Nucleases

<h2>What Are Nucleases?</h2>
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Nucleases are enzymes that cleave phosphodiester bonds between nucleotide subunits in nucleic acids. Deoxyribonucleases (DNases) act on DNA; ribonucleases (RNases) act on RNA; and some nucleases (S1 Nuclease, Mung Bean Nuclease) act on both single-stranded DNA and RNA. Nucleases are further divided into endonucleases, which cleave internal phosphodiester bonds, and exonucleases, which progressively remove nucleotides from the 5' or 3' terminus of a strand. Major research nucleases include DNase I (non-specific endonuclease for both ss- and ds-DNA), RNase A (cleaves single-stranded RNA at pyrimidine residues), RNase H (degrades the RNA strand of RNA: DNA hybrids), Exonuclease III (removes nucleotides from 3'-recessed or blunt ends of duplex DNA), S1 Nuclease (degrades single-stranded DNA or RNA), and RNase R (degrades linear RNA but not circular RNA). Match the nuclease to the substrate type (single-stranded vs. double-stranded, DNA vs. RNA), the directionality required (endo vs. exo), and cofactor compatibility with your reaction buffer.
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<h2 dir="ltr">What you will find:</h2>
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PureRec RNase A (Recombinant): A ribonuclease free of animal-derived components, designed for the swift elimination of RNA from DNA samples, ensuring no threat of viral contamination.
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DNase I Set (RNase-free): A highly effective endonuclease formulated for complete DNA digestion in delicate RNA applications while preserving the integrity of the transcript.
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PureRec Duplex-Specific Nuclease (DSN): A unique enzyme designed to equalize high-abundance transcripts, greatly enhancing the identification of rare variants in cDNA libraries.
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RNase R: A distinctive 3'-to-5' exoribonuclease that breaks down linear RNA but preserves circular RNA forms, crucial for the identification of circRNA.
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RNaseOFF Inhibitor: A strong protein-based barrier that counteracts a wide range of RNases, maintaining the delicate transcriptional environment of your samples.
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<h2>How to Choose Nucleases</h2>
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DNase selection
DNase I (bovine pancreatic, recombinant) non-specifically cleaves both single- and double-stranded DNA in the presence of Mg2+ (random cleavage) or Mn2+ (double-strand cuts at approximately the same position on both strands). Use RNase-free DNase I for RNA preparations to remove genomic DNA contamination. Use Plasmid-Safe ATP-Dependent DNase to selectively degrade linear double-stranded DNA while preserving supercoiled and relaxed circular plasmid DNA. Baseline-ZERO DNase is optimized for the complete removal of trace DNA without damaging RNA.
RNase selection
RNase A cleaves single-stranded RNA at pyrimidine (C and U) residues to produce 3'-pyrimidine nucleotides; it is used to remove RNA from DNA preps, to perform RNase protection assays, and to analyze RNA secondary structure. RNase H degrades the RNA strand of RNA: DNA duplexes and is used after first-strand cDNA synthesis to remove the mRNA template. RNase R (3'-&gt;5' exoribonuclease) degrades all linear RNA without affecting circular RNA, and is used in circular RNA enrichment workflows and to characterize circular RNA splice junctions. Terminator 5'-Phosphate-Dependent Exonuclease (Terminator) digests linear RNA with a 5'-monophosphate, enriching for capped mRNA or circular RNA.
Exonuclease selection
Exonuclease III (Exo III) removes nucleotides from the 3' terminus of duplex DNA and generates single-stranded regions used in unidirectional nested deletions, mapping regulatory elements, and generating single-stranded templates for sequencing. Exonuclease I (Exo I) digests single-stranded DNA in the 3'-&gt;5' direction and is used after PCR to remove unincorporated primers before Sanger sequencing. Lambda Exonuclease removes nucleotides from 5'-phosphorylated duplex DNA in the 5'-&gt;3' direction and is used in isothermal amplification and strand displacement workflows.
Cofactor and inhibitor sensitivity
DNase I requires Mg2+ or Ca2+ for activity and is completely inhibited by EDTA at a 5 mM concentration. RNase A is active across a wide pH range (optimum 7.0-7.5) and is exceptionally stable; inactivation requires proteinase K digestion, phenol-chloroform extraction, or RNase inhibitor protein. RNase H requires Mg2+; RNase R requires Mg2+ and is most active between 37-50 degrees C.
Purity and application grade
For RNA-focused applications, all nucleases used on DNA substrates must be certified RNase-free. For DNA-focused work, DNase-free grades of RNases are required. Confirm lot-specific QC contamination data from the manufacturer before use in sensitive workflows.
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<h2>Specifications Context</h2>
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DNase I activity is expressed in Kunitz units: 1 unit increases A260 by 0.001 per minute per mL during DNA hydrolysis at pH 5.0. RNase A activity is expressed as the amount of enzyme hydrolyzing 50% of an RNA substrate under defined conditions; it remains active at a wide range of temperatures and is notoriously difficult to inactivate (requires boiling in SDS, proteinase K digestion, or phenol-chloroform extraction). RNase R from E. coli degrades linear RNA processively in the 3'-&gt;5' direction and is used at 2-10 U per microgram of total RNA to enrich for circular RNA species. RNase R treatment before library construction is the standard method for circular RNA sequencing (circRNA-seq) workflows on both short-read and long-read platforms. For protecting RNA from RNase contamination during nuclease-adjacent workflows, see&nbsp;<a href="https://mbpinc.net/reagents/molecular-biology/enzymes-and-inhibitors">RNase inhibitors</a>&nbsp;in the parent Enzymes and Inhibitors category.
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Safeguard your molecular images&mdash;<a href="https://mbpinc.net/contact-us">reach out to the MBP team</a> now to obtain a quote for our sophisticated nucleases and inhibitors.

