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      Transcription of Click-Linked DNA in Human Cells**

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          Abstract

          Click DNA ligation promises an alternative to the current enzymatic approaches for DNA assembly, with the ultimate goal of using efficient chemical reactions for the total chemical synthesis and assembly of genes and genomes. Such an approach would enable the incorporation of various chemically modified bases throughout long stretches of DNA, a feat not possible with current polymerase-based methods. An unequivocal requirement for this approach is the biocompatibility of the resulting triazole-linked DNA. The correct function of this unnatural DNA linker in human cells is demonstrated here by using a click-linked gene encoding the fluorescent protein mCherry. Reverse transcription of mRNA isolated from these cells and subsequent sequencing of the mCherry cDNA shows error-free transcription. Nucleotide excision repair (NER) is shown to not play a role in the observed biocompatibility by using a NER-deficient human cell line. This is the first example of a non-natural DNA linker being functional in a eukaryotic cell.

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          Most cited references32

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          Structural basis of transcription: an RNA polymerase II elongation complex at 3.3 A resolution.

          The crystal structure of RNA polymerase II in the act of transcription was determined at 3.3 A resolution. Duplex DNA is seen entering the main cleft of the enzyme and unwinding before the active site. Nine base pairs of DNA-RNA hybrid extend from the active center at nearly right angles to the entering DNA, with the 3' end of the RNA in the nucleotide addition site. The 3' end is positioned above a pore, through which nucleotides may enter and through which RNA may be extruded during back-tracking. The 5'-most residue of the RNA is close to the point of entry to an exit groove. Changes in protein structure between the transcribing complex and free enzyme include closure of a clamp over the DNA and RNA and ordering of a series of "switches" at the base of the clamp to create a binding site complementary to the DNA-RNA hybrid. Protein-nucleic acid contacts help explain DNA and RNA strand separation, the specificity of RNA synthesis, "abortive cycling" during transcription initiation, and RNA and DNA translocation during transcription elongation.
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            Chemical synthesis of the mouse mitochondrial genome.

            We describe a one-step, isothermal assembly method for synthesizing DNA molecules from overlapping oligonucleotides. The method cycles between in vitro recombination and amplification until the desired length is reached. As a demonstration of its simplicity and robustness, we synthesized the entire 16.3-kilobase mouse mitochondrial genome from 600 overlapping 60-mers.
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              Structural basis for the transition from initiation to elongation transcription in T7 RNA polymerase.

              To make messenger RNA transcripts, bacteriophage T7 RNA polymerase (T7 RNAP) undergoes a transition from an initiation phase, which only makes short RNA fragments, to a stable elongation phase. We have determined at 2.1 angstrom resolution the crystal structure of a T7 RNAP elongation complex with 30 base pairs of duplex DNA containing a "transcription bubble" interacting with a 17-nucleotide RNA transcript. The transition from an initiation to an elongation complex is accompanied by a major refolding of the amino-terminal 300 residues. This results in loss of the promoter binding site, facilitating promoter clearance, and creates a tunnel that surrounds the RNA transcript after it peels off a seven-base pair heteroduplex. Formation of the exit tunnel explains the enhanced processivity of the elongation complex. Downstream duplex DNA binds to the fingers domain, and its orientation relative to upstream DNA in the initiation complex implies an unwinding that could facilitate formation of the open promoter complex.
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                Author and article information

                Journal
                Angew Chem Int Ed Engl
                Angew. Chem. Int. Ed. Engl
                anie
                Angewandte Chemie (International Ed. in English)
                Wiley-VCH Verlag GmbH & Co (KGaA, Weinheim )
                1433-7851
                1521-3773
                24 February 2014
                22 January 2014
                : 53
                : 9
                : 2362-2365
                Affiliations
                Chemistry, University of Southampton Southampton, SO17 1BJ (UK)
                Cancer Sciences, Faculty of Medicine, University of Southampton Southampton, SO16 6YD (UK)
                Dept. of Science and Mathematics, Suez University Suez, 43721 (Egypt)
                Department of Chemistry, University of Oxford, Chemistry Research Laboratory Oxford, OX1 3TA (UK)
                Author notes
                [*]Dr. A. Tavassoli Chemistry, University of Southampton Southampton, SO17 1BJ (UK) E-mail: a.tavassoli@ 123456soton.ac.uk
                [[+]]

                These authors contributed equally to this work.

                [[**]]

                This work was supported by Cancer Research UK (Career Establishment Award 10263 to A.T.); Breast Cancer Campaign (grant 2010NovPR12 to J.P.B. and A.T.), and the BBSRC (sLOLA grant BB/J001694/1 to T.B. and A.T.). We thank Prof. Roger Tsien for providing the mCherry gene and Dr. Josephine Corsi for discussions that led to initiation of this work.

                Article
                10.1002/anie.201308691
                4016740
                24452865
                241432d4-eaeb-485d-83fb-0fba0d48cb8b
                © 2014 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

                This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

                History
                : 05 October 2013
                Categories
                Synthetic Biology

                Chemistry
                click chemistry,dna ligation,gene technology,nucleic acids,synthetic biology
                Chemistry
                click chemistry, dna ligation, gene technology, nucleic acids, synthetic biology

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