Yusof-Goode. These entire models are inspired by the molecular biological process of DNA Splicing. Hence, this paper focuses on the translucent DNA Splicing process, particularly on the generated language. Starting with some preliminaries in a limit graph, this paper also provides the experimental design with the predicted and actual result.
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Two stages Splicing system
2015Co-Authors: Mohammad Hassan Mudaber, Yuhani YusofAbstract:The study of the biological process of deoxyribonucleic acid (DNA) Splicing system in a translucent approach was investigated in 2012 by Yusof under the framework of formal language theory. In this work, the concepts of Splicing system in two stages as well as Splicing languages are mathematically and biologically discussed. Additionally, some theorems based on recognition site factor of initial strings at the existence of two initial strings and two rules are provided via Yusof-Goode (Y-G) approach. Besides, an example is also given in showing the biological meaning of the introduced concept.
Ankur B. Dalia - One of the best experts on this subject based on the ideXlab platform.
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Enhancing multiplex genome editing by natural transformation (MuGENT) via inactivation of ssDNA exonucleases
Nucleic acids research, 2017Co-Authors: Triana N. Dalia, Soo Hun Yoon, Elisa Galli, François-xavier Barre, Christopher M. Waters, Ankur B. DaliaAbstract:Recently, we described a method for multiplex genome editing by natural transformation (MuGENT). Mutant constructs for MuGENT require large arms of homology (>2000 bp) surrounding each genome edit, which necessitates laborious in vitro DNA Splicing. In Vibrio cholerae, we uncover that this requirement is due to cytoplasmic ssDNA exonucleases, which inhibit natural transformation. In ssDNA exonuclease mutants, one arm of homology can be reduced to as little as 40 bp while still promoting integration of genome edits at rates of ∼50% without selection in cis. Consequently, editing constructs are generated in a single polymerase chain reaction where one homology arm is oligonucleotide encoded. To further enhance editing efficiencies, we also developed a strain for transient inactivation of the mismatch repair system. As a proof-of-concept, we used these advances to rapidly mutate 10 high-affinity binding sites for the nucleoid occlusion protein SlmA and generated a duodecuple mutant of 12 diguanylate cyclases in V. cholerae. Whole genome sequencing revealed little to no off-target mutations in these strains. Finally, we show that ssDNA exonucleases inhibit natural transformation in Acinetobacter baylyi. Thus, rational removal of ssDNA exonucleases may be broadly applicable for enhancing the efficacy and ease of MuGENT in diverse naturally transformable species.
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Enhancing Multiplex Genome Editing by Natural Transformation (MuGENT) via inactivation of ssDNA exonucleases
2017Co-Authors: Triana N. Dalia, Soo Hun Yoon, Elisa Galli, François-xavier Barre, Christopher M. Waters, Ankur B. DaliaAbstract:Recently, we described a method for multiplex genome editing by natural transformation (MuGENT). Mutant constructs for MuGENT require large arms of homology (>2000 bp) surrounding each genome edit, which necessitates laborious in vitro DNA Splicing. In Vibrio cholerae, we uncover that this requirement is due to cytoplasmic ssDNA exonucleases, which inhibit natural transformation. In ssDNA exonuclease mutants, one arm of homology can be reduced to as little as 40 bp while still promoting integration of genome edits at rates of ~50% without selection in cis. Consequently, editing constructs are generated in a single PCR reaction where one homology arm is oligonucleotide encoded. To further enhance editing efficiencies, we also developed a strain for transient inactivation of the mismatch repair system. As a proof-of-concept, we used these advances to rapidly mutate 10 high-affinity binding sites for the nucleoid occlusion protein SlmA and generated a duodecuple mutant of 12 diguanylate cyclases in V. cholerae. Whole genome sequencing revealed little to no off-target mutations in these strains. Finally, we show that ssDNA exonucleases inhibit natural transformation in Acinetobacter baylyi. Thus, rational removal of ssDNA exonucleases may be broadly applicable for enhancing the efficacy and ease of MuGENT in diverse naturally transformable species.
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Enhancing multiplex genome editing by natural transformation (MuGENT) via inactivation of ssDNA exonucleases
Nucleic Acids Research, 2017Co-Authors: Triana N. Dalia, Soo Hun Yoon, Elisa Galli, François-xavier Barre, Christopher M. Waters, Ankur B. DaliaAbstract:Recently, we described a method for multiplex genome editing by natural transformation (MuGENT). Mutant constructs for MuGENT require large arms of homology (\textgreater2000 bp) surrounding each genome edit, which necessitates laborious in vitro DNA Splicing. In Vibrio cholerae, we uncover that this requirement is due to cytoplasmic ssDNA exonucleases, which inhibit natural transformation. In ssDNA exonuclease mutants, one arm of homology can be reduced to as little as 40 bp while still promoting integration of genome edits at rates of ∼50% without selection in cis. Consequently, editing constructs are generated in a single polymerase chain reaction where one homology arm is oligonucleotide encoded. To further enhance editing efficiencies, we also developed a strain for transient inactivation of the mismatch repair system. As a proof-of-concept, we used these advances to rapidly mutate 10 high-affinity binding sites for the nucleoid occlusion protein SlmA and generated a duodecuple mutant of 12 diguanylate cyclases in V. cholerae. Whole genome sequencing revealed little to no off-target mutations in these strains. Finally, we show that ssDNA exonucleases inhibit natural transformation in Acinetobacter baylyi. Thus, rational removal of ssDNA exonucleases may be broadly applicable for enhancing the efficacy and ease of MuGENT in diverse naturally transformable species.