Surveyor nuclease assay

Last updated
Diagram of the surveyor nuclease assay workflow Figure final 3.jpg
Diagram of the surveyor nuclease assay workflow

Surveyor nuclease assay is an enzyme mismatch cleavage assay used to detect single base mismatches or small insertions or deletions (indels).

Contents

Surveyor nuclease is part of a family of mismatch-specific endonucleases that were discovered in celery (CEL nucleases). [1] The enzyme recognizes all base substitutions and insertions/deletions, and cleaves the 3′ side of mismatched sites in both DNA strands with high specificity [2]

This assay has been used to identify and analyze mutations in a variety of organisms and cell types, as well as to confirm genome modifications following genome editing (using CRISPR/TALENs/zinc fingers).

Background

The ability to discover and detect known and unknown mutations is of great importance in biomedical research and genetic diagnosis (see Applications). Therefore, multiple methods have been developed to enable research-based and clinical diagnostic detection of such mutations.

The most direct manner to identify the sequence changes/differences is through reading the DNA sequence with traditional and high throughput DNA sequencing methods (see Sanger sequencing and DNA sequencing). However, these methods provide large amounts of unnecessary data and are costly to use. [3] In addition, traditional sequencing can be useful for detection of germline mutations, but may be less successful in detecting somatic minor alleles at low frequencies (mosaicism). Therefore, other non-sequencing based approaches to detect the mutation or polymorphisms are required.

Other widely used methods depend on physical properties of DNA, for example melting temperature-based systems such as Single-stranded conformational polymorphism analysis (SSCP) and Denaturing high-performance liquid chromatography (DHPLC). These techniques are generally limited to the analysis of short DNA fragments (< 1000 bp) and are only able to indicate the presence of polymorphism(s), but do not easily yield the location of a mutation within a DNA sequence. Therefore, this must be followed with additional techniques in order to pinpoint the mutation or map multiple mutations in the same fragment. [3]

Enzymatic mismatch cleavage assays exploit the properties of mismatch-specific endonucleases to detect and cleave mismatches. These methods are simple to run using standard laboratory techniques and equipment, and can detect polymorphisms, single base pair mismatches, and insertions and deletions at low frequencies. [4] Several such enzymes have been discovered (including CEL I, T4 endonuclease VII, Endonuclease V, T7 endonuclease I). [3]

One of the commonly used enzymes is Surveyor nuclease (CEL II), which cleaves the 3′ side of both DNA strands with high specificity at sites of base substitution or insertion/deletion. This enzyme is capable of cleaving at multiple mutations in large DNA fragments, and produces detectable cleavage products from mismatch DNA representing only a small proportion of the DNA in a population, thus making it suitable for use in enzyme mismatch cleavage assays. [2]

History

In 1998, Olekowski et al. [5] identified a new mismatch specific endonuclease. The enzyme was purified from celery and was given the name CEL I.

CEL I was shown to cut DNA with high specificity on both strands at the 3′ side of base-substitution mismatches, and can therefore be used in enzyme mutation detection methods to identify mutations and polymorphisms. Olekowski and colleagues demonstrated this technique by using this enzyme to detect a variety of mutations and polymorphisms in the human BRCA1 gene. [1] [5] [6]

While monitoring the purification of CEL I using polyacrylamide gel electrophoresis, Yang et al. [1] noticed that there were two nuclease bands that stayed together during all the purification steps. The major nuclease activity was designated CEL I, while the minor activity on SDS-PAGE was named CEL II. They concluded that CEL I and CEL II are similar, and that both are able to cleave a DNA mismatch.

In 2004, Qiu et al. developed a mutation detection technology based on CEL II, also known as Surveyor Nuclease. [2] Since then the method has been used to detect mutations and polymorphisms in many different organisms and cell types (see applications).

Surveyor nuclease was licensed from the Fox Chase Cancer Center by Transgenomic, Inc. and was subsequently sold to IDT, which currently distributes it.

Surveyor nuclease assay workflow

DNA Extraction

Initially, the DNA of interest (nuclear or mitochondrial DNA) is extracted from tissues or cell culture. This can be done by standard extraction methods such as Proteinase K digestion followed by ethanol precipitation or by other commercially available methods.

If the DNA is predicted to be heterogeneous, e.g. from a pool of differentially modified cells or from heterozygous mutation carriers, there is no need to add control DNA.

Polymerase chain reaction

The region of interest in both mutant and wild-type reference DNA is amplified by polymerase chain reaction (PCR). The PCR reaction should be carried out using a high-fidelity proofreading polymerase to avoid introducing PCR errors that will be interpreted by the nuclease. The PCR reaction should be optimized to create a single, strong PCR band, as non-specific bands will increase the background noise of the assay.

If the allele of interest is expected to be present in low frequency, such as in the case of somatic mosaicism or heteroplasmic mitochondrial DNA, a modified PCR protocol that enriches variant alleles from a mixture of wild-type and mutation-containing DNA might be considered (e.g. COLD-PCR).

