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Enzymes as Molecular Tools

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Bioresources and Bioprocess in Biotechnology

Abstract

Development of molecular techniques has led to revolutionary advancements in various fields of biosciences. Enzymes that modify nucleic acids are of paramount importance in these techniques. A wide range of enzymes involved in the catalysis of polymerization, ligation, cleavage, and other manipulations of DNA and RNA are currently available. Novel enzymes with improved properties are being developed by manufacturers. Molecular cloning is now a regular laboratory technique with a vast array of enzymes available from various commercial sources and to select an enzyme apt for a particular application has become a tedious task. This chapter aims to provide details on the different commercial enzymes available for routine molecular biology work, in addition to reviewing the important classes of enzymes that are used in molecular biology.

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References

  • Alsmadi O, Alkayal F, Monies D, Meyer BF (2009) Specific and complete human genome amplification with improved yield achieved by phi29 DNA polymerase and a novel primer at elevated temperature. BMC Res Note 2:48

    Article  Google Scholar 

  • Anfinsen CB, Haber E, Sela M, White FH (1961) The kinetics of formation of native ribonuclease during oxidation of the reduced polypeptide chain. Proc Natl Acad Sci U S A 47(9):1309–1314

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Angers M, Cloutier JF, Castonguay A, Drouin R (2001) Optimal conditions to use Pfu exo(-) DNA polymerase for highly efficient ligation-mediated polymerase chain reaction protocols. Nucleic Acids Res 29:E83

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Baluda MA, Perbal B, Rushlow KE, Papas TS (1983) Avian myeloblastosis virus: a model for the generation of viral oncogenes from potentially oncogenic cellular genetic elements. Folia Biol 29:18–34

    CAS  Google Scholar 

  • Belkin S, Jannasch HW (1985) A new extremely thermophilic, sulfur-reducing heterotrophic, marine bacterium. Arch Microbiol 141(3):181–186

    Article  CAS  Google Scholar 

  • Benedik MJ, Strych U (1998) Serratia marcescens and its extracellular nuclease. FEMS Microbiol Lett 165:1–13

    Article  CAS  PubMed  Google Scholar 

  • Blanco L, Bernad A, Lazaro JM, Martin G, Garmendia C, Salas M (1989) Highly efficient DNA synthesis by the phage phi 29 DNA polymerase. Symmetrical mode of DNA replication. J Biol Chem 264:8935–8940

    CAS  PubMed  Google Scholar 

  • Blondal T, Hjorleifsdottir SH, Fridjonsson OF, Ævarsson A, Skirnisdottir S, Hermannsdottir AG, Kristjansson JK (2003) Discovery and characterization of a thermostable bacteriophage RNA ligase homologous to T4 RNA ligase 1. Nucleic Acids Res 31(24):7247–7254

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Blondal T, Thorisdottir A, Unnsteinsdottir U, Hjorleifsdottir S, Ævarsson A, Ernstsson S, Kristjansson JK (2005) Isolation and characterization of a thermostable RNA ligase 1 from a Thermus scotoductus bacteriophage TS2126 with good single-stranded DNA ligation properties. Nucleic Acids Res 33(1):135–142

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Brock TD, Freeze H (1969) Thermus aquaticus gen. n. and sp. n., a nonsporulating extreme thermophile. J Bacteriol 98:289–297

    CAS  PubMed  PubMed Central  Google Scholar 

  • Burgers PM, Koonin EV, Bruford E, Blanco L, Burtis KC, Christman MF, Copeland WC, Friedberg EC, Hanaoka F, Hinkle DC, Lawrence CW, Nakanishi M, Ohmori H, Prakash L, Prakash S, Reynaud CA, Sugino A, Todo T, Wang Z, Weill JC, Woodgate R (2001) Eukaryotic DNA polymerases: proposal for a revised nomenclature. J Biol Chem 276:43487–43490

    Article  CAS  PubMed  Google Scholar 

  • Butler ET, Chamberlin MJ (1982) Bacteriophage SP6-specific RNA polymerase I. Isolation and characterization of the enzyme. J Biol Chem 257(10):5772–5778

    CAS  PubMed  Google Scholar 

  • Cai L, Hu C, Shen S, Wang W, Huang W (2004) Characterization of bacteriophage T3 DNA ligase. J Biochem 135(3):397–403

