Smart Enzyme Choices for Smarter Science: Matching Nucleases to Your Experimental Needs

In the intricate network of life, nucleases act like “molecular scissors”—enzymes that cut and reshape DNA or RNA with precision. Found across prokaryotes, eukaryotes, and even viruses, nucleases are essential guardians of genomic stability and nucleic acid metabolism.

From DNA repair and recombination during cell division, to mRNA turnover, to defending against invading nucleic acids, nucleases are involved in nearly every aspect of genetic information transfer and regulation.

Figure 1. Representative mechanisms of nucleases in nucleic acid processing.

With the rapid progress of molecular biology, the applications of nucleases now extend far beyond basic science. In both cutting-edge laboratories and healthcare frontlines, their ability to selectively degrade or edit nucleic acids has made them indispensable tools—bridging discovery research and industrial-scale applications.

As a professional enzyme manufacturer, Yeasen has developed a full portfolio of high-purity, high-activity nucleases, offering reliable solutions for researchers and biomanufacturers worldwide.

Two Core Nuclease Types—Made Simple

Based on mechanism, nucleases are broadly divided into exonucleases and endonucleases:

Exonucleases act like “craftsmen trimming from the ends.” They degrade DNA or RNA step by step from the 5’ or 3’ terminus, producing nucleotides or short oligos. Commonly used in nucleic acid cleanup, recycling, or sequencing preparation.

Endonucleases work like “precision scissors.” They cleave within a nucleic acid strand at specific recognition sites or structures, without needing free ends. These are essential in gene editing, mismatch detection, and pathogen assays.

Table 1. Yeasen Endonuclease Selection Guide

Product	Cat. No.	Key Features	Typical Applications
DNase I	10325ES / 14549ES / 10607ES	Randomly cleaves DNA in the presence of Mg²⁺/Mn²⁺	Removal of genomic DNA during RNA extraction, gDNA clearance before reverse transcription, digestion of DNA templates after in vitro transcription, rRNA removal during RNA library prep, DNA nick translation labeling, DNase I footprinting assays
Thermolabile dsDNase	14544ES	Specifically digests dsDNA into small fragments; heat-inactivatable	Removal of genomic DNA prior to reverse transcription
Micrococcal Nuclease	14547ES	Degrades ssDNA, dsDNA, linear or circular DNA/RNA	Chromatin immunoprecipitation (ChIP)
UltraNuclease	20157ES / 20159ES	Broad-spectrum nuclease, digests nucleic acids into 2–5 bp 5'-monophosphate oligonucleotides	Host DNA/RNA removal in virus purification, vaccine production, protein/polysaccharide biopharma; reduces viscosity of cell culture supernatants and lysates
T7 Endonuclease I	14548ES	Cleaves mismatched or cruciform DNA at the mismatch 5' side	Gene editing efficiency analysis
Endonuclease VIII	14536ES	DNA glycosylase + AP lyase activity	NGS library repair, cloning with uracil-containing fragments
T4 Endonuclease V	14542ES	Specifically cleaves pyrimidine dimers in DNA	UV-damage repair, photoreactivation studies
Endonuclease IV	14543ES	Cleaves oxidized/AP site DNA	DNA oxidative damage repair, comet assay, alkaline elution, alkaline unwinding
RNase A	10405ES / 10406ES / 10407ES	Specifically degrades ssRNA at C and U residues	Plasmid/genomic DNA prep, RNA removal from protein preps, RNase protection assays
RNase H	12906ES / 14545ES	Hydrolyzes RNA in DNA/RNA hybrids	rRNA removal, second-strand cDNA synthesis, poly(A) removal after Oligo(dT) priming, site-specific RNA cleavage
RNase HII	14539ES	Recognizes DNA–rN–DNA/DNA duplex; cleaves at single ribonucleotide sites from the 5’ end	LAMP probe-based detection, RNaseHII-dependent PCR (rhPCR), removal of misincorporated rNTPs, degradation of RNA primers in Okazaki fragments
Restriction Endonucleases	15001–15300ES	Recognize and cut dsDNA at specific sequences	Molecular cloning, DNA methylation analysis, mapping and fingerprinting, linearization of mRNA plasmid templates, library construction

