Application of Nucleases in Nucleic Acid Sample Processing, Contamination Control, and Molecular Experiment Quality Control

Nucleases are enzymes that catalyze the hydrolysis of phosphodiester bonds in DNA or RNA. They play fundamental roles in nucleic acid extraction, sample purification, contamination control, and molecular experiment quality control. Their application is not simply to “degrade nucleic acids,” but to selectively remove DNA, RNA, free nucleic acids, host nucleic acids, or residual amplification products according to the experimental objective, thereby improving sample purity, reducing background interference, and ensuring the reliability of downstream detection results.

Keywords: nuclease; DNase; RNase; Benzonase; MNase; nucleic acid sample processing; DNA contamination control; RNA contamination control; qPCR; RT-qPCR; NGS; molecular experiment quality control; nucleic acid degradation

1 Functional Positioning of Nucleases

1.1 Role in Nucleic Acid Sample Processing

(1) Removal of non-target nucleic acids

In nucleic acid sample processing, it is often necessary to retain one type of nucleic acid while removing another. For example, DNase is used after RNA extraction to remove genomic DNA contamination; RNase is used during plasmid DNA or genomic DNA preparation to remove RNA contamination; broad-spectrum nucleases are used in protein, virus-like particle, or extracellular vesicle samples to remove free host nucleic acids.

(2) Reduction of sample background

In qPCR, RT-qPCR, digital PCR, NGS library preparation, and protein purification, non-target nucleic acids can increase background, cause quantitative bias, or reduce library complexity. Nuclease treatment can reduce interference from free nucleic acids, host nucleic acids, and residual templates.

(3) Improvement of downstream compatibility

Nuclease treatment can reduce sample viscosity, minimize nucleic acid–protein complex interference, and improve column- or magnetic bead-based purification efficiency. For high-cell-count lysates, viscous tissue homogenates, blood-derived samples, and viral preparation samples, nucleases are often used to improve processing efficiency.

1.2 Role in Contamination Control

(1) DNA contamination control

DNA contamination in molecular experiments may originate from genomic DNA, plasmids, PCR products, aerosols, environmental surfaces, or reagent residues. DNase or composite nucleases can be used to degrade accessible DNA contamination, but their potential impact on target samples must be considered.

(2) RNA contamination control

RNA contamination can affect DNA quantification, DNA purification, transcription experiments, and some sequencing library preparation workflows. RNase can effectively remove RNA, but in RNA experiments, RNase itself is also one of the most critical contamination sources to control.

(3) Amplification product contamination control

PCR product contamination is a high-risk issue in molecular diagnostics and high-throughput amplification experiments. Nucleases can be used for environmental cleaning or non-target nucleic acid degradation. For carryover contamination within amplification systems, the dUTP/UNG system, physical workflow separation, and aerosol control are often required together.

1.3 Role in Quality Control

(1) Verification of sample purity

Comparing RT-qPCR signals before and after DNase treatment can help determine the degree of genomic DNA contamination in RNA samples. Comparing nucleic acid signals before and after RNase treatment can help evaluate RNA residue levels in DNA preparations.

(2) Verification of molecular form

Nucleases can be used to determine whether nucleic acids are protected by proteins, lipid membranes, exosome membranes, or viral capsids. Protected nucleic acids are relatively resistant to externally added nucleases, whereas free nucleic acids are more readily degraded.

(3) Verification of experimental specificity

In transcriptomics, viral nucleic acid detection, extracellular free nucleic acid research, and environmental nucleic acid detection, nuclease treatment can serve as a specificity validation step to distinguish free contaminating nucleic acids from structurally protected target nucleic acids.

2 Types of Nucleases and Functional Differences

2.1 DNase

(1) Substrate specificity

DNases mainly hydrolyze DNA, including single-stranded DNA, double-stranded DNA, or specific DNA structures. The most commonly used enzyme is DNase I, which cleaves DNA phosphodiester bonds to generate shorter DNA fragments.

(2) Application focus

DNase is mainly used to remove genomic DNA contamination from RNA samples. It can also be used to remove free DNA from protein samples, viral samples, or cell lysates. In RT-qPCR, RNA-seq, and transcriptional analysis, DNase treatment is an important step for controlling DNA contamination.

(3) Precautions

After DNase treatment, residual enzyme must be completely inactivated or removed; otherwise, it may affect subsequent DNA-related experiments. When DNase is used in RNA samples, RNase-free DNase should be selected, and reaction time, temperature, and buffer system should be controlled to avoid RNA degradation.

