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Table 5.3Types and examples of typical enzymes used in the manipulation
of nucleic acids

Enzyme Specific example Use in nucleic acid manipulation

DNA pol I DNA-dependent DNA polymerase 5^0! 30! 50

exonuclease activity

Klenow DNA pol I lacks 5^0! 30 exonuclease activity

T4 DNA pol Lacks 5^0! 30 exonuclease activity

DNA polymerases TaqDNA pol Thermostable DNA polymerase used in PCR

TthDNA pol Thermostable DNA polymerase with RT activity

T7 DNA pol Used in DNA sequencing

T7 RNA pol DNA-dependent RNA polymerase

RNA polymerases T3 RNA pol DNA-dependent RNA polymerase

Qß replicase RNA-dependent RNA polymerase, used in RNA

amplification

DNase I Non-specific endonuclease that cleaves DNA

Exonuclease III DNA-dependent 3^0! 50 stepwise removal of

nucleotides

Nucleases RNase A RNases used in mapping studies

RNase H Used in second strand cDNA synthesis

S1 nuclease Single-strand-specific nuclease

Reverse transcriptase AMV-RT RNA-dependent DNA polymerase, used in cDNA
synthesis

Transferases Terminal transferase
(TdT)

Adds homopolymer tails to the 3^0 end of DNA

Ligases T4 DNA ligase Links 5^0 -phosphate and 3^0 -hydroxyl ends via
phosphodiester bond

Kinases T4 polynucleotide
kinase (PNK)

Transfers terminal phosphate groups from ATP to

50 -OH groups

Phosphatases Alkaline phosphatase Removes 5^0 -phosphates from DNA and RNA

Transferases Terminal transferase Adds homopolymer tails to the 3^0 end of DNA

Methylases EcoRI methylase Methylates specific residues and protects from
cleavage by restriction enzymes

Notes:PCR, polymerase chain reaction; RT, reverse transcriptase; cDNA, complementary DNA; AMV, avian
myeloblastosis virus.

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163 5.6 The manipulation of nucleic acids – basic tools and techniques