Table 2. Yeasen Exonuclease Selection Guide

Product	Cat. No.	Key Features	Typical Applications
Exonuclease I	14535ES	3'→5' hydrolysis of ssDNA; no activity on dsDNA/RNA	Primer removal after PCR, ssDNA purification
Exonuclease III	14525ES	Digests dsDNA from the 3'-OH end, releasing nucleotides	Nested deletion, site-directed mutagenesis, strand-specific probe prep, ssDNA generation
T5 Exonuclease	14538ES	5'→3' digestion of DNA; no activity on supercoiled dsDNA	Seamless cloning, degradation of denatured plasmid DNA, removal of unligated linear templates
T7 Exonuclease	14272ES	5'→3' digestion of dsDNA or RNA/DNA hybrids	Seamless cloning, ssDNA preparation, degradation of denatured plasmids, removal of unligated linear templates
Lambda Exonuclease	14527ES	5'→3' high-efficiency degradation of dsDNA; requires 5'-phosphorylated ends	ssDNA generation, plasmid denatured DNA digestion
RNase R	14606ES / 14615ES	3'→5' exoribonuclease; digests linear RNA but spares circular RNA, lariat RNA, or structured RNA with <7 nt 3’ overhang	Enrichment of circular RNA (circRNA)

 

Proven Performance: Yeasen Nucleases vs. Imports

Our data shows Yeasen nucleases deliver import-quality performance—validated across multiple applications.

1. Recombinant DNase I (RNase-Free, Yeast) (Cat#14549ES)

High digestion efficiency: Compared side-by-side with leading Supplier A, Yeasen DNase I achieved equivalent DNA removal efficiency when digesting 1 μg plasmid DNA.

Figure 2. Plasmid DNA Removal Efficiency Verification

RNA-friendly: In RNA extraction workflows, treatment of 12 mouse liver samples with 20 U of Yeasen DNase I removed contaminating DNA without compromising RNA integrity, as confirmed by agarose gel analysis. Ideal for RNA prep workflows.

Figure 3. RNA Extraction Application Verification

2. Thermolabile dsDNase (Cat#14544ES)

Strong activity, easy inactivation: At only 0.2 U, Yeasen Thermolabile dsDNase fully digested 1 μg calf thymus DNA.

Convenient heat inactivation: Incubation at 65 °C for 10 min completely inactivated the enzyme, matching the performance of Suppliers A and B.

Figure 4. Thermolabile dsDNase Thermostability Verification Results 

3. Micrococcal Nuclease (Cat#14547ES)

DNA digestion efficiency equivalent to Supplier A*:

Yeasen Micrococcal Nuclease and Supplier A’s nuclease were tested side by side on a 1 μg λ DNA substrate in a 50 μL reaction system at 37 °C for 15 minutes. Agarose gel electrophoresis results confirmed that Yeasen Micrococcal Nuclease delivered DNA digestion performance on par with Supplier A’s product.

Figure 5. DNA Substrate Excision Capability Verification

4. T7 Endonuclease I (Cat#14548ES)

Mismatch cleavage power: Both Yeasen and Supplier A’s T7 Endonuclease I effectively digested 200 ng dsDNA containing mismatched bases. At 20 U, Yeasen’s enzyme delivered equivalent cutting activity, validated by agarose gel electrophoresis.

Figure 6. T7 Endonuclease I Cleavage Efficiency Verification (Note: Substrate Input - 200 ng)

Reference

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[2] Alexander M, Heppel LA, Hurwitz J. The purification and properties of micrococcal nuclease. Journal of Biological Chemistry. 1961;236:3014-3019.

[3] Wang M, Fu Z, Li B, et al. One-step, ultrasensitive, and electrochemical assay of microRNAs based on T7 exonuclease assisted cyclic enzymatic amplification[J]. Analytical Chemistry, 2014, 86(12): 5606-5610.

[4] Mol C D, Kuo C F, Thayer M M, et al. Structure and function of the multifunctional DNA-repair enzyme exonuclease III[J]. Nature, 1995, 374(6520): 381-386.

[5] Kushner S R, Nagaishi H, Templin A, et al. Genetic recombination in Escherichia coli: the role of exonuclease I[J]. Proceedings of the National Academy of Sciences, 1971, 68(4): 824-827.