2.2 RNase

(1) Substrate specificity

RNases mainly hydrolyze RNA. RNase A is commonly used to remove RNA contamination during DNA preparation, while RNase H specifically degrades the RNA strand in RNA-DNA hybrids and has special applications in cDNA synthesis and nucleic acid structure analysis.

(2) Application focus

RNase A is commonly used in plasmid extraction, genomic DNA extraction, and protein sample processing to reduce the effects of RNA residue on A260 quantification, gel electrophoresis, and purification efficiency. RNase H is often used to remove RNA-DNA hybrid structures and improve cDNA-related reactions.

(3) Risk control

RNase is highly stable, resistant, and prone to environmental contamination, making it one of the most common destructive contaminants in RNA experiments. During RNA extraction, RNA storage, RT-qPCR, and RNA-seq library preparation, unintended RNase entry into the system should be strictly avoided.

2.3 Broad-Spectrum Nucleases

(1) Activity range

Broad-spectrum nucleases can degrade both DNA and RNA and usually act on single-stranded, double-stranded, linear, and circular nucleic acids. Benzonase-type nucleases, universal nucleases, and salt-tolerant nucleases all fall within this application category.

(2) Application focus

Broad-spectrum nucleases are commonly used in protein purification, viral vector preparation, vaccine production, cell lysate viscosity reduction, host nucleic acid removal, and clearance of exogenous free nucleic acids. Their advantage lies in broad substrate range and high degradation efficiency, making them suitable for complex biological samples.

(3) Application boundary

If the experimental target itself is nucleic acid analysis, broad-spectrum nuclease treatment must be used cautiously. It can rapidly destroy target DNA or RNA and is therefore more suitable for processing non-nucleic-acid target samples, or for experimental designs that distinguish free nucleic acids from structurally protected nucleic acids.

2.4 Micrococcal Nuclease and Structure-Specific Nucleases

(1) Micrococcal nuclease

Micrococcal nuclease (MNase) can cleave DNA and RNA and is commonly used for chromatin fragmentation, nucleosome positioning, MNase-seq, and immunoprecipitation-related chromatin processing. Its application focus is not simple contamination removal, but controlled fragmentation.

(2) Fusion MNases

pA-MNase, pAG-MNase, and pG-MNase bind antibodies through Protein A, Protein A/G, or Protein G and perform targeted chromatin cleavage after antibody localization. They are commonly used in CUT&RUN and related epigenetic research.

(3) Structure-specific nucleases

S1 nuclease, P1 nuclease, RNase T1, and RNase III have specific substrate preferences and are suitable for nucleic acid structure analysis, single-stranded region cleavage, double-stranded RNA processing, or nucleotide preparation. Selection of these enzymes should be based on substrate structure and experimental purpose.

Table 1. Common Nuclease Types and Application Characteristics

Nuclease Type	Main Substrate	Representative Enzymes	Main Uses	Risk Points
DNase	DNA	DNase I, DNase II	Removes genomic DNA from RNA samples; reduces DNA background	Residual enzyme may affect DNA experiments
RNase	RNA	RNase A, RNase H, RNase T1	Removes RNA during DNA preparation; processes RNA-DNA hybrids	Unintended contamination can destroy RNA samples
Broad-spectrum nuclease	DNA and RNA	Universal nuclease, Benzonase-type nuclease, SAN	Removes host nucleic acids; reduces lysate viscosity	Can destroy target nucleic acids
Micrococcal nuclease	DNA and RNA	MNase, pA-MNase, pAG-MNase	Chromatin fragmentation, nucleosome studies, CUT&RUN	Improper conditions may cause overdigestion
Structure-specific nuclease	Specific nucleic acid structures	S1 nuclease, P1 nuclease, RNase III	Single-stranded nucleic acid processing, dsRNA processing, nucleotide preparation	Strong substrate selectivity; conditions must be controlled

3 Applications in Nucleic Acid Sample Processing

3.1 DNA Removal from RNA Samples

(1) Application scenarios

RNA extracts often contain residual genomic DNA, especially in tissues, high-cell-count samples, incompletely lysed samples, or insufficiently washed column-purified samples. If DNA is not removed, no-reverse-transcription controls in RT-qPCR may still show amplification signals, leading to overestimation of expression levels.

(2) Treatment strategies

RNA samples can be treated with DNase on the extraction column or after elution in solution. On-column treatment is simple and causes less sample loss; in-solution treatment is more complete, but DNase and salts must be removed afterward.

(3) Quality control

RNA samples should include no-RT controls to determine whether DNA contamination is present. If the no-RT control still shows clear amplification, DNase treatment conditions should be optimized, or primers spanning exon-exon junctions should be redesigned to reduce the risk of genomic DNA amplification.

