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Deoxyribonuclease
Deoxyribonuclease
Deoxyribonuclease
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Deoxyribonuclease (DNase, for short) refers to a group of glycoprotein endonucleases which are enzymes that catalyze the hydrolytic cleavage of phosphodiester linkages in the DNA backbone, thus degrading DNA. The role of the DNase enzyme in cells includes breaking down extracellular DNA (ecDNA) excreted by apoptosis, necrosis, and neutrophil extracellular traps (NET) of cells to help reduce inflammatory responses that otherwise are elicited. A wide variety of deoxyribonucleases are known and fall into one of two families (DNase I or DNase II), which differ in their substrate specificities, chemical mechanisms, and biological functions. Laboratory applications of DNase include purifying proteins when extracted from prokaryotic organisms. Additionally, DNase has been applied as a treatment for diseases that are caused by ecDNA in the blood plasma. Assays of DNase are emerging in the research field as well.

Types

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The two main types of DNase found in animals are known as deoxyribonuclease I (DNase I) and deoxyribonuclease II (DNase II). These two families have subcategories within them.

The DNase I Family: DNase I, DNase1L1, DNase 1L2, DNase1L3

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The first set of DNases is DNase I. This family consisted of DNase I, DNase1L1, DNase 1L2, and DNase1L3. DNase I cleaves DNA to form two oligonucleotide-end products with 5'-phospho and 3'-hydroxy ends and is produced mainly by organs of the digestive system. The DNase I family requires Ca2+ and Mg2+ cations as activators and selectively expressed.[1] In terms of pH, the DNAses I family is active in normal pH of around 6.5 to 8.

The DNase II Family: DNase II α and DNase II β

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The second set of DNAases is DNase II. This family consisted of DNase II α and DNase II β. Like DNAase I, DNAase II cleaves DNA to form two oligonucleotide-end products with 5'-hydroxy and 3'-phospho ends. This type of DNAase is more widely expressed in tissues due to high expression in macrophages but limited cell-type expression. Unlike DNAase I, they do not need Ca2+ and Mg2+ cations as activators.[2] In terms of pH, the DNAase II family is expressed in acidic pH. The cleavage pattern of DNase II is altered in the presence of Dimethyl sulfoxide(DMSO), which significantly affects the structure of DNA.

Structure

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Although both DNase I and II are glycoprotein endonucleases, DNase I has a monomeric sandwich-type structure with a carbohydrate side chain whereas DNase II has a dimeric quaternary structure.

Glycoprotein DNase I 3D structure PDB: 3DNI

DNase I Structure: DNase I is a glycoprotein with a molecular weight of 30,000 Da and a carbohydrate chain of 8-10 residues attached to Asn18 (orange).[3] It is an 𝛼,𝛽-protein with two 6-stranded 𝛽-pleated sheets which form the core of the structure.[4] These two core sheets run parallel, and all others run antiparallel. The 𝛽-pleated sheets lie in the center of the structure while the 𝛼-helices are denoted by the coils on the periphery. DNase I contains four ion-binding pockets, and requires Ca2+ and Mg2+ for hydrolyzing double-stranded DNA.[5] Two of the sites strongly bind Ca2+ while the other two coordinate Mg2+. Little has been published on the number and location of the Mg2+ binding sites, although it has been proposed that Mg2+ is located near the catalytic pocket and contributes to hydrolysis.[6] The two Ca2+ are shown in red in the image. They are bound to DNase I under crystallization conditions and are important for the structural integrity of the molecule by stabilizing the surface loop Asp198 to Thr204 (cyan), and by limiting the region of high thermal mobility in the flexible loop to residues Gly97 to Gly102 (yellow).

Glycoprotein DNase II 3D structure PDB: 5UNB

DNase II Structure: DNase II contains a homodimeric quaternary structure that is capable of binding double-stranded DNA within a U-shaped clamp architecture. The interior of the U-shaped clamp is largely electropositive, capable of binding negatively-charged DNA. Similar to DNase I, DNase II structure consists of a mixed 𝛼/𝛽 secondary structure with 9 𝛼-helices and 20 𝛽-pleated sheets.[7] Although unlike DNase I, DNase II does not require divalent metal ions for catalysis.[7] The structure consists of protomer A (cyan) and protomer B (green). Each structure consists of two catalytic motifs, which are labeled on protomer B for simplicity: His100 and Lys102 compose the first motif (blue) and His279 and Lys281 compose the second catalytic motif (red).

Mechanism of action for DNase enzymes

Mechanism

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Some DNases cut, or "cleave", only residues at the ends of DNA molecules. This type of exonuclease is known as exodeoxyribonucleases. Others cleave anywhere along the chain, known as endodeoxyribonucleases (a subset of endonucleases.)[8] Some DNases are fairly indiscriminate about the DNA sequence at which they cut, while others, including restriction enzymes, are very sequence-specific. Other DNases cleave only double-stranded DNA, others are specific for single-stranded molecules, and others are active toward both.

The action of DNase occurs in three phases. The initial phase introduces multiple nicks in the phosphodiester backbone. The second phase produces acid-soluble nucleotides. The third phase, which is the terminal phase, consists of reduction of oligonucleotides, causing a hyperchromic shift in the UV data.[9]

DNase I Mechanism

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DNase I predominantly targets double-stranded DNA, and to a lesser extent, some single-stranded DNA for cleavage. DNase I catalyzes nonspecific DNA cleavage by nicking phosphodiester linkages in one of the strands. Its cleavage site lies between the 3′-oxygen atom and the adjacent phosphorus atom, yielding 3′-hydroxyl and 5′-phosphoryl oligonucleotides with inversion of configuration at the phosphorus. The DNase enzyme relies on the presence of a divalent cation, which is usually Ca2+, for proper function. The active site of DNase I includes two histidine residues (His134 and His252) and two acidic residues (Glu78 and Asp 212), all of which are critical for the general acid-base catalysis of phosphodiester bonds.[10]

DNase II Mechanism

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Deoxyribonuclease II (DNase II) is also known as acid deoxyribonuclease because it has optimal activity in the low pH environment of lysosomes where it is typically found in higher eukaryotes. Some forms of recombinant DNase II display a high level of activity in low pH in the absence of divalent metal ions, similar to eukaryotic DNase II.[7] Unlike DNase I, DNase II cleaves the phosphodiester bond between the 5'-oxygen atom and the adjacent phosphorus atom, yielding 3΄-phosphorylated and 5΄-hydroxyl nucleotides.