    Article  CAS  PubMed  Google Scholar 

  • Chamberlin M, Berg P (1962) Deoxyribonucleic acid-directed synthesis of ribonucleic acid by an enzyme from Escherichia coli. Proc Natl Acad Sci U S A 48(1):81–94

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chamberlin MJ, Ryan T (1982) Bacteriophage DNA-dependent RNA polymerases. In: Boyer PD (ed) The enzymes, vol 15. Academic, New York, pp 87–109

    Google Scholar 

  • Chamberlin M, McGrath J, Waskell L (1970) New RNA polymerase from Escherichia coli infected with bacteriophage T7. Nature 228(5268):227–231

    Article  CAS  PubMed  Google Scholar 

  • Chang LM, Bollum FJ (1986) Molecular biology of terminal transferase. CRC Crit Rev Bioeng 21:27–52

    CAS  Google Scholar 

  • Chase JW, Richardson CC (1974) Exonuclease VII of Escherichia coli. Mechanism of action. J Biol Chem 249:4553–4561

    CAS  PubMed  Google Scholar 

  • Danna K, Nathans D (1971) Specific cleavage of simian virus 40 DNA by restriction endonuclease of Hemophilus influenzae. Proc Natl Acad Sci U S A 68:2913

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Demple B, Harrison L (1994) Repair of oxidative damage to DNA: enzymology and biology. Annu Rev Biochem 63:915–948

    Article  CAS  PubMed  Google Scholar 

  • Desai NA, Shankar V (2003) Single-strand-specific nucleases. FEMS Microbiol Rev 26(5):457–491

    Article  CAS  PubMed  Google Scholar 

  • Diaz RS, Sabino EC (1998) Accuracy of replication in the polymerase chain reaction. Comparison between Thermotoga maritima DNA polymerase and Thermus aquaticus DNA polymerase. Braz J Med Biol Res 31(10):1239–1242

    Article  CAS  PubMed  Google Scholar 

  • Doherty AJ, Wigley DB (1999) Functional domains of an ATP-dependent DNA ligase. J Mol Biol 285(1):63–71

    Article  CAS  PubMed  Google Scholar 

  • Doherty AJ, Ashford SR, Subramanya HS, Wigley DB (1996) Bacteriophage T7 DNA ligase overexpression, purification, crystallization, and characterization. J Biol Chem 271:11083–11089

    Article  CAS  PubMed  Google Scholar 

  • Edmonds M (1982) Poly(A) adding enzymes. In: Boyer PD (ed) The enzymes, vol 15B. Academic, New York, pp 218–245

    Google Scholar 

  • Feng H, Dong L, Cao W (2006) Catalytic mechanism of endonuclease v: a catalytic and regulatory two-metal model. Biochemistry 45(34):10251–10259

    Article  CAS  PubMed  Google Scholar 

  • Franklin MC, Wang J, Steitz TA (2001) Structure of the replicating complex of a pol alpha family DNA polymerase. Cell 105:657–667

    Article  CAS  PubMed  Google Scholar 

  • Fujimura T, Tanaka T, Ohara K, Morioka H, Uesugi S, Ikehara M, Nishikawa S (1990) Secretion of recombinant ribonuclease T1 into the periplasmic space of Escherichia coli with the aid of the signal peptide of alkaline phosphatase. FEBS Lett 265(1–2):71–74

    Article  CAS  PubMed  Google Scholar 

  • Goodwin EC, Rottman FM (1992) The use of RNase H and poly(A) junction oligonucleotides in the analysis of in vitro polyadenylation reaction products. Nucleic Acids Res 20(4):916

    Google Scholar 

  • Günther S, Montes M, de DA, del VM, Atencia EA, Sillero A (2002) Thermostable Pyrococcus furiosus DNA ligase catalyzes the synthesis of (di)nucleoside polyphosphates. Extremophiles 6(1):45–50

    Article  PubMed  Google Scholar 

  • Halford SE (1971) Escherichia coli alkaline phosphatase. An analysis of transient kinetics. Biochem J 125(1):319–327

    Google Scholar 

  • Ho CK, Van Etten JL, Shuman S (1997) Characterization of an ATP-dependent DNA ligase encoded by Chlorella virus PBCV-1. J Virol 71(3):1931–1937

    Google Scholar 

  • Ho CK, Wang LK, Lima CD, Shuman S (2004) Structure and mechanism of RNA ligase. Structure 12:327–339

