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Enzymes for Molecular Biology

Reaction Cleanup & Improving Yields

Use these housekeepers to remove unwanted residues, improve yields and reduce artifacts

Reagents and reactants that are left behind can hinder downstream processes. Use the right enzyme preparation to clean up your samples before taking the next step. Speed up and enhance amplification and transcription with some not-so-secret additives. 

Enzymes for cleavage and cleanup of residual reagents

Enzymatic cleanup of DNA samples with Exonuclease I, DNase I, RNase A and proteases removes residual primers, nucleotides and enzymes prior to SNP analysis, next-generation sequencing, Sanger DNA sequencing or other downstream analysis. 

The TAGZyme DAPase enzyme and TAGZyme system is used for His-tag removal from proteins containing an intrinsic DAPase stop point (expressed using the TAGZyme pQE-2 vector) or from proteins that contain an engineered glutamine stop point.

Enzyme   Activity Application
X8010L
Exonuclease I		 Coming soon Exonuclease I cleaves single-stranded DNA in the 3’→5’
direction, releasing 5’-mono/dinucleotides and leaving
double-stranded DNA molecules and the 5’-terminus
intact; digestionis inhibited by the presence of
a 3’-terminal phosphate
  • Removing single-stranded primers in PCR reactions prior
    to SNP analysis or Sanger DNA sequencing
  • Removing single-stranded primers for nested PCR reactions
  • Removing linear single-stranded DNA, leaving behind double-
    stranded DNA in the sample
79254
RNase-free DNase
(1500 Kunitz units)
Endonuclease that nonspecifically cleaves DNA to release
di-, tri- and oligonucleotide products with 5’-phosphorylated
and 3’-hydroxylated ends; acts on ssDNA and dsDNA,
chromatin and RNA:DNA hybrids
  • Removing contaminating DNA from RNA solutions prior
    to RNA cleanup and concentration
  • Removing DNA from protein samples
  • Nicking DNA as a first step to incorporating labeled bases
    into DNA
  • DNA-protein interaction analysis (Footprinting assay)
19101
RNase A
Endoribonuclease that degrades ssRNA at C and U residues
  • Removing contaminating RNA from plasmid and genomic
    DNA preparations
  • Removing RNA from recombinant protein preparations
  • Mapping single-base mutations in DNA or RNA
    (RNase protection assay)
19131
Proteinase K
QIAGEN Proteinase K is a subtilisin-type protease isolated
from the saprophytic fungus Tritirachium album
  • Protease digestion in DNA and RNA isolation procedures
  • Proteinase K possesses a high specific activity; stable over
    a wide range of temperatures and pH values; not inhibited
    by EDTA; suitable for short digestion times
19155
Protease
QIAGEN Protease is a serine protease isolated from
a recombinant Bacillus strain; an economical alternative
to Proteinase K 		Protease digestion in isolation of native DNA and RNA from
a variety of sources
34362
TAGzyme DAPase
Enyzme
TAGZyme DAPase (Recombinant dipeptidyl peptidase I)
  • Removing dipeptides sequentially from N-terminal His tags
    up to the "stop point" expressed using TAGZyme pQE vectors
  • Production of His-tag-free proteins for:
    • Protein structure determination
    • Therapeutic proteins

Improving yields

Improved yields and quality of templates may be achieved with the use of DNA-binding proteins in amplification and sequencing reactions. The DNA-binding protein, gene 32 protein from bacteriophage T4 (T4gp32), increases PCR amplification efficiency with a number of diverse templates. In addition, using E. coli single-stranded DNA-binding protein (SSB) in DNA sequencing reactions increases the resolution of sequencing runs.

An increased rate of in vitro transcription is made possible by treatment with inorganic pyrophosphatase, an essential component of reactions for RNA preparation. This enzyme cleaves pyrophosphate into two phosphate molecules and prevents pyrophosphate from precipitating with magnesium.

Reagent   Activity Application
Y9030L
E. coli ssDNA Binding
Protein		 Coming soon Binds with high specificity to single-stranded DNA;
thermostable
  • Useful in primer sequestering
  • Useful in enhancing the specificity of PCR
  • Useful in enabling the sequencing of problematic
    DNA templates
Y9130L
T4 Gene 32 Protein		 Coming soon
 Stabilizes ssDNA regions

Increases processivity of some DNA polymerases

Y9380L
E. coli pyrophosphatase		 Coming soon
An inorganic pyrophosphatase that catalyzes the hydrolysis of
inorganic pyrophosphate to form orthophosphate*
  • Increases RNA yield in transcription reaction
  • Enhancing DNA replication
Y9370L
Thermostable
pyrophosphatase		 Coming soon
 Thermostable pyrophosphatase is a recombinant enzyme
from Sulfolobus acidocaldarius that catalyzes the hydrolysis of
inorganic pyrophosphate to produce orthophosphate†

Useful for the enhancement of DNA replication in PCR

UDG strand cleavage

UDG-mediated strand cleavage is an important tool in molecular biotechnology, allowing for controlled and location-specific cleavage of single- and double-stranded DNA chemically or enzymatically synthesized with single or multiple incorporations of deoxyuridine. 

UDG treatments can reduce sequence artifacts, eliminate PCR carry over and generate specific gaps in DNA.
 Enzyme   Activity Application

19160, G5010L
Uracil DNA
Glycosylase (UDG)

G5020L
Thermolabile UDG

 Coming soon
 Uracil DNA glycosylase (UDG) is involved in base excision
repair; UDG creates abasic sites in uracil-containing DNA;
degrades uracil-containing DNA

  • DNA pretreatment with UDG reduces DNA artifacts during
    mutation detection by next-generation sequencing and other
    methods, without affecting capacity to detect real mutations

  • Removes uracil (deaminated cytosine) artifacts from FFPE
    preps

  • Thermolabile UDG can be used to eliminate PCR “carry over”
    contamination when dUTP is substituted for dTTP in the
    primary PCR reaction mix

Y9180L
10X Uracil Cleavage
System		 Coming soon
 The system consists of two enzyme components, Uracil
DNA Glycosylase and Endonuclease VIII. When the enzymes
are added sequentially to a reaction where a synthetic DNA
fragment contains a deoxyuracil, a single nucleotide gap
is generated at the location of the uracil residue
  • Enzymatically generates uracil nucleotide gaps in vitro
  • UDG is a DNA-specific enzyme that does not excise uracil
    from RNA substrates. Targeted incorporation of deoxyuridine
    nucleotides into oligonucleotides may be used with the
    enzyme system for the specific cleavage of sections of DNA,
    or DNA templates, from DNA:RNA hybrids.
Y9080L
Endonuclease VIII		 Coming soon
 Endonuclease VIII functions as both an N-glycosylase
(by excising oxidative base lesions) and an AP lyase (by
subsequently cleaving the phosphodiester backbone), leaving
terminal phosphates at the 5’ and 3’ ends; participates in base
excision repair of oxidatively generated DNA damage 
  • Excises damaged pyrimidines from duplex DNA
  • Used to measure DNA damage via single cell gel
    electrophoresis (Comet assay)

FAQs about reducing artifacts and reaction clean-up

Do you have any questions? 
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