3.2 RNA Removal from DNA Samples

(1) Application scenarios

RNA residue is common in genomic DNA or plasmid DNA preparations and may appear as elevated A260 values, low-molecular-weight smears on electrophoresis, or changes in sample viscosity. RNA contamination affects DNA concentration estimation, restriction digestion, sequencing, and downstream reaction systems.

(2) Treatment strategies

RNase A is often added to lysis buffers or pre-purification systems so that RNA is degraded before purification. For high-purity DNA preparation, RNase dosage and reaction time should be controlled, and residual protease and RNase should be removed through subsequent purification.

(3) Quality control

DNA samples can be evaluated using agarose gel electrophoresis, band pattern, A260/A280, A260/A230, and fluorescence-based quantification. If the A260-based concentration is much higher than fluorescence dye-based quantification, RNA contamination or free nucleotide interference should be considered.

3.3 Host Nucleic Acid Removal from Protein and Viral Samples

(1) Protein samples

Nucleic acids in cell lysates significantly increase viscosity and can form complexes with proteins, affecting centrifugation, filtration, chromatography, and electrophoretic analysis. Broad-spectrum nucleases can reduce nucleic acid viscosity and improve protein purification efficiency.

(2) Viral vector samples

Viral particle preparations often contain host-cell DNA, plasmid DNA, RNA, and free nucleic acids. Added broad-spectrum nucleases can degrade free nucleic acids not protected by capsids or membrane structures, helping reduce host nucleic acid residues.

(3) Exosome and extracellular vesicle samples

Nuclease treatment can be used to distinguish free nucleic acids outside vesicles from protected nucleic acids inside vesicles. Enzyme-treated, enzyme-plus-detergent, and untreated groups are usually required to determine whether nucleic acids are protected by membrane structures.

3.4 Controlled Fragmentation of Chromatin Samples

(1) MNase digestion

MNase can digest chromatin into DNA fragments associated with nucleosome-protected regions. Digestion degree is affected by enzyme amount, Ca²⁺, temperature, time, chromatin accessibility, and sample input.

(2) CUT&RUN-related cleavage

pA-MNase, pAG-MNase, and pG-MNase localize to target protein-binding regions through antibodies and then perform local chromatin cleavage, making them suitable for epigenetic locus analysis and low-background chromatin enrichment.

(3) Quality control focus

MNase-related experiments require control of fragment length distribution and overdigestion risk. Insufficient digestion results in long fragments and high background; excessive digestion may cause loss of specific fragments and affect downstream library preparation and sequencing.

Table 2. Nuclease Selection for Different Sample Processing Scenarios

Sample Type	Main Problem	Recommended Nuclease	Treatment Objective	Quality Control Focus
RNA sample	Residual genomic DNA	RNase-free DNase I, heat-labile dsDNase	Remove DNA contamination	No-RT control, RNA integrity
Genomic DNA	RNA residue	RNase A	Reduce RNA background	Difference between A260 and fluorescence quantification; electrophoretic smear
Plasmid DNA	RNA residue and low-molecular-weight nucleic acids	RNase A	Improve plasmid purity	Restriction digestion, sequencing, A260/A280
Protein lysate	Nucleic acid-induced viscosity	Universal nuclease, salt-tolerant nuclease	Reduce viscosity and improve purification efficiency	Protein activity, residual nucleic acids
Viral vector	Residual free host nucleic acids	Broad-spectrum nuclease, salt-tolerant nuclease	Reduce host DNA/RNA background	Distinguish capsid-protected nucleic acids from free nucleic acids
Chromatin sample	Controlled fragmentation required	MNase, pA-MNase, pAG-MNase	Nucleosome fragmentation or targeted cleavage	Fragment length distribution, overdigestion control

4 Applications in Contamination Control

4.1 DNA Contamination Control

(1) Sources of contamination

DNA contamination may originate from genomic DNA, plasmid DNA, PCR products, environmental aerosols, pipettes, benchtops, centrifuge tubes, and reagent residues. In PCR experiments, amplicon contamination can easily cause false positives.

(2) Scope of nuclease treatment

DNase can degrade exposed DNA contamination, but it cannot penetrate intact cells, viral particles, or protective protein complexes. Environmental surface contamination usually also requires chemical cleaners, UV irradiation, and laboratory workflow separation.

(3) Precautions

DNase cannot be directly added to PCR systems in which DNA templates must be preserved. If used for environmental or reagent pretreatment, DNase must be completely inactivated or removed afterward to avoid degrading subsequent target DNA.