Applications

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Laboratory applications

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DNase is commonly used when purifying proteins that are extracted from prokaryotic organisms. Protein extraction often involves the degradation of the cell membrane. It is common for the degraded and fragile cell membrane to be lysed, releasing unwanted DNA and the desired proteins. The resulting DNA-protein extract is highly viscous and difficult to purify, in which case DNase is added to break it down.[11] The DNA is hydrolyzed but the proteins are unaffected and the extract can undergo further purification.

Treatment

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Extracellular DNA (ecDNA) is DNA that is found in blood circulation. It appears as a result of apoptosis, necrosis, or neutrophil extracellular traps (NET)-osis of blood and tissue cells, but can also arise from the active secretion from living cells. EcDNA and their designated DNA binding proteins are able to activate DNA-sensing receptors, pattern recognition receptors (PRRs). PRRs are able to stimulate pathways that cause an inflammatory immune response. As a result, several studies of inflammatory diseases have found that there are high concentrations of ecDNA in blood plasma. For this reason, DNase has proven to be a possible treatment for the reduction of ecDNA in the blood plasma. DNases can be excreted both intracellularly and extracellularly and can cleave the DNA phosphodiester bond. This function can be used to maintain a low ecDNA concentration, therefore treating inflammation. Illnesses that result from DNA residue in blood have been targeted using the "breaking-down properties" of DNase. Studies have shown DNase to be able to act as a treatment by decreasing the viscosity of mucus.[12][13] Administration of DNase varies dependent on the disease. It can and has been administered orally, intrapleurally, intravenously, intraperitoneally, and via inhalation.[14] Several studies continue to examine the application of DNase as treatment as well as ways to monitor health. For example, recently, DNase derived from pathogenic bacteria has been used as an indicator for wound infection monitoring.[15]

Respiratory diseases

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Cystic fibrosis is a genetic disorder that affects the production of mucus, sweat, and digestive fluids, causing them to become more viscous rather than lubricant. DNase enzymes can be inhaled using a nebulizer by cystic fibrosis sufferers. DNase enzymes help because white blood cells accumulate in the mucus, and, when they break down, they release DNA, which adds to the 'stickiness' of the mucus. DNase enzymes break down the DNA, and the mucus is much easier to clear from the lungs. Specifically, DNase I, also known as FDA approved drug Pulmozyme (also known as dornase alfa) is used as a treatment to increase pulmonary function.

Other respiratory illness such as asthma,[16] pleural empyema,[12] and chronic obstructive pulmonary disease have also been found to be positively affected by DNases properties.

Furthermore, recent studies show that intrapleural tissue plasminogen activator (tPA), a protein that is responsible for the breakdown of blood clots, combined with deoxyribonuclease increase pleural drainage, decreases hospital length of stay, and decreases the need for surgery in parapneumonic effusions and empyema.

Other diseases

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Sepsis is a life-threatening inflammatory disease caused by the body's extreme response to an infection. The body begins to attack itself as an inflammatory response encompasses the human body. As a result, high levels of ecDNA have been associated with the bloodstream and therefore, researchers have looked to DNase as an appropriate treatment. Studies have shown that DNase was successful in disrupting NETs and decreasing inflammatory responses. More research on the type and time of administration is needed to further establish DNase as an official treatment.[17][18][19]

Systemic lupus erythematosus (SLE) is an autoimmune disease that results in auto-antibody generation causing inflammation that results in damage to organs, joints, and kidneys. SLE has been linked with low levels of DNase I as apoptotic cells become self-antigens in this disease. DNase I has been investigated as a possible treatment to decrease the amount of apoptotic debris in the human system. It has been suggested that their difficulty might be due to the inability for the enzyme to break down the cell membrane of chromatin. Studies have shown conflicting results on this treatment, however, further research is being conducted to examine the therapeutic benefits of DNase I.[14][18][20]

Anti-tumor treatment. DNase is known to hold anti-tumor effects due to its ability to break down DNA. High levels of DNA are found to be in cancer patients' blood, suggesting that DNase I might be a possible treatment. There is still a lack of understanding as to why there are such high levels of ecDNA and whether or not DNase will act as an effective treatment. Several mice studies have shown positive results in anti-tumor progression utilizing intravenous DNase I. However, more investigations need to be carried out before being introduced to the public.[21][14]

Assays

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DNA absorbs ultraviolet (UV) light with a wavelength of maximal absorbance near 260 nm. This absorption is due to the pi electrons in the aromatic bases of the DNA. In dsDNA, or even regions of RNA where double-stranded structure occurs, the bases are stacked parallel to each other, and the overlap of the base molecular orbitals leads to a decrease in absorbance of UV light. This phenomenon is called the hypochromic effect. When DNase liberates nucleotides from dsDNA, the bases are no longer stacked as they are in dsDNA, so that orbital overlap is minimized and UV absorbance increases. This increase in absorbance underlies the basis of the Kunitz unit of DNase activity. One Kunitz unit is defined as the amount of enzyme added to 1 mg/ml salmon sperm DNA that causes an increase in absorbance of 0.001 per minute at the wavelength of 260 nm when acting upon highly polymerized DNA at 25 °C in a 0.1 M NaOAc (pH 5.0) buffer. The unit's name recognizes the Russian-American biochemist Moses Kunitz, who proposed the standard test in 1946.[22]

A standard enzyme preparation should be run in parallel with an unknown because standardization of DNA preparations and their degree of polymerization in solution is not possible.

