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Klenow fragment

The Klenow fragment is a large proteolytic fragment of the multifunctional enzyme DNA polymerase I from Escherichia coli, generated by limited digestion with the protease subtilisin, which separates the enzyme into a polymerase domain and a distinct 5'→3' exonuclease domain.^[1] This fragment, named after Hans Klenow, who first described it in 1970 with I. Henningsen by selective proteolytic elimination of the 5'→3' exonuclease activity,^[2] consists of approximately 560 amino acids (molecular weight ~68 kDa) and retains the core 5'→3' DNA polymerase activity for nucleotide incorporation and the 3'→5' exonuclease activity for proofreading, while lacking the 5'→3' exonuclease function responsible for nick translation.^[1]^[3] Structurally, the Klenow fragment adopts a right-hand-like architecture typical of A-family DNA polymerases, with three subdomains—palm, fingers, and thumb—in the C-terminal polymerase domain that forms a cleft for binding double-stranded DNA, and an N-terminal 3'→5' exonuclease domain separated by about 35 Å from the polymerization active site.^[3] The palm subdomain houses the catalytic residues (including Asp705, Asp882, and Glu883) that coordinate two metal ions (typically Mg²⁺) essential for nucleotidyl transfer, enabling high-fidelity DNA synthesis by discriminating against incorrect nucleotides through induced-fit conformational changes in the fingers subdomain.^[3] Crystal structures solved in the 1980s and 1990s, often in complex with DNA and dNTP substrates, have made it a model for studying replication fidelity and polymerase mechanisms, revealing how it excludes ribonucleotides via steric hindrance from residues like Phe762.^[3]^[4] In vivo, DNA polymerase I, including its Klenow fragment domains, plays a key role in E. coli DNA replication by processing Okazaki fragments during lagging-strand synthesis and in DNA repair pathways, though the full enzyme's activities are more prominent; the isolated fragment's properties have been extensively exploited in vitro.^[3] In molecular biology, the Klenow fragment is widely used for generating blunt-ended DNA from sticky ends via fill-in or exonuclease resection, random priming for probe labeling, and second-strand cDNA synthesis due to its processive polymerization on single-stranded templates.^[5] An exonuclease-deficient variant (D355A/E357A) is particularly valuable for avoiding degradation during applications like Sanger sequencing, site-directed mutagenesis, and PCR bias reduction by treating partially single-stranded products.^[5]^[6] Its recombinant production in E. coli has facilitated structural and kinetic studies, underscoring its enduring utility as a tool enzyme despite the advent of thermostable polymerases.^[5]

Discovery and History

Discovery

The Klenow fragment emerged as a key tool in molecular biology following the discovery of DNA polymerase I (Pol I) by Arthur Kornberg in 1956, which was the first enzyme identified capable of catalyzing DNA synthesis in vitro.^[7] This full-length Pol I enzyme, isolated from Escherichia coli, possesses both polymerase and exonuclease activities, but researchers sought ways to dissect these functions to better understand DNA replication and repair mechanisms. In 1970, Hans Klenow and I. Henningsen achieved a breakthrough by performing limited proteolysis on the full-length Pol I using the protease subtilisin, resulting in the isolation of a stable fragment that retained polymerase activity while largely eliminating the 5'→3' exonuclease function.^[8] This ~68 kDa fragment, now known as the Klenow fragment, was produced under controlled conditions to cleave the N-terminal domain of Pol I without disrupting the core catalytic regions.^[9] The proteolysis was conducted at pH 6.5 in potassium phosphate buffer, yielding a product with approximately 30% enhanced polymerase activity compared to the intact enzyme.^[9] This selective modification highlighted the modular nature of Pol I and provided a purified tool for subsequent studies on DNA synthesis, as detailed in the seminal publication by Klenow and Henningsen.^[8]