Formation of hybrid DNA duplex

The DNA of interest is denatured and annealed in order to form heteroduplexes containing a mismatch at the point of the mutation, which can then be identified by the Surveyor nuclease. If the DNA is predicted to be homogenous (e.g. homoplasmic mitochondrial DNA or identical alleles on both chromosomes of genomic DNA) then DNA from a control sample is needed in order to form a heteroduplex which is then recognizable by the nuclease. If the DNA sample is heterogeneous, no additional control DNA is needed; however, the PCR products should still be denatured and annealed in order to create heteroduplexes.

Digestion

The annealed DNA is treated with Surveyor nuclease to cleave the heteroduplexes. All types of mismatches are identifiable by Surveyor nuclease, although the mismatch cutting preferences fall into four groups from most to least preferred: CT, AC, and CC are preferred equally over TT, followed by AA and GG, and finally followed by the least preferred, AG and GT. Sequence context also influences the Surveyor nuclease digestion rate. [2]

Analysis

Digested DNA products can be analyzed using conventional gel electrophoresis or high-resolution capillary electrophoresis. The detection of cleaved products indicates the presence of a heteroduplex formed by a mismatch. The location of the mutation/polymorphism can be inferred by observing the fragment length after cleavage. If fluorescent labelled primers are used to mark the 5’ and 3’ end of the PCR products, different colored bands will be observed in the analysis. The size of each band independently confirms the position of the mutation/polymorphism. Multiple mutations can be detected by the presence of several fragments. [1] [5]

Advantages and limitations

Advantages

Advantages of mismatch nuclease assays

One of the main advantages of detecting mutations and polymorphisms using mismatch nuclease methods is that no previous knowledge is required regarding the nature of the mutation, as opposed to other methods, such as restriction fragment length polymorphisms (RFLP) that has been used for SNP analysis in the past.

In comparison to methods based on melting temperature, mismatch-specific endonuclease methods are not only faster, but can also detect multiple mutations in large DNA fragments.

The method is feasible to use in high-throughput systems using automated injection, making it suitable for screening. [7]

Advantages of surveyor nuclease

Surveyor nuclease is a reasonably sensitive enzyme, producing detectable cleavage products from sequences representing only a small proportion of DNA in the population. It can detect a ratio of 1:32 heteroduplex to homoduplex for smaller PCR products (~0.6 kb), and 1:16 heteroduplex to homoduplex for longer PCR products (~2.3 kb). This property makes it possible to pool clinical samples in order to increase the heteroduplex formation and hence the sensitivity. [3] This is also useful for detection of minor variants in a heterogeneous population (such as heterogeneous tumor). In the case of genome editing by CRISPR or other methods, this property can enhance detection of rare editing events in a population of cells prior to creation and testing of individual edited clones.

Surveyor nuclease cleaves all types of mismatches, even if some are more preferred then others: CT, AC, and CC are preferred equally over TT, followed by AA and GG, and finally followed by the least preferred, AG and GT. It also detects Indels up to at least 12 bp. [2]

Surveyor nuclease assay can also detect multiple mutations in the same fragment. However, this requires several additional processing steps that may also increase the background of the assay (see Limitations).

Limitations

PCR amplification product

One of the main limitations of this assay is that it relies on PCR amplification, and is therefore influenced by the quality of the amplified product. PCR artifacts (e.g. primer-dimers or truncated products) can increase the background noise and obscure the signal. Primer-dimers can also inhibit the activity of surveyor nuclease, reducing the signal.

As the PCR method has the potential to introduce its own mutations during the amplification, these errors can also increase background noise. Therefore, it is best to use a high-fidelity polymerase to minimize the amplification errors.

Mitochondrial DNA analysis might be susceptible to contamination by nuclear mitochondrial DNA sequences co-amplified during the PCR reaction, thus confounding the analysis of homoplasmic versus heteroplasmic mitochondrial DNA. [8]

In order to detect multiple mutations in the same fragment, post-PCR clean-up must be done before Surveyor nuclease digestion. Detection of multiple mismatches can also be improved by increasing time and amount of surveyor nuclease in the reaction, but this also increases the background due to non-specific cleavage.

Limitations of the surveyor nuclease enzyme

Surveyor nuclease also has a 5′ exonuclease activity that attacks the ends of double‐stranded DNA increasing background signal during extended incubation. [2] This can be reduced by shortening the digestion time and by adding DNA polymerase.

Applications

Confirming genome modifications using CRISPR and other methods

A number of genome editing technologies have emerged in recent years, including zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) and the RNA-guided CRISPR/Cas9 nuclease system. These methods promote genome editing by introduction of a double strand DNA break, followed by repair through the non-homologous end-joining (NHEJ) or homology-directed repair (HDR) pathways. While HDR is expected to introduce a consistent modification to the genome, NHEJ can introduce a heterogeneous mix of mutations (usually small indels), which will be difficult to identify using Sanger sequencing. Point mutations and indels can be detected by surveyor nuclease assay, making it useful to detect genome editing in a pool of cells without the need for clonal expansion prior to analysis, and it can also provide an estimate of the targeting efficiency achieved. [9] [10] [11] Even after clonal expansion, detection of mutations using Sanger sequence may be difficult as each allele can undergo a different editing event. In this case, the Surveyor nuclease assay will actually use this effect to create the required heteroduplexes for detection by the mismatch endonuclease.