4.2 RNase Contamination Control in RNA Experiments

(1) Contamination characteristics

RNases have widespread sources, including skin, dust, untreated consumables, ordinary water, pipettes, and reagents. RNase is highly stable, and even small amounts of contamination can cause RNA degradation.

(2) Control strategies

RNA experiments should use RNase-free water, consumables, and reagents, and should be performed in a dedicated area. RNase inhibitors can be used when needed to protect RNA samples. Repeated freeze-thaw cycles and prolonged room-temperature exposure should be avoided.

(3) Quality control

RNA integrity can be assessed by electrophoresis, Bioanalyzer, TapeStation, or RIN value. If obvious RNA degradation occurs, sources of RNase contamination should be investigated step by step, including sampling, lysis, extraction, storage, and the operating environment.

4.3 PCR Product Contamination and Carryover Control

(1) Contamination characteristics

PCR products have high copy numbers and diffuse easily; very small amounts of contamination can cause false positives. Conventional DNase is not suitable for direct control of product contamination inside amplification reactions.

(2) UNG/dUTP system

Replacing dTTP with dUTP in PCR systems and adding UNG before amplification can degrade uracil-containing amplicons from previous reactions, reducing the risk of carryover contamination. UNG is not a typical nuclease, but it plays an important role in amplification contamination control.

(3) Workflow separation

Pre-amplification areas, template addition areas, and post-amplification analysis areas should be physically separated. Nuclease treatment is only part of contamination control and cannot replace aerosol prevention, negative controls, and standardized experimental workflows.

4.4 Removal of Environmental and Instrument Surface Contamination

(1) Targets for removal

Molecular laboratory benchtops, pipette exterior surfaces, centrifuge tube racks, PCR preparation areas, and pre-library preparation areas may contain residual DNA, RNA, or nuclease contamination. Ready-to-use cleaners can be used to reduce environmental background.

(2) Application boundaries

Nucleases and nucleic acid cleaners are suitable for environmental surface treatment. They should not directly replace enzymatic treatment inside samples, nor should they be mixed with reaction systems in which nucleic acid templates need to be preserved.

(3) Workflow control

Environmental cleaning should be combined with spatial separation, dedicated consumables, aerosol-resistant filter tips, negative controls, and routine monitoring. A single cleaning step cannot replace a long-term contamination control system.

5 Applications in Molecular Experiment Quality Control

5.1 qPCR and RT-qPCR Quality Control

(1) RNA experiments

In RT-qPCR, DNase treatment can reduce genomic DNA interference. A no-RT control must be included to determine whether DNA contamination affects Ct values. If the target gene has no intron or primers cannot span exon-exon junctions, DNase treatment is especially important.

(2) DNA experiments

When qPCR is used to detect DNA templates, residual DNase or broad-spectrum nuclease must be prevented from entering the system. If the DNA template is partially degraded, amplification efficiency may decrease, Ct values may increase, or long-fragment amplification may fail.

(3) Contamination assessment

Amplification in no-template controls indicates contamination in the reaction system, primers, probes, water, or environment. Such problems should not be solved only by adding nuclease; instead, the contamination source should be traced and key reagents should be freshly prepared.

5.2 NGS Library Preparation Quality Control

(1) RNA-seq

RNA-seq is highly sensitive to both DNA contamination and RNA integrity. DNase treatment can reduce the proportion of genomic DNA reads, but excessive treatment or RNase contamination can cause RNA degradation, affecting library complexity and coverage uniformity.

(2) DNA-seq

In DNA library preparation, residual RNA usually affects quantification and purification, but excessive nuclease treatment can damage target DNA. DNA sample pretreatment should distinguish between two goals: removing RNA contamination and preserving DNA integrity.

(3) Low-input samples

Single-cell samples, microdissected tissues, cfDNA, and degraded samples are highly sensitive to nuclease treatment. In such samples, any non-target nucleic acid removal step should be validated by pilot experiments to avoid irreversible sample loss.

5.3 Molecular Diagnostic Quality Control

(1) False-positive control

Molecular diagnostics are highly sensitive to contamination. Nucleases can be used for environmental and reagent pretreatment, but the core controls remain workflow separation, negative controls, positive controls, internal reference controls, and carryover prevention systems.

(2) False-negative control

Nuclease residue, excessive sample treatment, target nucleic acid degradation, and residual inhibitors can all cause false negatives. Therefore, nuclease use must be followed by inactivation, purification, or removal steps, and amplification capacity should be verified using internal references or exogenous quality controls.