Characterization and Early Research

Following the isolation of the Klenow fragment through limited proteolysis of Escherichia coli DNA polymerase I, early biochemical assays confirmed that it retained the 5'→3' polymerase activity, enabling the incorporation of deoxynucleotides into a growing DNA strand in a template-dependent manner, as well as the 3'→5' exonuclease activity for proofreading mismatched nucleotides.^[10] In contrast, the 5'→3' exonuclease activity, responsible for removing nucleotides from the 5' end during nick translation, was completely absent, as demonstrated by the fragment's inability to degrade single-stranded DNA from the 5' end under conditions where the full enzyme was active.^[10] Molecular weight determinations via gel filtration chromatography established the Klenow fragment at approximately 68 kDa, significantly smaller than the full DNA polymerase I at 103 kDa, indicating a substantial N-terminal truncation that removed roughly the first one-third of the polypeptide chain.^[11] Subsequent amino acid sequencing in the mid-1970s, as determined by N-terminal sequencing in 1974 by Jovin et al., revealed that the truncation began around residue 324, preserving the core polymerase and 3'→5' exonuclease domains while excising the N-terminal 5'→3' exonuclease domain.^[12] During the 1970s, the Klenow fragment proved instrumental in pioneering recombinant DNA techniques, particularly for blunting DNA ends by filling in 5' overhangs or removing 3' overhangs without unwanted degradation. It featured prominently in prototype oligonucleotide-directed mutagenesis protocols, where its polymerase activity extended synthetic oligonucleotides annealed to single-stranded templates, incorporating specific mutations; for instance, Shortle and Nathans (1978) utilized it to generate targeted base substitutions in simian virus 40 DNA, achieving mutant yields of up to 1% among progeny. Comparative studies in the 1970s highlighted the fragment's processivity and fidelity relative to the full enzyme, showing that it incorporated nucleotides with similar accuracy due to intact proofreading but exhibited reduced processivity on long templates, often synthesizing stretches of 10–50 nucleotides before dissociating, in contrast to the full polymerase I's enhanced processivity during nick translation.

Structure

Overall Architecture

The Klenow fragment of Escherichia coli DNA polymerase I adopts a right-hand-like overall architecture typical of A-family DNA polymerases, comprising three principal domains: the palm, fingers, and thumb. The palm domain, formed by a central β-sheet flanked by α-helices, serves as the core scaffold, while the fingers domain, rich in β-strands and α-helices, extends from the palm to interact with incoming nucleotides, and the thumb domain, primarily helical, grips the DNA substrate. This configuration creates a cleft that accommodates double-stranded DNA, with the active sites positioned to facilitate polymerization and proofreading.^[13] The first crystal structure of the Klenow fragment, in its apo form complexed with dTMP, was solved at 3.3 Å resolution by Ollis et al. in 1985, revealing this hand-shaped fold and the separation of polymerase and exonuclease domains by about 30 Å. Subsequent refinements, including structures with DNA substrates, have confirmed the dynamic nature of the fingers domain, which closes upon nucleotide binding to enclose the active site.^[13]^[14] The conserved architecture of the Klenow fragment underscores its evolutionary relationship within the A family, sharing structural homology with polymerases such as those from T7 phage and Thermus aquaticus, despite modest sequence identity (around 25-30% in core motifs). This fold similarity supports the universal mechanism of DNA synthesis across prokaryotic and related enzymes.^[15]

Domains and Active Sites

The Klenow fragment of Escherichia coli DNA polymerase I is organized into three principal domains—palm, fingers, and thumb—that form a cleft for DNA binding and position the active sites for catalysis. The palm domain, located in the C-terminal portion, contains the polymerase active site and is characterized by two conserved sequence motifs, A and B, which are pivotal for the enzyme's 5'→3' polymerase activity. Motif A encompasses residues including Asp705, part of a carboxylate cluster that anchors one of the catalytic Mg²⁺ ions, while motif B includes Asp882 and a series of six α-helices that coordinate the second Mg²⁺ ion, facilitating the two-metal-ion mechanism for nucleotidyl transfer.^[16]^[17] The fingers domain, adjacent to the palm, is primarily responsible for binding the incoming deoxynucleoside triphosphate (dNTP) substrate. Key residues in this domain, such as Tyr766 in the O-helix, enable π-π stacking interactions with the purine or pyrimidine base of the dNTP, stabilizing its position prior to incorporation.^[18] This domain's mobility allows it to close over the active site during the catalytic cycle, though its static structural features emphasize nucleotide selectivity through hydrophobic and hydrogen-bonding contacts. The thumb domain contributes to DNA stability by wrapping around the duplex, featuring helix-hairpin-helix motifs that interact with the minor groove of the DNA substrate. These motifs, including residues in helices around positions 450-500, provide sequence-independent binding that positions the primer-template junction at the polymerase site approximately 25-30 Å from the exonuclease site.^[14] Separate from the polymerase site, the 3'→5' exonuclease active site resides in a pocket at the interface between the thumb and palm domains, within the N-terminal region of the fragment. This site features a conserved Asp-Glu-Asp (DED) triad comprising Asp355, Glu357, and Asp501, which coordinate two Mg²⁺ ions to enable hydrolysis of mismatched nucleotides from the 3' end of the primer strand. The two Mg²⁺ ions in the polymerase site, positioned about 4 Å apart, similarly support the phosphoryl transfer reaction by activating the 3'-OH nucleophile and stabilizing the pentacoordinated transition state.^[16]

