Archaeal RNA ligase from thermoccocus kodakarensis for template dependent ligation

References

• Shuman S, Schwer B. Rna Capping Enzyme and DNA-Ligase - a Superfamily of Covalent Nucleotidyl Transferases. Mol Microbiol 1995; 17:405-10; PMID:8559059; http://dx.doi.org/10.1111/j.1365-2958.1995.mmi_17030405.x
   PubMed Web of Science ®Google Scholar
• Shuman S, Lima CD. The polynucleotide ligase and RNA capping enzyme superfamily of covalent nucleotidyltransferases. Curr Opin Struc Biol 2004; 14:757-64; PMID:15582400; http://dx.doi.org/10.1016/j.sbi.2004.10.006
   PubMed Web of Science ®Google Scholar
• Zhuang FL, Fuchs RT, Sun ZY, Zheng Y, Robb GB. Structural bias in T4 RNA ligase-mediated 3′-adapter ligation. Nucleic Acids Res 2012; 40; PMID:22241775; http://dx.doi.org/10.1093/nar/gkr1263
   Web of Science ®Google Scholar
• Zhelkovsky AM, McReynolds LA. Simple and efficient synthesis of 5′ pre-adenylated DNA using thermostable RNA ligase. Nucleic Acids Res 2011; 39:E117-U71; PMID:21724605; http://dx.doi.org/10.1093/nar/gkr544
   PubMed Web of Science ®Google Scholar
• Zhang XH, Chiang VL. Single-stranded DNA ligation by T4 RNA ligase for PCR cloning of 5′-noncoding fragments and coding sequence of a specific gene. Nucleic Acids Res 1996; 24:990-1; PMID:8600474; http://dx.doi.org/10.1093/nar/24.5.990
   PubMed Web of Science ®Google Scholar
• Ho CK, Shuman S. Bacteriophage T4 RNA ligase 2 (gp24.1) exemplifies a family of RNA ligases found in all phylogenetic domains (vol 99, pg 12709, 2002). Proc Natl Acad Sci USA 2002; 99:12709-14; PMID:12228725; http://dx.doi.org/10.1073/pnas.222559599
   PubMed Web of Science ®Google Scholar
• Chursov A, Kopetzky SJ, Bocharov G, Frishman D, Shneider A. RNAtips: analysis of temperature-induced changes of RNA secondary structure. Nucleic Acids Res 2013; 41:W486-W91; PMID:23766288; http://dx.doi.org/10.1093/nar/gkt486
   PubMedGoogle Scholar
• Torchia C, Takagi Y, Ho CK. Archaeal RNA ligase is a homodimeric protein that catalyzes intramolecular ligation of single-stranded RNA and DNA. Nucleic Acids Res 2008; 36:6218-27; PMID:18829718; http://dx.doi.org/10.1093/nar/gkn602
   PubMed Web of Science ®Google Scholar
• Brooks MA, Meslet-Cladiere L, Graille M, Kuhn J, Blondeau K, Myllykallio H, Van Tilbeurgh H. The structure of an archaeal homodimeric ligase which has RNA circularization activity. Protein Sci 2008; 17:1336-45; PMID:18511537; http://dx.doi.org/10.1110/ps.035493.108
   PubMed Web of Science ®Google Scholar
• Lohman GJS, Zhang YH, Zhelkovsky AM, Cantor EJ, Evans TC. Efficient DNA ligation in DNA-RNA hybrid helices by Chlorella virus DNA ligase. Nucleic Acids Res 2014; 42:1831-44; PMID:24203707; http://dx.doi.org/10.1093/nar/gkt1032
   PubMed Web of Science ®Google Scholar
• Larman HB, Scott ER, Wogan M, Oliveira G, Torkamani A, Schultz PG. Sensitive, multiplex and direct quantification of RNA sequences using a modified RASL assay. Nucleic Acids Res 2014; 42:9146-57; PMID:25063296; http://dx.doi.org/10.1093/nar/gku636
   PubMed Web of Science ®Google Scholar
