Special Issue "Molecular Cut and Paste"

Guest Editor
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
E-Mail: komiyama@tara.tsukuba.ac.jp
Interests: DNA;RNA; hydrolysis;site-selective scission;gene manipulation

Guest Editor
Prof. Dr. Weiguo Cao
Genetics and Biochemistry, Clemson University, Clemson, South Carolina, USA
Website: http://www.clemson.edu/genbiochem/people/wcao.php
E-Mail: wgc@clemson.edu
Interests: DNA damage; mutagenesis and repair; evolution of repair enzymes; nuclease; DNA glycosylase; ligase; nucleic acids amplification and detection; protein engineering

Dear Colleagues,

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
Guest Editors

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• restriction endonuclease
• nuclease
• hydrolase
• artificial restriction enzyme
• isomerase
• ligase
• chemical ligation
• molecular cloning
• replication
• transcription
• repair
• regulation

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: komiyama@tara.tsukuba.ac.jp
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: miyazaki-kentaro@aist.go.jp
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.

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; alenapance@sanger.ac .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