Single Radial Enzyme Diffusion (SRED) This simple method for DNase I activity measurement was introduced by Nadano et al. and is based on the digestion of DNA in the agarose gel by DNase, which is present in samples punched into the gel.[14] DNase activity is represented by the size of a dispensed circular well in an agarose gel layer, in which DNA stained by ethidium bromide is uniformly distributed. After the incubation, a circular dark zone is formed as the enzyme diffuses from the well radially into the gel and cleaves DNA. SRED underwent many modifications, which led to an increase in sensitivity and safety, such as the replacement of ethidium bromide with SYBR Green I or other DNA gel stains.[23]

Colorimetric DNase I Activity Assay

Kinetic colorimetric DNase I activity assay is developed for the assessment of the stability of the human recombinant DNase I (Pulmozyme). The method was adjusted from a colorimetric endpoint enzyme activity assay based on the degradation of a DNA/methyl green complex.[24]

Virulence factor

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Extracellular deoxribonucleases act as virulence factors for pathogens, including Plasmodium[25] and several Streptococcus species,[26][27] as they allow the pathogens to defend themselves against neutrophil extracellular traps which consist primarily of histone-linked extracellular DNA.[28][29]

See also

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References

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Revisions and contributorsEdit on WikipediaRead on Wikipedia

Deoxyribonuclease

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Deoxyribonuclease (DNase) refers to a family of enzymes that catalyze the hydrolytic cleavage of phosphodiester linkages in the DNA backbone, resulting in the degradation of DNA into smaller nucleotide fragments. These endonucleases or exonucleases primarily target deoxyribonucleic acid (many are glycoproteins), distinguishing most from ribonucleases that act on RNA; however, some like DNase II also degrade RNA. DNases are classified into several types based on their structure, optimal , cofactor requirements, and substrate specificity. The DNase I family includes DNase I, DNase1L1, DNase1L2, and DNase1L3, which are active at neutral to slightly alkaline (6.5–8) and require divalent cations such as Mg²⁺ and Ca²⁺ for activity; DNase I, the most studied member, preferentially cleaves double-stranded DNA to produce 5'-phosphorylated and 3'-hydroxyl ends. In contrast, the DNase II family, comprising DNase IIα, DNase IIβ, and L-DNase II, functions optimally at acidic (4.8–5.2) without needing cations and generates 3'-phosphorylated and 5'-hydroxyl ends, often acting as nicking endonucleases. Additional DNases, such as TREX1 and TREX2, operate as 3'–5' exonucleases involved in cytosolic DNA clearance. Biologically, DNases play critical roles in maintaining genomic integrity and modulating immune responses by degrading extracellular DNA (ecDNA) released during processes like , , and neutrophil extracellular trap (NET) formation. For instance, DNase I digests nucleoproteins in the bloodstream to prevent autoimmune reactions, such as those observed in systemic lupus erythematosus (SLE), while DNase IIα facilitates lysosomal DNA breakdown during and supports . DNase1L2 contributes to antimicrobial defense by disrupting bacterial biofilms on , and DNase1L3 helps regulate plasma ecDNA levels to avert . Deficiencies in these enzymes are linked to inflammatory and autoimmune disorders due to ecDNA accumulation, which can trigger excessive immune activation. In biomedical applications, recombinant human DNase I (rhDNase), marketed as Pulmozyme, is FDA-approved for treating cystic fibrosis, where it reduces mucus viscosity by cleaving DNA in sputum (administered as 2.5 mg daily via inhalation). DNases also show promise in disrupting bacterial biofilms in infections like those caused by Pseudomonas aeruginosa, treating sepsis (e.g., 20 mg/kg intraperitoneal in mouse models), and inhibiting tumor progression in preclinical cancer studies (e.g., 1.5 U intravenous in rat models). Ongoing research as of 2025 continues to explore their potential in conditions like SLE, Alzheimer's disease, acute injuries such as stroke and pleural infections, and others, though clinical efficacy varies.

Overview

Definition and Properties

Deoxyribonucleases (DNases) are a class of glycoprotein endonucleases that catalyze the hydrolytic cleavage of phosphodiester bonds within DNA strands. Members of the DNase I family generate oligonucleotides terminating in 5'-phosphate groups and 3'-hydroxyl ends, while those of the DNase II family produce 3'-phosphate and 5'-hydroxyl ends. These enzymes play a central role in DNA degradation by targeting internal linkages rather than terminal nucleotides, distinguishing them from exonucleases. Unlike ribonucleases (RNases), which specifically hydrolyze RNA, or restriction enzymes that exhibit sequence-specific cleavage, DNases generally perform non-sequence-specific hydrolysis to facilitate broad DNA breakdown for cellular homeostasis. Biochemical properties of DNases vary by family, with optimal activity influenced by environmental factors. For instance, DNase I-like enzymes operate efficiently at neutral levels of 7.5–8.0 and require divalent metal cations such as Mg²⁺ and Ca²⁺ as essential cofactors to stabilize the and promote catalysis. In contrast, DNase II-like enzymes function optimally under acidic conditions ( 4.8–5.2) and do not depend on metal ions for activity. Substrate preferences also differ, as DNase I-like variants preferentially cleave double-stranded DNA (dsDNA) over single-stranded DNA (ssDNA) by a factor of 100–500, often initiating digestion through random nicking. DNases embody an ancient enzymatic lineage conserved across prokaryotes and eukaryotes, reflecting their fundamental involvement in DNA maintenance and turnover in diverse biological systems. This evolutionary persistence underscores their indispensable function in processes like recycling and response to DNA damage, present from bacterial lineages to higher organisms. The term "deoxyribonuclease" was first used in around 1946.