MSDS

2X DSN Stop Solution (50 ml)

E1020-4-50 by Zymo Research — 2X DSN Stop Solution; 50 mL; designed to inactivate PureRec Duplex-Specific Nuclease (DSN) in DSN normalization and cDNA library subtraction workflows; made in USA.

Manufacturer

Shipping Condition

Storage Condition

DataSheet

Protocol

DNase I Set (RNase-free)

E1010 by Zymo Research is a recombinant DNase I Set (RNase-free), supplied lyophilized with DNA Digestion Buffer. One unit = 12 Kunitz units. Guaranteed RNase-free and protease-free; stable through ≥10 freeze-thaw cycles. Heat-inactivated at 75°C/10 min. Available in 250 U, 1500 U, and 5×1500 U.

Unit Definition

Storage

Reconstitution

Inactivation

DNase I Set (250 U) w/ DNA Digestion Buffer (4 ml)

DNase I Set (1500 U) w/ DNA Digestion Buffer (4 ml)

DNase I Set (5 x 1500 U) w/ DNA Digestion Buffer (16 ml)

PureRec Duplex-Specific Nuclease(Liquid)

E1020-200 by Zymo Research is PureRec Duplex-Specific Nuclease (DSN), 200&nbsp;U at 1&nbsp;U/&micro;l (200&nbsp;&micro;l, liquid). Selectively digests dsDNA and DNA-RNA hybrids; spares ssDNA and RNA. Purity &gt;95%, RNase-free. Optimal at 60&deg;C. Also available as E1020-1000.

Concentration

Optimal Temperature

Reaction Buffer

Stop Solution

PureRec Duplex-Specific Nuclease (1 U/µl, 200 µl) (Liquid)

PureRec Duplex-Specific Nuclease (1 U/ul, 1000 ul) (Liquid)

PureRec RNase A (Recombinant)

PureRec RNase A Recombinant (E1019-5) by Zymo Research — 5 mg at 1 mg/ml, tag-free recombinant RNase A. DNase-free, protease-free, and animal-free. Active across a wide range of buffer conditions. For RNA removal from DNA and protein samples, NGS, and cloning workflows. Made in the USA.

PureRec RNase A (0.1 mg, 100 µl) (Liquid)

PureRec RNase A (5 mg, 1 mg/ml (Liquid)

PureRec RNase A (20 mg, 1 mg/ml) (Liquid)

RNase A (30 mg)

RNase A (30 mg) (E1008-30) by Zymo Research — lyophilized, DNase-free, protease-free bovine pancreas RNase A, reconstitutable to 10 mg/ml. Thermostable; cleaves single-stranded RNA at 3' pyrimidine residues for RNA removal in DNA/plasmid purification workflows.

United States

Texas

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