(3) Batch consistency

Nuclease activity is affected by temperature, buffer, ionic strength, pH, and inhibitors. In molecular diagnostics or high-throughput experiments, enzyme amount, reaction time, and inactivation conditions should be fixed to reduce batch-to-batch variation.

Table 3. Role of Nucleases in Molecular Experiment Quality Control

Experiment Type	Main Risk	Nuclease Application	Required Controls
RT-qPCR	Genomic DNA contamination in RNA	DNase treatment of RNA	No-RT control, NTC
qPCR	Template contamination or nuclease residue	Environmental/reagent pretreatment	NTC, positive control, internal reference
RNA-seq	gDNA contamination, RNA degradation	Mild DNase treatment	RNA integrity assessment, library QC
DNA-seq	RNA contamination, DNA degradation	RNase treatment of DNA samples	DNA integrity and quantification QC
Viral nucleic acid detection	Free nucleic acid background, false positives	Nuclease distinguishes free/protected nucleic acids	Enzyme-treated group, untreated group, extraction negative control
Exosome nucleic acids	Exogenous free nucleic acid contamination	DNase/RNase treatment	Detergent-plus-enzyme group, untreated group
CUT&RUN	Non-specific chromatin background	pA-MNase/pAG-MNase targeted cleavage	IgG control, no-antibody control

6 Key Control Points in Nuclease Use

6.1 Enzyme Activity Conditions

(1) Buffer system

Nuclease activity depends on pH, salt concentration, metal ions, and buffer composition. DNase I usually requires Mg²⁺ or Ca²⁺ to maintain activity; some broad-spectrum nucleases also depend on magnesium ions. If the buffer system is incompatible, digestion may be incomplete.

(2) Temperature and time

Most nucleases show higher activity within specific temperature ranges. Insufficient time leaves residual nucleic acids, while excessive time may increase non-target damage or sample degradation risk. Conditions should be optimized according to sample complexity and target nucleic acid protection requirements.

(3) Effects of inhibitors

EDTA, strong denaturants, high salt, detergents, protease inhibitors, phenol, ethanol residues, and some lysis buffer components can affect nuclease activity. Reagent compatibility should be confirmed before treatment.

6.2 Enzyme Inactivation and Removal

(1) Heat inactivation

Some nucleases can be inactivated by heating, but not all enzymes can be completely heat-inactivated. RNase A is highly stable, and heating alone is usually not suitable as a complete inactivation strategy. Heat-labile dsDNase is suitable for DNA removal scenarios requiring mild inactivation.

(2) Chelation-based inactivation

For metal ion-dependent nucleases, EDTA can chelate metal ions and reduce activity. However, residual EDTA may affect subsequent enzymatic reactions, such as PCR, reverse transcription, ligation, and restriction digestion.

(3) Purification-based removal

Column purification, magnetic bead purification, phenol-chloroform extraction, or protease treatment can be used to remove nucleases and reaction components. For downstream sensitive experiments, purification-based removal is more reliable than inactivation alone.

6.3 Protection of Target Nucleic Acids

(1) Clarify what must be retained

Before using nuclease, it must be clear whether DNA, RNA, protein, viral particles, or vesicle structures should be preserved. If the experimental target is nucleic acid itself, nucleases with broad substrate range or harsh treatment conditions should be avoided.

(2) Set digestion controls

Nuclease treatment experiments should include at least an untreated group, an enzyme-treated group, and, when necessary, an enzyme-plus-detergent group. This helps distinguish whether nucleic acids are structurally protected, freely exposed, or inherently digestion-resistant.

(3) Avoid cross-contamination

DNase, RNase, and broad-spectrum nucleases should be stored and used in separate areas to avoid entering unrelated experimental systems. RNase-related operations should be especially isolated from RNA experiment environments.

7 Common Problems and Troubleshooting Directions

7.1 DNA Contamination Persists After DNase Treatment

Possible causes include insufficient enzyme amount, insufficient reaction time, tight association of DNA with proteins or chromatin, insufficient metal ions in the buffer, or excessive sample input. DNase amount can be increased, reaction time extended, lysis conditions optimized, and treatment effects verified using no-RT controls.

7.2 RNA Samples Degrade After DNase Treatment

Common causes include RNase contamination in the DNase reagent, RNase contamination in the operating environment, excessively long reaction time, or repeated freeze-thaw cycles. RNase-free DNase and RNase-free consumables should be used, treatment time should be shortened, and RNase inhibitors may be added when necessary.