Enzymatic Activities

Polymerase Activity

The Klenow fragment of Escherichia coli DNA polymerase I catalyzes the 5'→3' synthesis of DNA through the template-directed incorporation of deoxyribonucleoside triphosphates (dNTPs) onto the 3'-hydroxyl terminus of a primer strand base-paired to a single-stranded DNA template. This polymerase activity requires a divalent metal ion, typically Mg²⁺, coordinated in the active site to facilitate nucleophilic attack by the primer's 3'-OH on the α-phosphate of the incoming dNTP, releasing pyrophosphate as a byproduct. The enzyme exhibits substrate specificity for dNTPs over ribonucleotides or other analogs, primarily through interactions in the nucleotide-binding pocket that favor the deoxyribose sugar conformation. Kinetic parameters for this activity include Michaelis constants (K_m) of approximately 1–10 μM for dNTP substrates, reflecting efficient binding under physiological nucleotide concentrations. Optimal polymerization occurs at 37°C and pH 7.5, conditions that support maximal catalytic turnover while maintaining enzyme stability. The processivity of the Klenow fragment is moderate, with the enzyme typically incorporating 10–20 nucleotides per template-primer binding event before dissociating, which limits its efficiency for long-strand synthesis compared to more processive replicative polymerases. Fidelity during polymerization arises from base-pairing selectivity enforced by geometric exclusion, where the active site accommodates only Watson-Crick base pairs, and induced fit, a conformational change that aligns catalytic residues only upon correct dNTP binding. This results in an intrinsic error rate of about 10⁻⁵ errors per nucleotide incorporated, predominantly from base substitution mismatches. Additionally, the absence of 5'→3' exonuclease activity enables strand displacement synthesis, allowing the enzyme to extend primers past downstream duplex regions by displacing the non-template strand.^[19]

Exonuclease Activity

The 3'→5' exonuclease activity of the Klenow fragment involves the hydrolysis of phosphodiester bonds at the 3' terminus of DNA, specifically removing mismatched nucleotides to correct errors during DNA synthesis. This proofreading function operates by cleaving the bond between the mismatched nucleotide and the preceding phosphate, releasing a dNMP and leaving a 3'-OH group for subsequent correct incorporation. The activity is localized to a dedicated domain in the Klenow fragment, distinct from the polymerase site, and is crucial for post-insertion error correction.^[20] The rate of nucleotide excision by this exonuclease is approximately 10–100 s⁻¹ for mismatched termini, which is slower than the single-nucleotide polymerization rate constant (~50 s⁻¹) but allows selective proofreading without degrading correctly paired DNA, as excision of matched nucleotides occurs at rates orders of magnitude slower. This kinetic partitioning favors extension after correct incorporation while promoting excision after mismatches. For example, excision of a terminal mismatched dNMP occurs at rates within this range under physiological conditions with Mg²⁺.^[21] The exonuclease exhibits specificity for single-stranded DNA substrates and mismatched primer termini, where the destabilized duplex facilitates transfer of the 3' end from the polymerase active site to the exonuclease site, approximately 35 Å away. This transfer involves minimal conformational changes in the enzyme–DNA complex, with the mismatched base positioning for hydrolysis; correctly paired termini bind more stably to the polymerase site, reducing transfer efficiency by orders of magnitude. The activity preferentially processes ssDNA or the single-stranded overhang generated upon mismatch-induced melting of 3–4 base pairs at the primer terminus.^[22] The hydrolysis reaction requires divalent cations, primarily Mg²⁺ (or Mn²⁺ as an alternative), which coordinate with the Asp-Glu-Asp triad (residues Asp355, Glu357, Asp501) in the active site to position and activate a water molecule as the nucleophile. This two-metal-ion mechanism facilitates the inline attack on the scissile phosphodiester bond, with one metal activating the hydroxide and the other neutralizing the leaving group oxyanion. Optimal activity occurs at 1–10 mM Mg²⁺, reflecting the physiological role in replication fidelity.^[20]^[23] Coupled with the polymerase activity, the 3'→5' exonuclease enhances the overall fidelity of DNA synthesis by 10²–10³ fold, primarily by excising ~99% of mismatched nucleotides before extension can occur. This improvement stems from the kinetic discrimination against mismatches, where excision outcompetes forward polymerization, reducing error rates from ~10⁻⁵ (base selection alone) to ~10⁻⁷–10⁻⁸ per base pair.^[24]