Historical Background

The enzymatic activity capable of degrading deoxyribonucleic acid was first identified in bovine extracts in 1906 by Fritz Sachs, who demonstrated that pancreatic preparations could hydrolyze nucleic acids, laying the groundwork for understanding DNase function. This initial observation highlighted the presence of a in pancreatic tissue, though the specific was not yet isolated. Subsequent studies in the early confirmed similar activities in other organs, but it was not until 1950 that Moses Kunitz achieved the first isolation and crystallization of bovine pancreatic deoxyribonuclease I (DNase I) from fresh beef , enabling detailed characterization and paving the way for its commercial production as a research tool. Kunitz's work also introduced a spectrophotometric for measuring DNase activity, which became a standard method and facilitated broader biochemical investigations. Parallel efforts revealed a second major deoxyribonuclease, initially termed "acid DNase" due to its optimal activity at low . In the late 1940s, researchers including Catchside and Holmes observed this activity in mammalian tissues, particularly high in extracts, distinguishing it from the neutral -preferring pancreatic DNase. The was formally characterized and named DNase II in 1952 by Vincent Allfrey and Alfred Mirsky, who purified it from and described its properties, including its independence from divalent cations and role in DNA degradation under acidic conditions. By the , studies began noting variations in DNase activities across tissues and individuals, with early reports of polymorphic forms in serum and DNase I emerging around 1964, suggesting genetic influences on expression and function. In the 1970s, research milestones included investigations into DNases' involvement in cellular processes, with links to DNA breakdown during cell death observed in studies of tissue autolysis and nuclear degradation. In subsequent decades, these findings contributed to understanding their role in programmed cell death. The 1990s marked a leap in production technology, exemplified by the development of recombinant human DNase I (rhDNase I), approved as Pulmozyme (dornase alfa) in 1993 for treating cystic fibrosis by reducing mucus viscosity through extracellular DNA cleavage. This recombinant form, produced in Chinese hamster ovary cells, represented the first protein therapeutic approved specifically for the treatment of cystic fibrosis. Advancing into the early 2000s, the completion of the enabled the full genomic sequencing of human DNase genes, including DNASE1 on and DNASE2 on , revealing their evolutionary conservation and regulatory elements by 2003. These sequences facilitated genetic studies, confirming polymorphisms such as the Q222R variant in DNASE1 associated with autoimmune conditions, and supported ongoing research into DNase functions up to 2025, including their roles in and disease pathology.

Classification

DNase I Family

The DNase I family comprises a group of calcium- and magnesium-dependent endonucleases that cleave DNA at neutral pH, primarily in mammals. In humans, the family includes four paralogous genes: DNASE1 encoding DNase I, a secreted enzyme predominantly produced in the pancreas; DNASE1L1 (also known as DNase X), which is testis-enriched; DNASE1L2, expressed mainly in skin and sweat glands; and DNASE1L3 (also called DNase γ), associated with immune cells such as dendritic cells and macrophages. These proteins share sequence similarity ranging from 30-50% and exhibit tissue-specific roles in DNA degradation. The genes encoding these enzymes are distributed across different chromosomes and display conserved exon-intron architectures typical of the family. The DNASE1 gene is located on chromosome 16p13.3 and spans approximately 4 kb with 9 exons and 8 introns, including two alternative transcription start sites. DNASE1L1 resides on the X chromosome at Xq28, covering about 11 kb with 10 exons. DNASE1L2 is also on 16p13.3, adjacent to DNASE1, and consists of 8 exons over 3 kb. DNASE1L3 maps to 3p21.31, encompassing 22 kb with 7 exons. Polymorphisms in these genes can influence enzymatic activity; for instance, the A2317G single nucleotide polymorphism and a 56-bp variable number tandem repeat in DNASE1 are associated with reduced DNase I activity levels in populations. Similarly, the Q222R variant in DNASE1 has been linked to altered activity and increased risk for autoimmune conditions like systemic lupus erythematosus. Tissue-specific expression patterns reflect the specialized functions of each member, with regulation often tied to developmental or inflammatory cues. DNase I (DNASE1) is highly expressed in exocrine glands such as the , parotid, and submandibular salivary glands, as well as in the and , and its expression is upregulated during inflammatory responses via cytokines like IL-1β. DNase1L1 (DNASE1L1) shows preferential expression in testicular germ cells and , though detectable at lower levels in other non-brain tissues. DNase1L2 (DNASE1L2) is predominantly transcribed in of the and ducts, with upregulation during terminal differentiation and cornification. DNase1L3 (DNASE1L3) is enriched in immune-responsive tissues like and lymphoid organs, particularly in dendritic cells and macrophages, where its expression supports clearance. Evolutionarily, the DNase I family arose from successive gene duplications of an ancestral endonuclease predating vertebrate divergence, with the core repertoire established in early mammals. Phylogenetic analyses indicate that the four human paralogs form a monophyletic within the broader DNase1 superfamily, conserved across mammals but with lineage-specific losses, such as the absence of DNASE1L1 orthologs in some and DNASE1L2 in certain . This diversification likely drove tissue specialization, as evidenced by syntenic clustering of DNASE1 and DNASE1L2 on from a tandem duplication event.