    Article  CAS  PubMed  Google Scholar 

  • Hofstetter H, Schambock A, Van Den Berg J, Weissmann C (1976) Specific excision of the inserted DNA segment from hybrid plasmids constructed by the poly(dA). poly (dT) method. Biochim Biophys Acta 454:587–591

    Article  CAS  PubMed  Google Scholar 

  • Hosfield DJ, Guan Y, Haas BJ, Cunningham RP, Tainer JA (1999) Structure of the DNA repair enzyme endonuclease IV and its DNA complex: double-nucleotide flipping at abasic sites and three-metal-ion catalysis. Cell 98(3):397–408

    Article  CAS  PubMed  Google Scholar 

  • Housby JN, Thorbjarnardóttir SH, Jónsson ZO, Southern EM (2000) Optimised ligation of oligonucleotides by thermal ligases: comparison of Thermus scotoductus and Rhodothermus marinus DNA ligases to other thermophilic ligases. Nucleic Acids Res 28(3):e10

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Houts GE, Miyagi M, Ellis C, Beard D, Beard JW (1979) Reverse transcriptase from avian myeloblastosis virus. J Virol 29(2):517–522

    CAS  PubMed  PubMed Central  Google Scholar 

  • Huang Z, Fasco MJ, Kaminsky LS (1996) Optimization of Dnase I removal of contaminating DNA from RNA for use in quantitative RNA-PCR. BioTechniques 20:1012–1014, 1016, 1018–1020

    Google Scholar 

  • Huber HE, Tabor S, Richardson CC (1987) Escherichia coli thioredoxin stabilizes complexes of bacteriophage T7 DNA polymerase and primed templates. J Biol Chem 262:16224–16232

    CAS  PubMed  Google Scholar 

  • Jannasch HW, Wirsen CO, Molyneaux SJ, Langworthy TA (1992) Comparative physiological studies on hyperthermophilic Archaea isolated from deep-sea hot vents with emphasis on Pyrococcus strain GB-D. Appl Environ Microbiol 58(11):3472–3481

    CAS  PubMed  PubMed Central  Google Scholar 

  • Johnson PH, Laskowski M Sr (1970) Mung bean nuclease I. II. Resistance of double stranded deoxyribonucleic acid and susceptibility of regions rich in adenosine and thymidine to enzymatic hydrolysis. J Biol Chem 245:891–898

    CAS  PubMed  Google Scholar 

  • Keller W, Crouch R (1972) Degradation of DNA- RNA hybrids by ribonuclease H and DNA polymerases of cellular and viral origin. Proc Natl Acad Sci U S A 69:3360–3364

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kilpatrick MW, Wei CF, Gray HB Jr, Wells RD (1983) BAL 31 nuclease as a probe in concentrated salt for the B-Z DNA junction. Nucleic Acids Res 11:3811–3822

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Klenow H, Henningsen I (1970) Selective elimination of the exonuclease activity of the deoxyribonucleic acid polymerase from Escherichia coli B by limited proteolysis. Proc Natl Acad Sci U S A 65(1):168–175

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kornberg A (1957) Enzymatic synthesis of deoxyribonucleic acid. Harvey Lect 53:83–112

    PubMed  Google Scholar 

  • Lehman IR (1974) DNA ligase: structure, mechanism, and function. Science 186(4166):790–797

    Article  CAS  PubMed  Google Scholar 

  • Lehman IR, Nussbaum AL (1964) The deoxyribonucleases of Escherichia coli. V. on the specificity of exonuclease I (phosphodiesterase). J Biol Chem 239:2628–2636

    CAS  PubMed  Google Scholar 

  • Levin JD, Johnson AW, Demple B (1988) Homogeneous Escherichia coli endonuclease IV. Characterization of an enzyme that recognizes oxidative damage in DNA. J Biol Chem 263(17):8066–8071

    CAS  PubMed  Google Scholar 

  • Little JW (1981) Lambda exonuclease. Gene Amplif Anal 2:135–145

    CAS  PubMed  Google Scholar 

  • Lohman GJ, Zhang Y, Zhelkovsky AM, Cantor EJ, Evans TC Jr (2014) Efficient DNA ligation in DNA–RNA hybrid helices by Chlorella virus DNA ligase. Nucleic Acids Res 42(3):1831–1844

    Article  CAS  PubMed  Google Scholar 

  • Luo J, Bergstrom DE, Barany F (1996) Improving the fidelity of Thermus thermophilus DNA ligase. Nucleic Acids Res 24(15):3071–3078