Mechanism of Action

DNA Binding

The Klenow fragment of Escherichia coli DNA polymerase I binds double-stranded DNA substrates primarily through electrostatic interactions between positively charged residues lining its central binding cleft and the negatively charged phosphate backbone of the DNA. This cleft, formed by the palm, fingers, and thumb subdomains, positions the DNA at a right angle to the overall enzyme axis, facilitating specific recognition of the primer-template junction. The binding site accommodates approximately 8-11 base pairs of duplex DNA, with the structure-specific nature of the interaction ensuring stable occlusion of this segment within the cleft.^[14]^[25] The affinity of the Klenow fragment for primer-template DNA is notably high, with dissociation constants (K_d) typically ranging from 1 to 20 nM under physiological conditions, varying slightly with DNA length and temperature (e.g., 7.7 nM for a 13/20-mer at 25°C). This tight binding reflects the enzyme's preference for primed-template structures over single-stranded DNA or blunt-ended double-stranded DNA alone, to which it exhibits much weaker affinity, particularly at moderate salt concentrations like 150 mM NaCl. The initial binding event occurs in an open conformation, where the fingers subdomain is extended away from the active site, allowing the DNA to access the cleft without steric hindrance.^[26]^[27]^[26] Key stabilizing interactions involve contacts to the minor groove of the DNA, primarily mediated by the thumb subdomain, which wraps around the duplex like a vise to grip the phosphate backbone and enhance overall complex stability. These minor groove interactions contribute to the enzyme's ability to discriminate primer-template junctions during initial binding, positioning the 3′ end of the primer for subsequent engagement while the thumb's helical elements (such as α-helices H1 and H2) insert into the groove for secure hold. Mutational studies disrupting thumb residues, such as deletion of amino acids 590-613, reduce DNA binding affinity by over 100-fold (e.g., K_d increasing to 42 nM), underscoring the thumb's critical role in maintaining grip and specificity without altering the enzyme's overall thermal stability.^[14]^[28]

Catalysis and Proofreading

The catalytic cycle of the Klenow fragment begins with the binding of an incoming deoxyribonucleoside triphosphate (dNTP) to the binary complex formed by the enzyme and primer-template DNA. Nucleotide selection occurs primarily through Watson-Crick base pairing with the template base, ensuring specificity during replication. Upon selection of a cognate dNTP, the fingers domain undergoes a conformational change, closing over the active site to position the substrates optimally for catalysis; this induced fit transition is crucial for fidelity, as mismatched dNTPs induce slower or incomplete closure, promoting dissociation rather than incorporation.^[29] In the closed conformation, phosphodiester bond formation proceeds via a two-metal-ion mechanism, where two Mg²⁺ ions, coordinated by conserved residues (Asp705, Asp882, and Glu883 in the Klenow fragment), facilitate the nucleophilic attack by the primer's 3'-OH on the dNTP's α-phosphate. This generates a pentacoordinate transition state, leading to polymerization described by the equation:

(\ce{DNA})_n + \ce{dNTP} \rightarrow (\ce{DNA})_{n+1} + \ce{PPi}

Pyrophosphate (PPi) is then released, marking the completion of the chemistry step, followed by translocation of the enzyme along the DNA to the next template position, allowing the cycle to repeat. The induced fit model enhances fidelity by excluding water from the active site upon fingers closure for correct base pairs, preventing non-specific hydrolysis, while mismatches fail to trigger full closure, reducing the rate of bond formation by orders of magnitude and allowing error correction.^[29] If a mismatch is incorporated, proofreading is initiated through detection of the distorted base pair geometry, often involving wobble configurations that destabilize the primer terminus and reduce binding affinity at the polymerase site. The mismatched terminus is then transferred intramolecularly to the 3'-5' exonuclease active site, approximately 30 Å away, where hydrolysis occurs via another two-metal-ion mechanism involving conserved residues (Asp355, Glu357, Asp424, and Asp501) and Mg²⁺ ions. This exonuclease reaction yields:

(\ce{DNA})_n \rightarrow (\ce{DNA})_{n-1} + \ce{dNMP}

for the mismatched nucleotide (m), excising it as a 5'-deoxymonophosphate and returning the corrected primer to the polymerase site for resumption of synthesis.^[30]^[31] The rate-limiting step in the catalytic cycle is the fingers domain closure during induced fit, occurring at approximately 100-300 s⁻¹, which is slower than the subsequent chemical step (~10³ s⁻¹), ensuring that fidelity checkpoints are enforced before bond formation. In contrast, for processive synthesis, PPi release can become limiting under steady-state conditions.^[29]^[32]

Applications

DNA End Processing

The Klenow fragment plays a key role in DNA end processing by leveraging its 5'→3' polymerase and 3'→5' exonuclease activities to convert sticky ends into blunt ends, facilitating downstream cloning and ligation procedures.^[33] This process is essential for preparing DNA fragments with cohesive or protruding termini generated by restriction enzyme digestion. For fill-in of 5' overhangs, the Klenow fragment extends the recessed 3' hydroxyl end using its polymerase activity, incorporating nucleotides complementary to the overhanging template strand in the presence of all four dNTPs.^[34] This reaction generates flush, double-stranded blunt ends suitable for ligation. In contrast, removal of 3' overhangs relies on the 3'→5' exonuclease activity to progressively degrade the protruding 3' single-stranded tail until a blunt end is achieved, often combined with polymerase fill-in if a recessed 3' end results.^[34]^[33] Typical protocols involve incubating 0.1–4 μg of DNA with 1–5 units of Klenow fragment in a reaction buffer containing 33–50 μM each dNTP, at 25–37°C for 10–30 minutes, followed by heat inactivation at 75°C for 10–20 minutes or addition of EDTA to 10 mM.^[34] These conditions ensure efficient end modification without excessive degradation. In molecular cloning, the Klenow fragment is widely applied to prepare vectors and inserts by blunting restriction-generated ends, thereby enabling compatible ligation into blunt-ended sites. Although blunt-end ligation is generally less efficient than sticky-end ligation (by 10–100 fold), blunting provides uniform interfaces necessary for joining incompatible ends.^[35]^[36] A primary advantage of the Klenow fragment over full DNA polymerase I is the absence of 5'→3' exonuclease activity, which prevents unwanted nicking or degradation of double-stranded DNA from the 5' end during processing.^[33]