DNase II Family

The DNase II family comprises acid-activated endonucleases primarily involved in intracellular DNA degradation, in contrast to the DNase I family, which consists of secreted enzymes active at neutral pH. The family includes two main members in humans: DNase II α, encoded by the DNASE2 gene, and DNase II β, encoded by the DNASE2B gene. Additionally, L-DNase II, derived post-translationally from the serpin leukocyte elastase inhibitor (LEI/SERPINB1), exhibits DNase II-like endonucleolytic activity in acidic conditions, particularly during caspase-independent apoptosis. DNase II α is a well-characterized lysosomal enzyme that hydrolyzes DNA in acidic compartments, while DNase II β is less studied but shares sequence similarity and structural homology with DNase II α, functioning similarly in specialized tissues. The DNASE2 gene for DNase II α is located on chromosome 19p13.13 and consists of six exons, encoding a protein targeted to lysosomes where it facilitates the breakdown of ingested or damaged DNA. Expression of DNase II α is prominent in macrophages and liver cells, particularly in lysosomal compartments of Kupffer cells in the fetal liver and bone marrow macrophages, supporting its role in clearing nuclear debris from apoptotic or enucleated cells. DNase II β, encoded by DNASE2B on chromosome 1p22.3, exhibits restricted expression mainly in the eye lens and salivary glands, contributing to DNA degradation during lens fiber cell differentiation. These enzymes are optimally active in acidic environments at pH 4.5–5.5, without requiring divalent cations, enabling efficient hydrolysis of DNA within lysosomes for intracellular catabolism. This activity is crucial for processing exogenous or endogenous DNA fragments, preventing accumulation that could trigger inflammatory responses. Evolutionarily, the DNase II family represents an ancient lineage conserved across metazoans, with orthologs identified in invertebrates such as Drosophila, indicating its fundamental role in DNA turnover predating vertebrate divergence. The β paralog (DNase II β) arose as a gene duplication event, with its synteny conserved alongside the uricase gene over approximately 700 million years, though it diversified in primates to support tissue-specific functions like lens development.

Other DNases

Prokaryotic DNases include the restriction endonucleases classified into Types I through IV, which function primarily as defense mechanisms against invading foreign DNA, such as from s, by cleaving DNA at or near specific recognition sequences. Type I enzymes are multisubunit complexes that recognize unmethylated DNA and cleave at random sites far from the recognition sequence, requiring ATP for activity. Type II enzymes, the most commonly utilized in , cleave DNA precisely within or adjacent to their recognition sites without ATP dependence. Type III enzymes resemble Type I in complexity but cleave at sites proximal to the recognition sequence, often in a bidirectional manner. Type IV enzymes specifically target modified or methylated DNA, cleaving it to prevent integration of foreign genetic material. An example of a specialized prokaryotic DNase is the A product of phiX174, which exhibits both endonucleolytic nicking of the viral strand during replication and associated exonucleolytic processing to displace the cleaved strand, facilitating single-stranded . Among eukaryotic outliers, TREX1 functions as a DNase III-like , acting as a major 3'→5' localized to the where it degrades single-stranded and double-stranded DNA to prevent aberrant activation of innate immune responses. Similarly, TREX2 is a 3'→5' that prefers double-stranded DNA with mismatched 3' termini and plays a role in and replication. DNase X, also known as DNase1L1, represents another outlier in the DNase I superfamily; while it shares with canonical DNase I members, it is distinguished by its anchoring to cell membranes and tissue-specific expression, particularly in , where it may contribute to localized DNA clearance. Viral DNases, such as the UL12 protein encoded by type 1, exhibit alkaline activity with 5'→3' exonucleolytic function, processing DNA ends during and recombination; this activity is enhanced by interaction with the viral single-strand ICP8, increasing processivity on substrates. Emerging classifications of DNases extend to members of the (PLD) superfamily, which harbor conserved HKD motifs enabling in both and nucleic acids; notable examples include bacterial toxins like colicins and viral proteins that display DNase activity as part of their cytotoxic mechanisms. Metagenomic discoveries up to 2025 have further expanded this diversity, identifying antiphage nucleases in uncultured microbial communities, such as those targeting modified phage DNA or acting as outer membrane proteins to degrade invading genomes, highlighting previously unrecognized enzymatic variations in environmental microbiomes.

Molecular Structure

DNase I Structure

DNase I adopts an α/β fold characterized by two predominantly antiparallel six-stranded β-sheets that form a sandwich-like core, flanked by three α-helices and extensive loop regions, resulting in overall dimensions of approximately 45 × 40 . This architecture positions the at the interface between the β-sheets, facilitating substrate access. The enzyme is a , with a chain attached at Asn18 in the bovine form, protruding about 15 from the core. The molecular weight of human DNase I is approximately 31 kDa, comprising 260 residues in its mature form. The includes a involving glutamate (Glu78) and aspartate (Asp212) as acceptors that coordinate two divalent metal ions (typically Mg²⁺ or Ca²⁺) in a two-metal-ion mechanism, alongside residues (His134 and His252) that act as general acid-base catalysts. Stability is enhanced by Ca²⁺-binding loops that accommodate two calcium ions near the , shielding it from nonspecific interactions. Crystal have elucidated these features, with the bovine DNase I determined at 2.5 resolution in 1984 (PDB: 1DNK) and refined to 2.0 (PDB: 3DNI). The human variant was solved at 1.95 resolution in 2013, bound to magnesium and phosphate ions (PDB: 4AWN), confirming the conserved fold and metal coordination. DNase I family variants, including DNase1L1, DNase1L2, and DNase1L3, display high structural homology to DNase I, with root-mean-square deviations (RMSD) around 1.8 for core domains upon superposition. For instance, DNase1L3 shares the α/β sandwich fold but features an extended positively charged C-terminal domain (residues 283–305) that enhances binding to DNA-protein complexes for immune clearance, along with unique disulfide bonds and cation-binding sites. The of the core domain of DNase1L3 (residues 22–282, lacking the C-terminal domain) was determined at 2.2 resolution, confirming these features.