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Makeyev EV, Bamford DH (2000) Replicase activity of purified recombinant protein P2 of double-stranded RNA bacteriophage phi6. EMBO J 19(1):124–133

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Makeyev EV, Bamford DH (2001) Primer-independent RNA sequencing with bacteriophage phi6 RNA polymerase and chain terminators. RNA 7:774–781

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Martin G, Keller W (1998) Tailing and 3′-end labeling of RNA with yeast poly(A) polymerase and various nucleotides. RNA 4:226–230

    CAS  PubMed  PubMed Central  Google Scholar 

  • McGraw NJ, Bailey JN, Cleaves GR, Dembinski DR, Gocke CR, Joliffe LK, McAllister WT (1985) Sequence and analysis of the gene for bacteriophage T3 RNA polymerase. Nucleic Acids Res 13(18):6753–6766

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Melton DA, Krieg PA, Rebagliati MR, Maniatis T, Zinn K, Green MR (1984) Efficient in vitro synthesis of biologically active RNA and RNA hybridization probes from plasmids containing a bacteriophage SP6 promoter. Nucleic Acids Res 12(18):7035–7056

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Minakhin L, Nechaev S, Campbell EA, Severinov K (2001) Recombinant Thermus aquaticus RNA polymerase, a new tool for structure-based analysis of transcription. J Bacteriol 183(1):71–76

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Moelling K (1974) Characterization of reverse transcriptase and RNase H from friend-murine leukemia virus. Virology 62:46–59

    Article  CAS  PubMed  Google Scholar 

  • Mohr S, Thach R (1969) Application of ribonuclease T1 to the synthesis of oligoribonucleotides of defined base sequence. J Biol Chem 244:6566

    CAS  PubMed  Google Scholar 

  • Mössner E, Boll M, Pfleiderer G (1980) Purification of human and bovine alkaline phosphatases by affinity chromatography. Hoppe-Seyler’s Zeitschrift fur physiologische Chemie 361(4):543–549

    Article  PubMed  Google Scholar 

  • Mullis K, Faloona F, Scharf S, Saiki R, Horn G, Erlich H (1986) Specific enzymatic amplification of DNA in vitro: the polymerase chain reaction. Cold Spring Harb Symp Quant Biol 51(1):263–273

    Article  CAS  PubMed  Google Scholar 

  • Murray N, Bruce S, Murray K (1979) Molecular cloning of DNA ligase gene from bacteriophage T4. II. Amplification and preparation of the gene product. J Mol Biol 132:493

    Article  CAS  PubMed  Google Scholar 

  • Myers TW, Gelfand DH (1991) Reverse transcription and DNA amplification by a Thermus thermophilus DNA polymerase. Biochemistry 30(31):7661–7666

    Article  CAS  PubMed  Google Scholar 

  • Nossal NG (1984) Prokaryotic DNA replication systems. Annu Rev Biochem 53:581–615

    Google Scholar 

  • Panasenko SM, Alazard RJ, Lehman IR (1978) A simple, three-step procedure for the large scale purification of DNA ligase from a hybrid λ lysogen constructed in vitro. J Biol Chem 253:4590–4592

    CAS  PubMed  Google Scholar 

  • Perbal B (2008) Avian myeoloblastosis virus (AMV): only one side of the coin. Retrovirology 5:49

    Article  PubMed  PubMed Central  Google Scholar 

  • Pray L (2008) Restriction enzymes. Nat Educ 1(1):38

    Google Scholar 

  • Raines RT (1998) Ribonuclease A. Chem Rev 98(3):1045–1066

    Article  CAS  PubMed  Google Scholar 

  • Rittié L, Perbal B (2008) Enzymes used in molecular biology: a useful guide. J Cell Commun Signal 2(1–2):25–45

    Article  PubMed  PubMed Central  Google Scholar 

  • Rogers SG, Weiss B (1980) Cloning of the exonuclease III gene of Escherichia coli. Gene 11:187–195

    Article  CAS  PubMed  Google Scholar 

  • Saïda F, Odaert B, Uzan M, Bontems F (2004) First structural investigation of the restriction ribonuclease RegB: NMR spectroscopic conditions, 13C/15N double-isotopic labelling and two-dimensional heteronuclear spectra. Protein Expr Purif 34(1):158–165