Labeling and Sequencing

The Klenow fragment, particularly its exonuclease-deficient variant (exo-), plays a key role in random primer labeling for generating high-specific-activity DNA probes. This method involves annealing short random oligonucleotide primers, typically hexamers, to denatured template DNA, followed by extension using the exo- Klenow fragment in the presence of deoxynucleotide triphosphates (dNTPs), one of which is radiolabeled or fluorescently tagged. The process enables uniform incorporation of labels along the DNA strand, producing probes suitable for hybridization-based detection in Southern blots or microarrays. Developed by Feinberg and Vogelstein, this technique yields specific activities exceeding 10⁹ disintegrations per minute per microgram (dpm/μg) of DNA, often reaching 2–5 × 10⁹ dpm/μg, which enhances sensitivity in nucleic acid detection assays.^[37] As an alternative to nick translation, random primer labeling with the exo- Klenow fragment is preferred for probe generation because it avoids the degradative action of the 5'→3' exonuclease activity present in full DNA polymerase I, which can lead to excessive DNA fragmentation during nick translation. This approach works efficiently with small quantities of starting DNA (10–20 ng) and produces longer, more stable probes without the size limitations imposed by nick-induced nicking and displacement synthesis. The exo- variant ensures processive extension without proofreading removal of incorporated labels, maintaining high labeling efficiency.^[38] In early DNA sequencing, the Klenow fragment was instrumental in the Sanger dideoxy chain-termination method, where it performed processive DNA synthesis to extend primers in the presence of chain-terminating dideoxynucleotides. Lacking the 5'→3' exonuclease activity of full DNA polymerase I, it prevented unwanted degradation of the template or newly synthesized strands, enabling reliable generation of termination fragments for gel electrophoresis and size-based readout. This enzyme was the polymerase of choice in the original Sanger protocol, providing the fidelity and processivity needed for sequencing up to several hundred bases before thermostable polymerases like Taq were adopted for automated and cycle-based improvements in the late 1980s.^[39] The Klenow fragment also facilitates second-strand cDNA synthesis by filling in and extending from RNA-DNA hybrids generated during first-strand reverse transcription. In this application, the enzyme uses the RNA strand as a template to synthesize the complementary DNA strand, often employing random primers or hairpin loops for initiation, resulting in double-stranded cDNA suitable for cloning or further amplification. Its polymerase activity ensures accurate extension with moderate strand displacement, making it effective for constructing cDNA libraries from mRNA templates. This use was demonstrated in early cloning experiments, such as the insertion of rabbit β-globin gene sequences into plasmids.

Variants

Exo-Klenow Fragment

The Exo-Klenow fragment, also known as Klenow fragment lacking 3'→5' exonuclease activity, is a modified version of the Klenow fragment derived from Escherichia coli DNA polymerase I that retains 5'→3' polymerase activity but eliminates the proofreading function. This variant is primarily generated through site-directed mutagenesis targeting the 3'→5' exonuclease active site, with the double mutation D355A/E357A being a common approach to abolish the activity while preserving the polymerase domain.^[40] The first descriptions of such exonuclease-deficient mutants appeared in the late 1980s, developed for studies on DNA labeling where proofreading could degrade incorporated nucleotides.^[41] Key properties of the Exo-Klenow fragment include its full retention of DNA polymerase activity for primer extension and strand displacement, but without the 3'→5' exonuclease, resulting in an error rate increase of approximately 100-fold due to the absence of proofreading. This lack of degradation activity makes it particularly useful in applications requiring stable incorporation of modified nucleotides, as it prevents the removal of labeled or tagged bases that could otherwise be excised by the wild-type enzyme's exonuclease.^[42]^[43] Commercially, the Exo-Klenow fragment is available in high-concentration formulations, typically 5–10 U/μL or higher (up to 50 U/μL), optimized for efficient random priming reactions in probe generation.^[44] These preparations are supplied by major biotech suppliers and are stored in buffers with glycerol for stability. Specific applications leverage its non-degradative nature, such as in microarray labeling where it incorporates fluorescent dNTPs via random priming without removing the labels, enabling high-sensitivity detection of gene expression.^[42] It is also widely used for dA-tailing of blunt-ended DNA fragments in next-generation sequencing workflows, adding adenine residues to 3' ends without excising preexisting overhangs or added tails, facilitating adapter ligation.^[42]