• Nilsson M, Antson DO, Barbany G, Landegren U. RNA-templated DNA ligation for transcript analysis. Nucleic Acids Res 2001; 29:578-81; PMID:11139629; http://dx.doi.org/10.1093/nar/29.2.578
   PubMed Web of Science ®Google Scholar
• Fareed GC, Richards CC. Enzymatic breakage and joining of deoxyribonucleic acid .2. structural gene for polynucleotide ligase in bacteriophage T4. P Natl Acad Sci USA 1967; 58:665-72; PMID:25008400; http://dx.doi.org/10.1073/pnas.58.2.665
   PubMed Web of Science ®Google Scholar
• Ho CK, VanEtten JL, Shuman S. Characterization of an ATP-dependent DNA ligase encoded by Chlorella virus PBCV-1. J Virol 1997; 71:1931-7; PMID:9032324
   PubMed Web of Science ®Google Scholar
• Fukui T, Atomi H, Kanai T, Matsumi R, Fujiwara S, Imanaka T. Complete genome sequence of the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 and comparison with Pyrococcus genomes. Genome Res 2005; 15:352-63; PMID:15710748; http://dx.doi.org/10.1101/gr.3003105
   PubMed Web of Science ®Google Scholar
• Seo MS, Kim YJ, Choi JJ, Lee MS, Kim JH, Lee JH, Kwon ST. Cloning and expression of a DNA ligase from the hyperthermophilic archaeon Staphylothermus marinus and properties of the enzyme. J Biotechnol 2007; 128:519-30; PMID:17118474; http://dx.doi.org/10.1016/j.jbiotec.2006.09.024
   PubMed Web of Science ®Google Scholar
• Lovett ST, Clark AJ. Genetic-Analysis of the recj-gene of escherichia-coli-K-12. J Bacteriol 1984; 157:190-6; PMID:6317649
   PubMed Web of Science ®Google Scholar
• Petro TM, Agarkova IV, Zhou Y, Yolken RH, Van Etten JL, Dunigan DD. Response of mammalian macrophages to challenge with the chlorovirus acanthocystis turfacea chlorella virus 1. J Virol 2015; 89:12096-107; PMID:26401040; http://dx.doi.org/10.1128/JVI.01254-15
   PubMed Web of Science ®Google Scholar
• Coleman G. Novel method for achieving cell-free synthesis of protein. Nature 1969; 222:666-7; PMID:5768275; http://dx.doi.org/10.1038/222666a0
   PubMed Web of Science ®Google Scholar
• Bretscher MS, Grunbergmanago M. Polyribonucleotide-directed protein synthesis using an E. coli cell-free system. Nature 1962; 195:283-4; PMID:13872932; http://dx.doi.org/10.1038/195283a0
   PubMed Web of Science ®Google Scholar
• Wainwright SD. Mediation of the genetic control of protein synthesis in cell-free extracts of neurospora-crassa. Nature 1960; 185:314-5; http://dx.doi.org/10.1038/185314a0
   Web of Science ®Google Scholar
• Shimizu Y, Inoue A, Tomari Y, Suzuki T, Yokogawa T, Nishikawa K, Ueda T. Cell-free translation reconstituted with purified components. Nat Biotechnol 2001; 19:751-5; PMID:11479568; http://dx.doi.org/10.1038/90802
   PubMed Web of Science ®Google Scholar
• Niederholtmeyer H, Xu L, Maerkl SJ. Real-Time mRNA measurement during an in vitro transcription and translation reaction using binary probes. Acs Synth Biol 2013; 2:411-7; PMID:23654250; http://dx.doi.org/10.1021/sb300104f
   PubMed Web of Science ®Google Scholar
• Jackson K, Kanamori T, Ueda T, Fan ZH. Protein synthesis yield increased 72 times in the cell-free PURE system. Integr Biol-Uk 2014; 6:781-8; http://dx.doi.org/10.1039/C4IB00088A