7.3 RNA Smearing Persists in DNA Samples After RNase Treatment

This may be related to insufficient RNase amount, RNA secondary structure, incomplete lysis, or excessive RNA content in the sample. RNase can be added during the lysis stage, reaction time can be extended, and degradation fragments can be removed through subsequent purification.

7.4 Protein Recovery Decreases After Broad-Spectrum Nuclease Treatment

Broad-spectrum nucleases usually do not directly degrade proteins, but salt concentration, metal ions, incubation time, and viscosity changes during treatment may affect the stability of protein complexes. It is necessary to evaluate whether the target protein depends on nucleic acids or nucleic acid-binding structures and to optimize reaction conditions.

7.5 Abnormal MNase Digestion Fragment Distribution

When MNase digestion is insufficient, fragments are longer and background is higher. When digestion is excessive, nucleosome-protected fragments or targeted cleavage fragments may be lost. Appropriate conditions should be determined through enzyme amount gradients, time gradients, and fragment analysis.

Table 4. Common Problems in Nuclease Applications

Problem	Possible Cause	Effect on Results	Adjustment Direction
Amplification remains in no-RT after DNase treatment	Incomplete DNA digestion	RT-qPCR expression level is overestimated	Increase enzyme amount, optimize buffer, design exon-spanning primers
RNA sample degradation	RNase contamination or overtreatment	RNA integrity decreases	Use an RNase-free system and shorten treatment time
Low-molecular-weight smearing in DNA sample	RNA residue or DNA degradation	Quantification and library preparation are affected	Perform RNase treatment and optimize purification workflow
Sample remains viscous	Insufficient nucleic acid degradation	Protein purification and pipetting are difficult	Increase broad-spectrum nuclease amount or extend reaction time
Downstream PCR failure	Residual nuclease or inhibitor	False negative or reduced amplification efficiency	Purify to remove enzyme and salts
Abnormal MNase fragments	Insufficient digestion or overdigestion	Abnormal library fragment distribution	Set enzyme amount and time gradients
Large batch-to-batch variation	Inconsistent enzyme activity, temperature, or time	Quantitative results are unstable	Fix processing workflow and include QC samples

8 Nuclease and Related Reagent Selection

Table 5. Nuclease Products for Nucleic Acid Sample Processing and Molecular Experiment Quality Control