Other Engineered Forms

High-fidelity variants of the Klenow fragment have been developed through site-directed mutagenesis to improve nucleotide selectivity and reduce error rates during DNA synthesis. Mutations such as R754A and Q849A in the polymerase active site enhance discrimination against mismatched base pairs during the extension step, leading to lower mutation frequencies in lacZ forward mutation assays compared to the wild-type enzyme. These anti-mutator variants demonstrate increased fidelity by stabilizing the enzyme's closed conformation for correct nucleotides while destabilizing it for mismatches, providing insights into proofreading-independent error avoidance mechanisms.^[45] Processivity-enhanced forms of the Klenow fragment often involve mutations or fusions that extend the length of DNA synthesis per binding event. The D424A substitution in the exonuclease domain, commonly combined with other modifications, prevents premature termination due to proofreading degradation, allowing for improved processivity compared to the wild-type enzyme, enabling synthesis of longer DNA stretches. Additional engineering, such as fusion with DNA-binding domains inspired by viral polymerases, has been explored to further boost processivity, though applications remain primarily research-oriented rather than routine.^[46] Thermostable analogs of the Klenow fragment, such as Klentaq1 (the large fragment of Thermus aquaticus DNA polymerase I), have been engineered for PCR-like applications by leveraging structural similarities to the E. coli Klenow while conferring heat stability up to 95°C. These variants enable repeated cycles of denaturation and extension without enzyme inactivation, outperforming mesophilic Klenow in high-temperature amplification protocols. Glycerol-free formulations of exo-Klenow derivatives further support lyophilized preparations for next-generation sequencing workflows, enhancing stability in reagent mixes.^[47]^[48] Post-2000 research has utilized Klenow mutants as models for studying cancer-associated polymerase variants, particularly in translesion synthesis (TLS) pathways that bypass DNA lesions. Engineered mutants mimicking structural features of Y-family polymerases, such as altered active site residues for lesion tolerance, have revealed mechanisms of error-prone replication in tumor cells, with implications for mutagenesis in oncogenesis. For therapeutic potential, fusions of exonuclease-deficient Klenow with nCas9 in click editing systems facilitate template-directed gene editing, achieving precise insertions and corrections with reduced off-target effects compared to reverse transcriptase-based methods as of 2023; however, clinical translation is limited by delivery challenges and ongoing optimization needs.^[49]^[50]

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Site-directed mutagenesis of the large fragment of DNA polymerase I (Klenow fragment) yielded two mutant proteins lacking 3',5'-exonuclease activity but ...Missing: First Exo- 1980s labeling<|separator|>
[37]
Klenow Fragment (3'→5' exo–) - QIAGEN
The enzyme is supplied with 10X Blue Buffer (B0110) containing 500 mM NaCl, 100 mM Tris-HCl, 100 mM MgCl2, 10 mM DTT; pH 7.9 at 25°C. Performance. Assay ...Missing: optimal | Show results with:optimal
[38]
Mapping DNA polymerase errors by single-molecule sequencing - NIH
May 16, 2016 · We measured the average error rates of 3′→5′ exonuclease deficient Klenow Fragment (Klenow (exo-)), Taq, E. coli Y-family DNA Polymerase IV ...
[39]
Klenow (3'-5' exo-) - Enzo
Klenow (3′-5′ exo-) is a mesophilic DNA polymerase deficient in both proofreading (3′-5′) and nick-translation (5′-3′) nuclease activities, ...
[40]
https://www.biosearchtech.com/molecular-biology-enzymes/polymerases/dna-and-rna-polymerases/exo-minus-klenow-dna-polymerase-%2528d355a%252C-e357a%2529/p/NXGENZ-004
[41]
Engineered viral DNA polymerase with enhanced DNA amplification ...
Sep 14, 2020 · The new variant, B35-HhH, has enhanced DNA amplification capacity, and overall similar DNA replication fidelity and TLS capacity to the parental ...
[42]
Crystal structure of the large fragment of Thermus aquaticus DNA ...
Beese L. S., Derbyshire V., Steitz T. A. Structure of DNA polymerase I Klenow fragment bound to duplex DNA. Science. 1993 Apr 16;260(5106):352–355. doi ...
[43]
Glycerol-Free DNA Pol I Klenow Fragment exo- (HC)
The enzyme displays moderate strand displacement activity and can also be ... What is the difference between DNA Pol I Klenow Fragment and DNA Pol I Klenow ...
[44]
Family A and B DNA Polymerases in Cancer - PubMed Central - NIH
The Klenow fragment (KF) [20] of E. coli DNA polymerase I (pol I) is the prototypical DNA polymerase that has been used to understand the biochemical mechanism ...
[45]
https://www.jbc.org/article/S0021-9258(19)88090-0/fulltext