DNase II Structure

DNase II enzymes adopt a homodimeric quaternary structure, with each monomer consisting of approximately 360 amino acid residues and a molecular weight of around 40 kDa, forming a stable dimer through an extensive interface burying about 3070 Ų of surface area. The overall fold is a mixed α/β architecture characteristic of the phospholipase D (PLD) superfamily, featuring 9 α-helices and 20 β-strands that assemble into a U-shaped clamp-like monomer with a central cavity approximately 16–17 Å wide, suitable for accommodating double-stranded DNA substrates. This fold is conserved across DNase II family members, including bacterial homologs like that from Burkholderia thailandensis, which shares 28% sequence identity with human DNase IIα and serves as a structural model for the eukaryotic enzymes. The resides in the central cavity at the dimer interface and does not require divalent metal ions for , distinguishing DNase II from metal-dependent nucleases like DNase I. Instead, proceeds via a protonation-based mechanism facilitated by two conserved HxK motifs (HxKxxxxxxD/G/Q) in the N- and C-terminal domains, where the residues (e.g., H100 and H279 in the bacterial enzyme, corresponding to H113 and H295 in DNase IIα) act as nucleophiles to form a covalent phosphohistidine intermediate. Additional residues, such as conserved tryptophans (W239, W282) and arginines (R298), contribute to substrate positioning and alignment within the cleft. As a lysosomal enzyme, human DNase IIα is targeted to lysosomes via N-linked glycosylation sites that acquire mannose-6-phosphate (M6P) modifications in the Golgi apparatus, enabling binding to M6P receptors for trafficking from the trans-Golgi network to endosomes and ultimately lysosomes. This ensures delivery to the acidic lysosomal environment ( 4.5–5.0), where the maintains conformational stability and optimal activity, unlike at neutral where it is inactive. The first high-resolution structure of a DNase II family member was determined for the B. thailandensis enzyme at 2.15 Å resolution (PDB ID: 5UNB), revealing the dimeric assembly and active site architecture without bound DNA or metals. No crystal structure exists for human DNase IIα, but homology models based on the bacterial template highlight conserved features, including the catalytic HxK motifs. Human DNase IIβ, a paralog sharing ~40% sequence identity with DNase IIα and expressed primarily in salivary glands and alveolar macrophages, exhibits similar overall fold but minor variations in surface loops that may influence tissue-specific localization and substrate specificity.

Catalytic Mechanism

DNase I Mechanism

DNase I employs a two-metal-ion catalytic mechanism to hydrolyze phosphodiester bonds in double-stranded DNA, requiring both Ca²⁺ and Mg²⁺ for activity. The two Ca²⁺ ions bind at structural sites I and II, stabilizing the enzyme's active site loop and facilitating proper positioning of the DNA substrate within the minor groove. Meanwhile, the Mg²⁺ ions occupy catalytic sites III and IV; the Mg²⁺ at site IVa helps orient the scissile phosphate, while the Mg²⁺ at site IVb activates a bound water molecule as the nucleophile by lowering its pKa through coordination with Asp190 and Glu61. The catalytic cycle begins with non-sequence-specific binding of the enzyme to DNA via electrostatic interactions and minor groove contacts, which distort the DNA helix by kinking it at the binding site to align the phosphodiester bond for inline attack. His252 then acts as a general base to abstract a proton from the activated water, enabling nucleophilic attack on the phosphorus atom and formation of a pentacoordinate transition state. This state is stabilized by the catalytic Mg²⁺ ions, leading to breakage of the P-O3′ bond with stereochemical inversion and release of the 3′-oxygen as a leaving group, protonated by His134 functioning as a general acid. The reaction yields oligonucleotide products terminating in 5′-phosphate and 3′-hydroxyl groups, followed by rapid product dissociation and enzyme turnover. DNase I exhibits a preference for supercoiled double-stranded DNA substrates, where torsional stress enhances initial nicking and subsequent rates compared to relaxed or linear forms. Under physiological conditions (pH 7.5, with 5 mM Mg²⁺ and 10 mM Ca²⁺), the enzyme displays Michaelis-Menten kinetics, reflecting efficient turnover. Activity is notably inhibited by globular actin (G-actin), which binds competitively at the DNA-interaction surface with a K_i in the nanomolar range, preventing substrate access. The DNase1L1, DNase1L2, and DNase1L3 variants conserve this two-metal-ion mechanism and active site architecture, with minor adaptations in substrate specificity; notably, DNase1L3 demonstrates higher affinity for single-stranded DNA regions within chromatin substrates, enabling more effective cleavage of nucleosome-associated DNA.

DNase II Mechanism

DNase II catalyzes the hydrolysis of DNA phosphodiester bonds through an acid-dependent, non-metal-requiring mechanism that contrasts with the divalent cation-dependent process of DNase I. In this proton-transfer mechanism, a conserved histidine residue acts as a general acid to protonate the 3'-oxygen leaving group, facilitating bond cleavage, while an adjacent aspartate residue stabilizes the transition state and aids in proton shuttling. The reaction yields DNA fragments with 3'-phosphate and 5'-hydroxyl termini, reflecting the enzyme's role in generating oligonucleotides suitable for further lysosomal degradation. The is activated in the acidic environment of lysosomes (pH ~4.5–5.0), where low pH protonates key residues to enable ; at neutral pH, activity is negligible. DNase II performs random endonucleolytic cleavages on both single-stranded and double-stranded DNA, initiating with single-strand nicks that propagate to full degradation. Dimerization of the , observed in its , enhances substrate binding and catalytic efficiency by forming a clamp-like interface that accommodates DNA. Kinetically, DNase II exhibits optimal activity at pH 5.0. Its turnover rate is slower than that of DNase I, reflecting a more deliberate degradation process suited to lysosomal conditions. DNase II displays broad substrate specificity, cleaving native, denatured, and chromatin-associated DNA without strict sequence preference, though it shows a mild bias for motifs like AGAGGA. This versatility allows it to process diverse DNA forms encountered in phagocytic and degradative pathways. The catalytic dyad involving histidine and lysine motifs, conserved across DNase II family members, underpins this pH-driven hydrolysis.