Product Category	Cat. No.	Product Name	Grade / Specification	Role in the System	Applicable Direction
DNase	D406460	DNase I	Recombinant, PharmPure™, endotoxin tested, EnzymoPure™, ≥95%, 1.8KU/ml-2.2KU/ml	Degrades DNA and reduces DNA contamination or sample viscosity	Removal of genomic DNA from RNA samples; DNA background control in protein samples
DNase	R1373644	Recombinant DNase I, RNase-free	EnzymoPure™, ≥95%(SDS-PAGE), 1 U/μl	Degrades DNA while reducing RNase risk	Post-RNA-extraction treatment; DNA contamination control before RT-qPCR and RNA-seq
DNase	D755014	Deoxyribonuclease I from bovine pancreas	Type IV, lyophilized powder,≥2,000 Kunitz units/mg protein	Hydrolyzes DNA phosphodiester bonds	Routine DNA removal, sample viscosity reduction, nucleic acid contamination control
DNase	D755012	Deoxyribonuclease I from bovine pancreas	Type II, lyophilized powder, Protein≥80 %,≥2,000 units/mg protein	Degrades DNA	DNA residue treatment in biological samples; routine laboratory DNase digestion
DNase	D755016	Deoxyribonuclease I from bovine pancreas	lyophilized powder, Protein≥85 %,≥400 Kunitz units/mg protein	Degrades DNA	DNA removal from RNA samples, protein samples, or lysates
DNase II	D755001	Deoxyribonuclease II from bovine spleen	Type V, essentially salt-free, lyophilized powder,≥1,000 units/mg protein	Hydrolyzes DNA under acidic conditions	DNA degradation in specific acidic systems; nuclease activity research
DNase II	D128600	Deoxyribonuclease II from porcine spleen	EnzymoPure™, ≥800 units/mg dry weight	Acidic DNase activity	DNA degradation research and special sample processing
DNase II	D128605	Deoxyribonuclease II from porcine spleen(Purified,Solution)	EnzymoPure™, ≥12,000 units/mg protein	DNA hydrolysis under acidic conditions	Specific enzymology research and DNA degradation experiments
RNase A	R665518	RNase A	EnzymoPure™, DNase free, Protease Free, sterile, ≥90%(SDS-PAGE), 10 mg/mL	Degrades RNA and removes RNA contamination from DNA samples	RNA removal in plasmid DNA and genomic DNA preparation
RNase A	R128619	Ribonuclease A from bovine pancreas(DNase & Protease Free)	Bioactive,ActiBioPure™,Native,High Performance,EnzymoPure™,DNase free,Protease Free,≥2,000 units/mg protein	Removes RNA while reducing DNase and protease contamination risk	High-purity DNA preparation, plasmid purification, genomic DNA sample processing
RNase H	R754998	Ribonuclease H (RNase H)	from <I>Escherichia coli</I> H 560 <I>pol</I> A1	Specifically degrades RNA in RNA-DNA hybrids	Post-cDNA synthesis processing; RNA-DNA hybrid structure analysis
RNase III	R749972	RNase III (dsRNA-specific)	ActiBioPure™, EnzymoPure™, Bioactive, Animal Free, Carrier Free, sterile, DNase free, 2.0 U/µL	Degrades double-stranded RNA	dsRNA processing, RNA structure research, specific RNA sample quality control
RNase T1	R128610	Ribonuclease T1 from Aspergillus oryzae(Chromatographically Purif.)	EnzymoPure™, ≥300,000 units/mg protein	Specifically cleaves guanylate-related sites in RNA	RNA structure analysis, RNA fragmentation, nuclease mapping
Broad-spectrum nuclease	B401536	Binuclease	Bioactive,Recombinant,ActiBioPure™,endotoxin tested,High Performance,EnzymoPure™,expressed in Pichia pastoris，Protein Content ≥95% (Biuret test); ≥20 KU/mg enzyme powder	Broad-spectrum degradation of DNA and RNA	Protein purification, cell lysate viscosity reduction, host nucleic acid removal
Broad-spectrum nuclease	rp221814	Recombinant UltraNuclease	Carrier Free,Bioactive,ActiBioPure™,EnzymoPure™,His Tag,≥99%(SDS-PAGE)	Broad-spectrum nucleic acid degradation	Viral vector preparation, host nucleic acid removal from protein samples, molecular background control
Broad-spectrum nuclease	O775185	Omnipotent nuclease	ActiBioPure™, Bioactive, EnzymoPure™, Carrier Free, sterile, ≥99%(SDS-PAGE), ≥250 U/uL	Efficient DNA/RNA degradation	High-purity protein preparation, free nucleic acid removal from viral samples, sample viscosity reduction
Salt-tolerant nuclease	rp221815	Salt Active UltraNuclease	Carrier Free, Bioactive, ActiBioPure™, EnzymoPure™, Recombinant, ≥99%(SDS-PAGE), 250U/μL, expressed in E. coli	Maintains nucleic acid degradation capacity under relatively high-salt conditions	High-salt lysates, protein purification, host nucleic acid removal from complex samples
Salt-tolerant nuclease	S755009	Salt Active Nuclease (SAN)	Recombinant, expressed in <I>Pichia pastoris</I>	Degrades nucleic acids under high-salt conditions	High-salt sample processing; nucleic acid residue control in viral or protein samples
Heat-labile DNase	T751064	Thermolabile dsDNase	Animal Free,Carrier Free,Bioactive,Recombinant,ActiBioPure™,High Performance,EnzymoPure™,free of RNase and other DNA endonuclease and exonuclease. expressed in Pichia pastoris	Specifically degrades double-stranded DNA and can be heat-treated to reduce residual activity	RT-qPCR, DNA removal from RNA samples, molecular experiments requiring mild inactivation
S1 nuclease	N128634	Nuclease S1 from Aspergillus oryzae	EnzymoPure™,Native,≥100,000-500,000 units/ml	Degrades single-stranded DNA/RNA regions	Single-stranded nucleic acid removal, nucleic acid structure analysis, hybridization assay quality control
P1 nuclease	N1442771	Nuclease P1		Hydrolyzes nucleic acids into nucleotide-related products	Nucleic acid degradation analysis, nucleotide sample preparation
Micrococcal nuclease	N755004	Nuclease micrococcal from Staphylococcus aureus	100-300 units/mg protein	Cleaves DNA/RNA; commonly used for chromatin fragmentation	Chromatin digestion, nucleosome research, sample nucleic acid fragmentation
Micrococcal nuclease	N128635	Nuclease micrococcal from Staphylococcus aureus(Strain ATCC #27735)	EnzymoPure™, ≥6,000 units/mg protein	High-activity MNase digestion of nucleic acids	Chromatin fragmentation, nucleosome positioning, molecular quality control
Micrococcal nuclease	M1518341	Micrococcal Nuclease (MNase)	Bioactive,Recombinant,ActiBioPure™,High Performance,EnzymoPure™,≥95%(SDS-PAGE),expressed in E.coli;2000 gel units/μl	Chromatin and nucleic acid fragmentation	MNase-seq, chromatin accessibility research, nucleosome analysis
MNase kit	M1509374	Micrococcal Nuclease, MNase	BioReagent,for IP,ready-to-use	Provides an MNase treatment system	Immunoprecipitation-related chromatin digestion, nucleic acid sample fragmentation

