Special Issue "Molecular Cut and Paste"
Deadline for manuscript submissions: closed (15 October 2013)
Prof. Dr. Makoto Komiyama
Life Science Center of Tsukuba Advanced Research Alliance, University of Tsukuba, Ten-noudai 1-1-1, Tsukuba, Ibaraki 305-8577, Japan
Interests: DNA;RNA; hydrolysis;site-selective scission;gene manipulation
Prof. Dr. Weiguo Cao
Genetics and Biochemistry, Clemson University, Clemson, South Carolina, USA
Interests: DNA damage; mutagenesis and repair; evolution of repair enzymes; nuclease; DNA glycosylase; ligase; nucleic acids amplification and detection; protein engineering
Anyone who has used a word processing application knows the convenience of “cut”, “copy” and “paste”. It is unimaginable to manipulate words digitally without these clever functions. It turns out that the creation of “cut”, “copy” and “paste” is far more ancient than modern day word processing. Through evolution, a vast set of tools has been developed for molecular surgery much like the way we delete, duplicate, translocate, and connect words. The birth of biotechnology in the 1970’s–1980’s was the direct outcome of the understanding of restriction enzymes, DNA polymerases and DNA ligases and their ingenious uses. In living cells, a large set of elaborative tools has been developed to manipulate DNA molecules to meet the needs of cellular maintenance and reproduction, whether it is DNA replication, DNA repair or DNA degradation. Tools to cut other macromolecules such as RNA, proteins, carbohydrates and lipids have also been invented. In recent years, much progress has been made to understand and develop chemical and enzymological tools for molecular cutting and pasting. From an ever expanding list of native restriction enzymes to artificial chemical restriction enzymes; from DNA ligases to chemical ligation agents; from cut-paste-based cloning to topo-cloning; from protein splicing to site-specific protein tagging; from site-defined restriction endonucleases to site-designed zinc finger nucleases; these amazing tools are helping researchers to meet the needs of molecular biology, biotechnology, medicine and therapy, nanotechnology, and other new bioprocesses. This special issue is designed to be a collection of articles reporting the exciting progress in the broad areas of molecular cutting and pasting. Both original research articles and review articles in chemical and enzymological manipulations of DNA, RNA, carbohydrates and lipids are welcome.
Prof. Dr. Makoto Komiyama
Prof. Dr. Weiguo Cao
Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. Papers will be published continuously (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.
Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are refereed through a peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed Open Access monthly journal published by MDPI.
- restriction endonuclease
- artificial restriction enzyme
- chemical ligation
- molecular cloning
Article: Molecular Diversity Assessment Using Sequence Related Amplified Polymorphism (SRAP) Markers in Vicia faba L.
Int. J. Mol. Sci. 2012, 13(12), 16457-16471; doi:10.3390/ijms131216457
Received: 2 October 2012; in revised form: 9 November 2012 / Accepted: 12 November 2012 / Published: 4 December 2012| Download PDF Full-text (243 KB) | Download XML Full-text
Int. J. Mol. Sci. 2013, 14(2), 3343-3357; doi:10.3390/ijms14023343
Received: 5 December 2012; in revised form: 28 January 2013 / Accepted: 30 January 2013 / Published: 5 February 2013| Download PDF Full-text (868 KB) | Download XML Full-text
Article: Quick, Selective and Reversible Photocrosslinking Reaction between 5-Methylcytosine and 3-Cyanovinylcarbazole in DNA Double Strand
Int. J. Mol. Sci. 2013, 14(3), 5765-5774; doi:10.3390/ijms14035765
Received: 20 December 2012; in revised form: 12 February 2013 / Accepted: 26 February 2013 / Published: 12 March 2013| Download PDF Full-text (1433 KB) | Download XML Full-text | Supplementary Files
Article: Thermostable Mismatch-Recognizing Protein MutS Suppresses Nonspecific Amplification during Polymerase Chain Reaction (PCR)
Int. J. Mol. Sci. 2013, 14(3), 6436-6453; doi:10.3390/ijms14036436
Received: 31 January 2013; in revised form: 28 February 2013 / Accepted: 11 March 2013 / Published: 21 March 2013| Download PDF Full-text (2137 KB) | Download XML Full-text | Supplementary Files
Int. J. Mol. Sci. 2013, 14(4), 7583-7597; doi:10.3390/ijms14047583
Received: 6 March 2013; in revised form: 22 March 2013 / Accepted: 26 March 2013 / Published: 8 April 2013| Download PDF Full-text (296 KB) | Download XML Full-text
Int. J. Mol. Sci. 2013, 14(5), 9305-9318; doi:10.3390/ijms14059305
Received: 28 February 2013; in revised form: 16 April 2013 / Accepted: 17 April 2013 / Published: 29 April 2013| Download PDF Full-text (433 KB) | Download XML Full-text | Supplementary Files
Article: A Chimeric UDP-Glucose Pyrophosphorylase Produced by Protein Engineering Exhibits Sensitivity to Allosteric Regulators
Int. J. Mol. Sci. 2013, 14(5), 9703-9721; doi:10.3390/ijms14059703
Received: 1 March 2013; in revised form: 10 April 2013 / Accepted: 18 April 2013 / Published: 6 May 2013| Download PDF Full-text (976 KB) | Download XML Full-text | Supplementary Files
Int. J. Mol. Sci. 2013, 14(7), 13137-13153; doi:10.3390/ijms140713137
Received: 2 May 2013; in revised form: 4 June 2013 / Accepted: 7 June 2013 / Published: 25 June 2013| Download PDF Full-text (632 KB) | Download XML Full-text
The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.