Biological Functions

Physiological Roles

Deoxyribonucleases (DNases) play critical roles in maintaining DNA homeostasis by clearing extracellular and intracellular DNA fragments generated during cell death processes such as apoptosis and necrosis. DNase I, the predominant serum nuclease, facilitates the degradation of extracellular DNA (ecDNA) from apoptotic and necrotic cells, preventing the accumulation of nuclear antigens that could trigger autoimmune responses. In DNase I-deficient models, impaired ecDNA clearance leads to features of systemic autoimmunity, underscoring its protective function. Complementing this, DNase II, localized in lysosomes, degrades ingested DNA from phagocytosed apoptotic bodies in macrophages and other phagocytes, ensuring efficient clearance during efferocytosis. This lysosomal activity is essential for processing DNA in the acidic environment of phagolysosomes, with DNase IIα (also known as DNase2a) specifically responsible for hydrolyzing DNA transported to lysosomes post-phagocytosis. In immune modulation, DNases contribute to resolving by degrading (NETs), web-like structures of DNA and proteins released by neutrophils to trap pathogens. DNase1L3, a secreted DNase highly expressed in dendritic cells and liver, works in tandem with DNase I to fragment circulating NETs, preventing their pro-thrombotic and inflammatory effects. Deficiency in DNase1L3 impairs NET breakdown, leading to persistent and vascular occlusion in vivo. Additionally, DNase II supports by enabling the digestion of engulfed DNA, thereby facilitating immune cell recycling and preventing lysosomal overload during the uptake of dying cells. DNases are integral to developmental processes, particularly in tissue differentiation requiring DNA elimination. DNase IIα is indispensable for definitive erythropoiesis, where macrophages in the fetal liver phagocytose and degrade the extruded nuclei from maturing erythroid precursors, ensuring enucleation. Mice lacking DNase IIα exhibit perinatal lethality due to defective nuclear clearance in erythroid cells, highlighting its non-redundant role. Similarly, DNase IIβ (DLAD), specifically expressed in lens fiber cells, degrades nuclear DNA during lens differentiation to maintain optical transparency; its absence results in DNA accumulation and formation. In spermatogenesis, DNase I-like 1 (DNase1L1), a testis-enriched member of the DNase I family, is expressed in spermatogenic cells, suggesting a role in DNA remodeling or fragmentation during sperm maturation. DNase I also serves a digestive function, secreted by the pancreas into the intestinal tract to hydrolyze dietary DNA from ingested food, aiding in nutrient absorption. This exocrine role complements its systemic activities, with pancreatic DNase I contributing to the breakdown of nucleic acids in the gastrointestinal lumen.

Pathological Roles

Dysregulation of deoxyribonuclease (DNase) activity plays a significant role in autoimmune diseases, particularly through deficiencies in DNase I, which impair the clearance of extracellular DNA and contribute to systemic lupus erythematosus (SLE). Heterozygous nonsense mutations in the DNASE1 gene have been identified in SLE patients, leading to reduced enzymatic activity and accumulation of self-DNA that triggers autoantibody production and immune complex formation. Similarly, DNase1-deficient mice spontaneously develop an SLE-like phenotype, characterized by elevated autoantibodies and renal damage by 12 months of age. In vasculitis, such as IgA vasculitis and ANCA-associated vasculitis, low DNase I activity results in elevated neutrophil extracellular traps (NETs), exacerbating vascular inflammation and tissue damage due to impaired NET degradation. Pathogenic microbes exploit DNases as virulence factors to evade host immunity. For instance, secretes the DNase Sda1, which degrades the DNA backbone of NETs, allowing the bacteria to escape neutrophil-mediated killing and disseminate from the initial infection site. Inhibition of this DNase activity with G-actin enhances bacterial clearance , underscoring its role in . Among viruses, gammaherpesviruses encode DNases that impair recognition by virus-specific CD8+ T cells, facilitating immune evasion and the establishment of latency by reducing the presentation of viral antigens on infected cells. In cancer, aberrant DNase expression contributes to tumor progression and . Tumor cells can induce NET formation, and while therapeutic DNase administration inhibits by degrading these structures, endogenous low DNase activity in the allows NET persistence, which supports migration and invasion. DNase II mutations are associated with developmental disorders, including severe autoinflammatory syndromes resembling monogenic , where biallelic loss-of-function variants in DNASE2 lead to lysosomal DNA accumulation, type I overproduction, and early-onset with neurological involvement. Knockout models reveal perinatal lethality due to multiple developmental defects, such as impaired . Reduced DNase activity is implicated in other pathologies, including , where hypercholesterolemia impairs the DNase response to NETs, leading to their accumulation in plaques and promotion of and plaque instability. Recent 2025 studies highlight the persistence of (ecDNA) in neurodegeneration, such as in , where microglial DNase II deficiency causes double-stranded DNA buildup, sustaining and neuronal damage; impaired DNase activity correlates with elevated ecDNA levels that bind protein aggregates, exacerbating disease progression in and other neurodegenerative conditions.

Applications

Laboratory and Research Uses

Deoxyribonucleases, particularly DNase I, serve as essential tools in molecular biology laboratories for manipulating DNA in experimental protocols. One primary application is the removal of contaminating genomic DNA during RNA extraction workflows, where RNase-free variants like RQ1 DNase are employed to degrade double- and single-stranded DNA without affecting RNA integrity, ensuring high-purity samples for downstream applications such as RT-PCR. Similarly, in protein purification processes, DNase I is added to cell lysis buffers to hydrolyze released chromosomal DNA, which otherwise increases solution viscosity and co-purifies with target proteins through nonspecific binding, thereby improving yield and purity. DNase I footprinting assays exploit the enzyme's sequence-nonspecific cleavage to map protein-DNA interactions and structure. In accessibility studies, DNase I digestion identifies hypersensitive sites—regions of open where nucleosomes are displaced—enabling genome-wide profiling via DNase-seq to locate regulatory elements like enhancers and promoters. For transcription factor binding analysis, limited DNase I digestion reveals protected "footprints" on DNA probes, delineating specific binding motifs essential for constructing reporter plasmids or validating regulatory sequences. In cloning and sequencing pipelines, DNase I facilitates the generation of random fragments for construction, as seen in approaches where controlled digestion produces sheared inserts for ligation into vectors, supporting high-throughput genomic analysis. This fragmentation complements restriction enzyme-based methods by providing unbiased coverage, particularly useful in de novo assembly projects. Beyond nucleic acid handling, recombinant DNase I enhances cell culture techniques by preventing aggregation during passaging; it degrades extracellular DNA from apoptotic or necrotic cells that acts as a sticky scaffold, yielding uniform single-cell suspensions critical for transfection and flow cytometry. In recent CRISPR workflows as of 2025, optimized protocols integrate recombinant DNase I during cell preparation for electroporation, reducing clumping in primary cells like NK cells to boost delivery efficiency of Cas9 ribonucleoproteins and improve editing outcomes.

