Nucleases
S1 nuclease - Exonuclease that degrade both 3' and 5' termini of duplex DNA. Endonuclease cuts at nicks and gaps and single-stranded regions.
Mung Bean nuclease - a single-stranded specific DNA and RNA endonuclease which will degrade single-stranded extensions from the ends of DNA and RNA leaving blunt, ligatable ends.
Bal 31 nuclease - Exonuclease that degrade both 3' and 5' termini of duplex DNA. Endonuclease cuts at nicks and gaps and single-stranded regions.
Exo III nuclease - 3' exonuclease that acts at blunt or 3' recessed ends. Is not active on on single-stranded DNA (i.e., 3' overhangs => 4 bases).
Exo I nuclease - Degrades single-stranded DNA primers from annealed PCR products.
Lambda exonuclease - highly processive enzyme that acts in the 5'->3' direction, catalyzing the removal of 5' mononucleotides from duplex DNA. 5' phosphrylated DNA greatly preferred . It is unable to cut DNA at nick or gaps.
DNase I - nonspecifically cleaves DNA to release di, tri, and oligonucleotide products with 5' P and 3' OH .
T7 Endonuclease - cleaves non-perfectly matched DNA at the first, second, or third phophodiester bonds 5' to the mismatch.
RNase I - cuts all single-stranded RNA bonds leaving a 5' -OH and a 2', 3' cyclic monophosphate.
RNase III - When used with Mn2+ it converts long double-stranded RNA into a mix of short 18-25 bp RNAs suitable to serve as siRNA for RNA interference in mammalian cells.
RNase H - endonuclease which specifically hydrolyzes RNA which is hybridized to DNA. It does not digest single- or double-stranded DNA.
Polymerases
DNA Polymerase I - DNA-dependent DNA plymerase with inherent 3'->5' exonuclease activity (proofreading) and 5'->3' exonuclease activity (nick translation). Good for copying short stretches of DNA.
Large Klenow Fragment DNA Polymerase I - DNA polymerase I without the 5'-3' activity.
Klenow Fragment DNA Polymerase I - Large Klenow fragment with mutation that also eliminated the 3'->5' exonuclease activity.
T7 DNA Polymerase - highly processive DNA polymerase capable of copying long stretches of DNA. Modified forms reduce the very strong 3'->5' exonuclease activity.
Taq DNA Polymerase - a therostable DNA polymerase that possesses a 5'->3' polymerase activity and a double strand specific 5'->3' exonuclease activity. (No proofreading).
Vent DNA Polymerase - A thermostable 5'->3' DNA polymerase with 3'->5' exonuclease activity (proofreading). Also available in a proofreading minus form for DNA sequencing.
Reverse Transcriptase - An RNA directed DNA polymerase that uses RNA or DNA as a template and makes complementary DNA by extending an RNA or DNA primer. Lacks 3'->5' exonuclease activity (proofreading) .
Terminal transferase - a template independent polymerase that add dNTPs to the 3' OH of DNA (protruding, recessed, blunt-ended, double- or single-stranded DNA.
Sp6 RNA Polymerase - RNA Polymerase that has a highly specific recognition site, CATACGATTTAGGTGACACTATAG.
T7 RNA Polymerase - RNA Polymerase that has a highly specific recognition site, CTCGAGTAATACGACTCACTATAGG.
T3 RNA Polymerase - RNA Polymerase that has a highly specific recognition site, ATTAACCCTCACTAAAGGGA.
Poly(A) Polymerase - Adds As onto the end of single-stranded RNA.
Modifying enzymes
Alkaline Phosphatase - catalyzes the removal of 5' phosphates from DNA, RNA, and NTPs or dNTPs.
Polynucleotide Kinase - catalyzes the transfer and exchange of Pi from the gamma position of ATP to the 5' hydroxyl terminus of double- and single-stranded DNA and RNA
Ligases
T4 DNA Ligase - Catalyzes the formation a phosphodiester bond between justaposed 5' phosphate and 3' hydroxyl group in duplex DNA or RNA. Will join blunt or cohesive ends.
Taq DNA Ligase - Catalyzes the formation a phosphodiester bond between justaposed 5' phosphate and 3' hydroxyl termini of two adjacent oligomucleotides that are hybridized to a complementary target DNA. Ligation will only occur if the oligonucleotides are perfectly paired to the complementary target DNA, a single-base mismatch can be detected.
E.coli DNA Ligase - Catalyzes the formation a phosphodiester bond between justaposed 5' phosphate and 3' hydroxyl group in duplex DNA containing cohesive ends.
T4 RNA Ligase - Catalyzes the formation a phosphodiester bond between 5' phosphate and 3' hydroxyl group in DNA or RNA.
DNA methylases
CpG methylase - methylates C at:
C(me)G
Alu I methylase - methylates C at:
AGC(me)T
BamHI methylase - methylates C
at: GGATC(me)C
dam methylase - methylates
A at: TA(me)TC
EcoRI methylase - methylates A at: GAA(me)TTC
Hae methylase - methylates C at: GGC(me)C
HhaI methylase - methylates C at: GC(me)GC
Hpa II methylase - methylates C at: CC(me)GG
MspI methylase - methylates C at: C(me)CGG
TaqI methylase - methylates A at: TCGA(me)
topoisomerases
Topoisomerase I (E. coli) - relaxes negatively supercoiled DNA.
TA cloning
Recombinases
Cre Recombinase - A type I topoisomerase that catalyzes the site-specific recombination of DNA between loxP sites.
Gelantis Xi-Clone