Type of Paper: Review
Title: Cut-and-paste DNA Manipulation Using Artificial Restriction DNA Cutter
Author: Makoto Komiyama
Affiliation: Life Science Center of Tsukuba Advanced Research Alliance, University of Tsukuba, Japan; E-Mail: email@example.com
Abstract: We recently developed completely chemistry-based DNA cutter which selectively cuts double-stranded DNA at designated site. They are composed of (1) Ce(IV)/EDTA complex as molecular scissors and (2) pseudo-complementary peptide nucleic acid. The scission-site and site-specificity are freely chosen, and thus even human genome can be cut at one predetermined site. Importantly, all the DNA scission proceeds via hydrolysis of the targeted phosphodiester linkages exactly as naturally occurring enzymes cut DNA. Accordingly, the DNA fragments obtained by the site-selective scission of these cutters can be easily ligated by using ligase. This cut-and-paste technology provides recombinant DNA, which expresses the corresponding protein in various cells. The present cutter is also applicable to targeted homologous recombination in human cells. Various applications of this new cut-and-paste method are described.
Type of Paper: Article
Title: Cut and Paste of Bacterial Genomes in Vivo
Author: Ken Miyazaki
Affiliation: Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan; E-Mail: firstname.lastname@example.org
Abstract: Arranging bacterial genomes as desired is important for biotechnology. This article deals gene knock-out (disruption), point mutation introduction, and knock-in of heterologous genes on bacterial genomes via "cut and paste technologies", which exploit homologous recombination ability of bacterial cells.
Title: Size-augmented sugar-modified nucleoside-5’-triphosphate analogues as tools to investigate DNA polymerase fidelity
Authors: Mira Elbasyouny, Janina Cramer, Frank Streckenbach, Gopinath Rangam, Andreas Marx and Tobias Restle
Affiliation: Institut für Molekulare Medizin, Universitätsklinikum Schleswig–Holstein, Campus Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany, Fax: (+49) 451-5002729; E-Mail: email@example.com (T.R.)
Abstract: DNA polymerase fidelity is crucial for the survival of any living species, yet varies significantly among different DNA polymerases. Understanding the basis for these differences in fidelity between polymerases mainly involved in repair processes and those responsible for replication might help to unravel the underlying molecular details. Inaccuracy during DNA polymerase-catalyzed DNA synthesis results from the incorporation of noncanonical nucleotides and extension of misaligned DNA substrates. Besides factors like hydrogen bonding and base stacking, nascent base pair/active site geometry is believed to play the most important role. In the present study we analysed pre-steady state kinetics of nucleotide binding, incorporation and primer extension of Dbh (DinB homolog) polymerase of Sulfolobus acidocaldarius, HIV reverse transcriptase (RTwt, RTM184V) and Pyrococcus furiosus (Pfu) DNA polymerase (exo-) using size augmented nucleoside-5’-triphosphate (TTP) analogues as steric probes. Overall, the pattern we observed resembles what one might have expected: the more accurate the polymerase (i.e. the more “rigid” the active site) and the larger the steric constrain within the incoming nucleotide, the primer terminus or the templating nucleotide the stronger the discrimination is. However, there are interesting exceptions to this general concept.
Type of Paper: Review
Title: Tailoring the Models of Transcription
Authors: Alena Pance
Affiliation: The Wellcome Trust Sanger Institute, Genome Campus Hinxton, Cambridge CB10 1SA, UK; firstname.lastname@example.org .uk. Tel.: 44 1223 834244 (ext. 8710)
Abstract: Molecular biology is a rapidly evolving field that has led to the development of increasingly sophisticated technologies to improve our capacity to study cellular processes in much finer detail. This has made it possible to start unravelling the molecular mechanisms underpinning cellular life and death. One of these vital cellular processes is transcriptional regulation which, as the first step in protein expression is the major point of regulation of the components that determine the characteristics, fate and functions of cells. Some of the technologies that have helped unravelling this process have resorted to the introduction of reporter genes to measure transcriptional activity. Reporter constructs rapidly became versatile tools that provided the possibility of manipulating promoters as well as transcription factors in order to examine their function. The understanding of promoter complexity and transcription factor structure offered an insight into the mechanisms of transcriptional control and their impact on cell behaviour. This review focuses on some of the many applications of molecular tools leading to the understanding of crucial aspects of transcriptional regulation.
Keywords: transcription; promoter; reporter gene; transcription factor; chimera
Last update: 27 February 2013