Therapeutic Applications

Deoxyribonucleases, particularly DNase I, have established therapeutic roles in managing respiratory conditions associated with excessive extracellular DNA. Dornase alfa, a recombinant form of human DNase I marketed as Pulmozyme, was approved by the FDA in 1993 for nebulized administration in patients with cystic fibrosis (CF). It cleaves neutrophil-derived DNA in airway mucus, reducing viscosity and facilitating clearance, which improves pulmonary function and decreases the frequency of respiratory exacerbations when used alongside standard therapies like antibiotics and bronchodilators. Clinical evidence from randomized trials demonstrates that daily inhalation of dornase alfa leads to sustained improvements in forced vital capacity (FVC) and forced expiratory volume in one second (FEV1) over placebo, with benefits observed in both pediatric and adult CF populations. In , systemic DNase I formulations are advancing through clinical trials to target extracellular DNA structures that promote tumor progression and resistance. An exploratory Phase 1 trial initiated in July 2025, with the first patient dosed on July 8, 2025, evaluates XBIO-015, a DNase I therapy, in combination with for first-line treatment of unresectable or metastatic , aiming to degrade circulating cell-free DNA and enhance chemotherapeutic efficacy. Similarly, in March 2025, XBIO-015 entered clinical testing for rare bone cancers such as and , building on preclinical data showing reduced tumor burden via DNA degradation. These approaches also potentiate by degrading (NETs) in the , which promote tumor progression and immune evasion. Therapeutic strategies leveraging DNase I are emerging in autoimmune and inflammatory diseases, particularly those involving (NETs), which contribute to tissue damage through DNA-based scaffolds. A 2025 study in the demonstrated that (AAV)-mediated delivering enhanced DNase I significantly ameliorates anti-myeloperoxidase (MPO) in murine models by promoting sustained NET degradation and reducing glomerular inflammation, outperforming short-acting exogenous DNase infusions. In (RA), DNase I treatments targeting NETs have shown promise in preclinical models by mitigating joint inflammation and production, with ongoing research exploring nanoparticle-encapsulated formulations for targeted delivery to synovial tissues. For (MS), elevated extracellular DNA correlates with disease activity. Beyond these areas, DNase I holds diagnostic and preventive potential in and applications in wound management. Circulating DNase I activity serves as a for silent (CAD) in high-risk populations, such as those with and ; a 2025 study found elevated serum levels predict subclinical progression, enabling early intervention to prevent acute events. In wound healing, topical DNase I disrupts bacterial by degrading extracellular DNA matrices, accelerating re-epithelialization and reducing infection rates in chronic wounds; for instance, DNase I combined with nanoparticles enhanced biofilm eradication and healing in models.

Assays and Detection

Assays for deoxyribonuclease (DNase) activity typically monitor the enzymatic degradation of DNA substrates, while detection methods quantify DNase protein levels or activity in biological samples such as serum, tissues, or fluids. These techniques are crucial for research, clinical diagnostics, and evaluating DNase as potential biomarkers in diseases like systemic lupus erythematosus (SLE), cancer, and myocardial infarction.

Spectrophotometric Assays

The classic spectrophotometric method, developed by Kunitz in 1950, measures the increase in ultraviolet absorbance at 260 nm (hyperchromicity) resulting from the hydrolysis of phosphodiester bonds in DNA. This assay uses purified DNA as a substrate and is simple and widely used for DNase I activity, though it lacks high specificity for different DNase types.

Fluorometric Assays

Fluorometric methods offer higher sensitivity by detecting changes in fluorescence upon DNA cleavage. The PicoGreen assay employs a dye that intercalates with double-stranded DNA (dsDNA); DNase activity causes a decrease in fluorescence as the DNA is degraded. Typically, 0.2 μg of DNA substrate is used, making it suitable for low-activity samples. Another variant uses ethidium bromide, where fluorescence increases due to enhanced binding to single-stranded DNA fragments. These assays are adaptable to high-throughput 96-well plate formats.

Radial Enzyme Diffusion Assays

In single radial enzyme diffusion (SRED), DNase diffuses through an agarose gel containing DNA and a DNA-binding dye like methyl green or SYBR Green I, creating a clear zone where DNA is degraded. The diameter of the zone is proportional to enzyme activity, allowing quantification. This method is effective for measuring DNase I in tissues and fluids but can be limited by diffusion kinetics.

Immunochemical and ELISA-Based Assays

Immunochemical assays detect DNase protein levels rather than activity. uses antibodies specific to DNase I to quantify the in serum, providing insights into expression levels independent of catalytic function. For activity, microtiter plate assays employ biotinylated or fluorescently labeled DNA substrates, where cleavage reduces signal intensity. These are valuable for clinical samples and biomarker studies.

Other Advanced Methods

Emerging techniques include microchip for rapid (under 10 minutes) analysis via changes and lateral flow assays for point-of-care detection. Electrochemical biosensors and high-throughput -based assays have also been developed for screening DNase inhibitors. As of 2020, no major new assay paradigms have superseded these established methods, though adaptations for specific applications continue.

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