Table 6. Products Related to Contamination Removal, Specialized Nucleases, and Quality Control Detection

Product Category	Cat. No.	Product Name	Grade / Specification	Role in the System	Applicable Direction
Nucleic acid / nuclease remover	R749975	RNase, DNase and DNA Away	BioReagent, ready-to-use	Removes environmental or surface DNA and related nuclease contamination	Contamination control for PCR areas, qPCR areas, nucleic acid experiment benches, and instruments
Nucleic acid / nuclease remover	R749976	RNase, DNase, RNA and DNA Away	BioReagent, ready-to-use	Removes RNA, DNA, and nuclease contamination	Environmental cleaning for RNA experiments, PCR experiments, and molecular detection
Nuclease remover	R749971	RNase and DNase Away	BioReagent, ready-to-use	Reduces RNase/DNase contamination risk	RNA experiment areas, nucleic acid extraction areas, pre-library preparation areas
Soil nuclease activity detection	S1522242	Soil Nuclease Activity Assay Kit (Micro Method)	BioReagent	Detects nuclease activity in soil samples	Environmental sample nuclease activity evaluation, soil microbiology-related research
Soil nuclease activity detection	S1522243	Soil Nuclease Activity Assay Kit (Colorimetric Method)	BioReagent	Detects soil nuclease activity by colorimetric method	Soil enzyme activity and environmental nucleic acid degradation capacity evaluation
pA-MNase fusion enzyme	P752086	Protein A-MNase (pA-MNase)	EnzymoPure™, ActiBioPure™, Animal Free, Carrier Free, Bioactive, sterile, 2000 gel units/μL	Performs local chromatin cleavage after antibody localization	CUT&RUN, targeted chromatin fragmentation
pAG-MNase fusion enzyme	P752085	Protein A/G-MNase (pAG-MNase)	EnzymoPure™, ActiBioPure™, Animal Free, Carrier Free, sterile, Bioactive, 2000 gel units/μL	Binds multiple antibody Fc regions to enable targeted MNase cleavage	CUT&RUN and CUT&Tag-related chromatin research
pG-MNase fusion enzyme	P752087	Protein G-MNase (pG-MNase)	EnzymoPure™, ActiBioPure™, Bioactive, Animal Free, Carrier Free, sterile, 2000 gel units/μL	Performs nucleic acid cleavage after Protein G-mediated antibody localization	Targeted chromatin digestion, epigenetic sample processing
Structure / target detection	EJ1514603	Human Flap Structure Specific Endonuclease 1 (FEN1) ELISA Kit	BioReagent	Detects FEN1 protein level	DNA repair mechanism research, FEN1 expression analysis
Nuclease inhibitor	L288189	LNT 1	≥98%(HPLC)	Inhibits FEN1 activity	DNA replication/repair mechanism research; not a routine sample-processing nuclease
RNase H inhibitor	N170153	NSC727447	Moligand™,≥98%	Inhibits viral RNase H activity	Antiviral mechanism research; not a routine nucleic acid sample-processing reagent

The value of nucleases in molecular experiments lies in their selectivity and controllability. Rational use of DNase, RNase, broad-spectrum nucleases, and MNase tools can improve nucleic acid sample purity, reduce contamination background, and strengthen experimental quality control. However, any nuclease treatment must be designed together with target nucleic acid protection, enzyme inactivation or removal steps, and necessary controls.

For more related articles, please see below:

[1] Nucleic Acid and Nuclease Decontamination in Biopharmaceutical Manufacturing and Molecular Testing Workflows

[2] Deoxyribonuclease (DNase): DNA Hydrolytic Cleavage Properties, Methodological Value, and Multi-Context Applications

[3] dsDNase-Mediated Hydrolysis of Double-Stranded DNA: Enzymatic Characteristics, Methodological Strategies, and Bioanalytical Applications

[4] Micrococcal Nuclease (MNase): A Technical Review of Enzymatic Properties, Reaction Control, and Research and Biomanufacturing Applications

[5] Proteinase K and Ribonuclease A