    Article  PubMed  Google Scholar 

  • Saiki RK, Gelfand DH, Stoffel S, Scharf SJ, Higuchi R, Horn GT, Mullis KB, Erlich HA (1988) Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239(4839):487–491

    Article  CAS  PubMed  Google Scholar 

  • Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A 74:5463–5467

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Stahl SJ, Zinn K (1981) Nucleotide sequence of the cloned gene for bacteriophage T7 RNA polymerase. J Mol Biol 148(4):481–485

    Article  CAS  PubMed  Google Scholar 

  • Stein H, Hausen P (1969) Enzyme from calf thymus degrading the RNA moiety of DNA-RNA hybrids: effect on DNA-dependent RNA polymerase. Science 166:393–395

    Article  CAS  PubMed  Google Scholar 

  • Steitz TA (1998) A mechanism for all polymerases. Nature 391:231–232

    Article  CAS  PubMed  Google Scholar 

  • Stenesh J, Roe B (1972) DNA polymerase from mesophilic and thermophilic bacteria. I. Purification and properties from Bacillus licheniformis and Bacillus stearothermophilus. Biochim Biophys Acta 272:167

    Article  CAS  Google Scholar 

  • Struhl K (1997) Enzymatic manipulation of DNA and RNA. In: Bensonchanda V (ed) Current protocols in molecular biology. Wiley, Boston, pp 311–316

    Google Scholar 

  • Tabor S, Richardson CC (1989) Selective inactivation of the exonuclease activity of bacteriophage T7 DNA polymerase by in vitro mutagenesis. J Biol Chem 264:6447–6458

    CAS  PubMed  Google Scholar 

  • Tabor S, Huber HE, Richardson CC (1987) Escherichia coli thioredoxin confers processivity on the DNA polymerase activity of the gene 5 protein of bacteriophage T7. J Biol Chem 262:16212–16223

    CAS  PubMed  Google Scholar 

  • Takagi M, Nishioka M, Kakihara H, Kitabayashi M, Inoue H, Kawakami B, Imanaka T (1997) Characterization of DNA polymerase from Pyrococcus sp. strain KOD1 and its application to PCR. Appl Environ Microbiol 63(11):4504–4510

    CAS  PubMed  PubMed Central  Google Scholar 

  • Takahashi K (1966) The structure and function of ribonuclease T1. VII. Further investigations on amino acid composition and some other properties of ribonuclease T1. J Biochem 60:239

    Article  CAS  PubMed  Google Scholar 

  • Talmadge K, Stahl S, Gilbert W (1980) Eukaryotic signal sequence transports insulin antigen in Escherichia coli. Proc Natl Acad Sci U S A 77:3369–3373

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Vanecko S, Laskowski M (1961) Studies of the specificity of deoxyribonuclease I. III. Hydrolysis of chains carrying a monoesterified phosphate on carbon 5. J Biol Chem 236:3312–3316

    CAS  PubMed  Google Scholar 

  • Verjee ZHM (1969) Isolation of three acid phosphatases from wheat germ. Eur J Biochem 9(3):439–444

    Article  CAS  PubMed  Google Scholar 

  • Wang LK, Lima CD, Shuman S (2002) Structure and mechanism of T4 polynucleotide kinase: an RNA repair enzyme. EMBO J 21(14):3873–3880

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Williams RJ (2003) Restriction endonucleases: classification, properties, and applications. Mol Biotechnol 23(3):225–243

    Article  CAS  PubMed  Google Scholar 

  • Zhelkovsky AM, McReynolds LA (2012) Structure-function analysis of Methanobacterium thermoautotrophicum RNA ligase – engineering a thermostable ATP independent enzyme. BMC Mol Biol 13(1):24

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhou MY, Gomez-Sanchez CE (2000) Universal TA cloning. Curr Issues Mol Biol 2:1–7

    CAS  PubMed  Google Scholar 

  • Zinn K, DiMaio D, Maniatis T (1983) Identification of two distinct regulatory regions adjacent to the human b-interferon gene. Cell 34:865–879

    Article  CAS  PubMed  Google Scholar 

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Valsala, G., Sugathan, S. (2017). Enzymes as Molecular Tools. In: Sugathan, S., Pradeep, N., Abdulhameed, S. (eds) Bioresources and Bioprocess in Biotechnology. Springer, Singapore. https://doi.org/10.1007/978-981-10-4284-3_4

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