Exonuclease I

• Excises bases from single-stranded DNA in 3ʹ→ 5ʹ direction

Exonuclease I cleaves single-stranded DNA in the 3ʹ→5ʹ direction, releasing 5ʹ mono/di-nucleotides and leaving double-stranded DNA molecules and the 5ʹ terminus intact. The enzyme is processive though digestion is inhibited by the presence of a 3ʹ terminal phosphate. Exonuclease I is tolerant of a wide-range of buffer conditions and can typically be added to reactions containing magnesium (1–3).

This enzyme is supplied in 10 mM Tris-HCl, 100 mM NaCl, 1 mM DTT, 0.5 mM EDTA and 50% glycerol: pH 7.5 at 25°C.

SDS is available on request.

Enzyme properties

• Storage temperature: –25°C to –15°C
• Molecular weight: 54,500 Daltons

Source of recombinant enzyme protein
The protein is produced by a strain of E. coli that expresses the recombinant Exonuclease I gene.

Unit definition: One unit is defined as the amount of enzyme required to produce 10 nmol of acid-soluble total nucleotide in 30 minutes at 37°C.

References

1. Lehman, I.R., and Nussbaum, A.L. (1964) J. Biol. Chem. 239, 2628.
2. Kushner, S.R., et al. (1971) Proc. Natl. Acad. Sci. USA 68, 824.
3. Kushner, S.R., et al. (1972) Proc. Natl. Acad. Sci. USA 69, 1366.

Exonuclease I can be heat-inactivated by incubation at 80°C for 15 minutes.

Exonuclease I will preferentially degrade single-stranded oligonucleotide primers in a reaction containing amplification products or other sources of double-stranded DNA, leaving double-stranded molecules intact.

Exonuclease I, in combination with Lambda Exonuclease (cat. no. X8030L) is effective in removing linear DNA species from plasmid preparations.

Exonuclease I works well in most molecular biology buffers that contain magnesium in excess of 1.5 mM.

Quality control analysis

Unit activity was measured using a twofold serial dilution method. Dilutions of enzyme were made in an Exonuclease I storage solution containing glycerol (50%) and added to 50 µl reactions containing a single-stranded tritiated DNA fragment and 67 mM glycine-KOH (pH 9.5), 10mM DTT, 6.7 mM MgCl₂. Reactions were incubated 10 minutes at 37°C, placed on ice, and analyzed using a TCA-precipitation method.

Protein concentration is determined by OD₂₈₀ absorbance.

Physical purity is evaluated by SDS-PAGE of concentrated and diluted enzyme solutions followed by silver-stain detection. Purity is assessed by comparing the aggregate mass of contaminant bands in the concentrated sample to the mass of the band corresponding to the protein of interest in the diluted sample.

Double-stranded endonuclease activity is determined in a 50 µl reaction containing 0.5 µg of plasmid DNA and 10 µl of enzyme solution incubated for 4 hours at 37°C.

E. coli contamination is evaluated using 5 µl replicate samples of enzyme solution that are denatured and screened in a TaqMan qPCR assay for the presence of contaminating E. coli genomic DNA using oligonucleotide primers corresponding to the 16S rRNA locus.

This OEM by QIAGEN product is available for bulk purchase for the following commercial assay applications.

• Plasmid prep cleanup
• Generates single-stranded DNA from linear double-stranded DNA
• Removes oligonucleotide primers after PCR