   Google Scholar
• Karig DK, Iyer S, Simpson ML, Doktycz MJ. Expression optimization and synthetic gene networks in cell-free systems. Nucleic Acids Res 2012; 40:3763-74; PMID:22180537; http://dx.doi.org/10.1093/nar/gkr1191
   PubMed Web of Science ®Google Scholar
• Kirk N, Cowan D. Optimizing the Recovery of Recombinant Thermostable Proteins Expressed in Mesophilic Hosts. J Biotechnol 1995; 42:177-84; PMID:7576536; http://dx.doi.org/10.1016/0168-1656(95)00078-5
   PubMed Web of Science ®Google Scholar
• Manavalan P, Johnson WC. Sensitivity of circular-dichroism to protein tertiary structure class. Nature 1983; 305:831-2; http://dx.doi.org/10.1038/305831a0
   Web of Science ®Google Scholar
• Barela TD, Darnall DW. Practical aspects of calculating protein secondary structure from circular-dichroism spectra. Biochemistry-Us 1974; 13:1694-700; PMID:4831358; http://dx.doi.org/10.1021/bi00705a022
   PubMed Web of Science ®Google Scholar
• Landegren U, Kaiser R, Sanders J, Hood L. A ligase-mediated gene detection technique. Science 1988; 241:1077-80; PMID:3413476; http://dx.doi.org/10.1126/science.3413476
   PubMed Web of Science ®Google Scholar
• Kuhn H, Frank-Kamenetskii MD. Template-independent ligation of single-stranded DNA by T4 DNA ligase. Febs J 2005; 272:5991-6000; PMID:16302964; http://dx.doi.org/10.1111/j.1742-4658.2005.04954.x
   PubMed Web of Science ®Google Scholar
• Zhang L, Wang JJ, Coetzer M, Angione S, Kantor R, Tripathi A. One-Step ligation on RNA amplification for the detection of point mutations. J Mol Diagn 2015; 17:679-88; PMID:26322949; http://dx.doi.org/10.1016/j.jmoldx.2015.07.001
   PubMed Web of Science ®Google Scholar
• Fujiwara S, Takagi M, Imanaka T. Archaeon Pyrococcus kodakaraensis KOD1: application and evolution. Biotechnol Ann Rev 1998; 4:259-84; PMID:9890143; http://dx.doi.org/10.1016/S1387-2656(08)70073-5
   PubMedGoogle Scholar
• Salomonsson M, Arendshorst WJ. Calcium recruitment in renal vasculature: NE effects on blood flow and cytosolic calcium concentration. Am J Physiol 1999; 276:F700-10; PMID:10330052
   PubMed Web of Science ®Google Scholar
• Hiramatsu A, Ouchi T. On proteolytic enzymes from commercial protease preparation of streptomyces griseus (Pronase P). J Biochem-Tokyo 1963; 54:462-4; PMID:14089742
   PubMed Web of Science ®Google Scholar
• Cohn EJ, Hughes WL, Weare JH. Preparation and Properties of serum and plasma proteins .13. crystallization of serum albumins from ethanol water mixtures. J Am Chem Soc 1947; 69:1753-61; PMID:20251413; http://dx.doi.org/10.1021/ja01199a051
   PubMed Web of Science ®Google Scholar
• Soding J, Biegert A, Lupas AN. The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res 2005; 33:W244-W8; PMID:15980461; http://dx.doi.org/10.1093/nar/gki408
   PubMed Web of Science ®Google Scholar
• Kelley LA, Mezulis S, Yates CM, Wass MN, Sternberg MJE. The Phyre2 web portal for protein modeling, prediction and analysis. Nat Protoc 2015; 10:845-58; PMID:25950237; http://dx.doi.org/10.1038/nprot.2015.053
   PubMed Web of Science ®Google Scholar