Detection of germline mutations in human genes

Surveyor nuclease assay has been used to detect germline mutations in human genes. For example, ATRX for X-linked mental retardation, [12] and the HBB gene linked to β-thalassemia. [7] The assay has also been used to detect mitochondrial and nuclear DNA mutations associated with respiratory chain defects, [13] and mutations associated with kidney disease. [14] [15]

Detection of somatic mutations in cancer

Surveyor nuclease assay has been used to detect somatic mutations in various cancer-related genes, and as stated above, can be used even when the sample is heterogeneous and the mutant allele only comprises 1%–5% of the total alleles. [16] The method has been used to detect mutations in epidermal-growth-factor-receptor (EGFR), [16] [17] [18] [19] Janus Kinase 2 (JAK2), [20] [21] p53 [22] and others.

Other applications

The method has been used to detect mutations that cause drug resistance in Mycobacterium tuberculosis. [23]

Related Research Articles

A restriction enzyme, restriction endonuclease, REase, ENase orrestrictase is an enzyme that cleaves DNA into fragments at or near specific recognition sites within molecules known as restriction sites. Restriction enzymes are one class of the broader endonuclease group of enzymes. Restriction enzymes are commonly classified into five types, which differ in their structure and whether they cut their DNA substrate at their recognition site, or if the recognition and cleavage sites are separate from one another. To cut DNA, all restriction enzymes make two incisions, once through each sugar-phosphate backbone of the DNA double helix.

<span class="mw-page-title-main">Nuclease</span> Class of enzymes

A nuclease is an enzyme capable of cleaving the phosphodiester bonds between nucleotides of nucleic acids. Nucleases variously effect single and double stranded breaks in their target molecules. In living organisms, they are essential machinery for many aspects of DNA repair. Defects in certain nucleases can cause genetic instability or immunodeficiency. Nucleases are also extensively used in molecular cloning.

<span class="mw-page-title-main">Locked nucleic acid</span> Biological molecule

A locked nucleic acid (LNA), also known as bridged nucleic acid (BNA), and often referred to as inaccessible RNA, is a modified RNA nucleotide in which the ribose moiety is modified with an extra bridge connecting the 2' oxygen and 4' carbon. The bridge "locks" the ribose in the 3'-endo (North) conformation, which is often found in the A-form duplexes. This structure provides for increased stability against enzymatic degradation. LNA also offers improved specificity and affinity in base-pairing as a monomer or a constituent of an oligonucleotide. LNA nucleotides can be mixed with DNA or RNA residues in a oligonucleotide.

In molecular biology, endonucleases are enzymes that cleave the phosphodiester bond within a polynucleotide chain. Some, such as deoxyribonuclease I, cut DNA relatively nonspecifically, while many, typically called restriction endonucleases or restriction enzymes, cleave only at very specific nucleotide sequences. Endonucleases differ from exonucleases, which cleave the ends of recognition sequences instead of the middle (endo) portion. Some enzymes known as "exo-endonucleases", however, are not limited to either nuclease function, displaying qualities that are both endo- and exo-like. Evidence suggests that endonuclease activity experiences a lag compared to exonuclease activity.

TILLING is a method in molecular biology that allows directed identification of mutations in a specific gene. TILLING was introduced in 2000, using the model plant Arabidopsis thaliana, and expanded on into other uses and methodologies by a small group of scientists including Luca Comai. TILLING has since been used as a reverse genetics method in other organisms such as zebrafish, maize, wheat, rice, soybean, tomato and lettuce.

Mung bean nuclease is a nuclease derived from sprouts of the mung bean that removes nucleotides in a step-wise manner from single-stranded DNA molecules (ssDNA) and is used in biotechnological applications to remove such ssDNA from a mixture also containing double-stranded DNA (dsDNA). This enzyme is useful for transcript mapping, removal of single-stranded regions in DNA hybrids or single-stranded overhangs produced by restriction enzymes, etc. It has an activity similar to Nuclease S1, but it has higher specificity for single-stranded molecules.

<span class="mw-page-title-main">Heteroduplex analysis</span>

Heteroduplex analysis (HDA) is a method in biochemistry used to detect point mutations in DNA since 1992. Heteroduplexes are dsDNA molecules that have one or more mismatched pairs, on the other hand homoduplexes are dsDNA which are perfectly paired. This method of analysis depend up on the fact that heteroduplexes shows reduced mobility relative to the homoduplex DNA. heteroduplexes are formed between different DNA alleles. In a mixture of wild-type and mutant amplified DNA, heteroduplexes are formed in mutant alleles and homoduplexes are formed in wild-type alleles. There are two types of heteroduplexes based on type and extent of mutation in the DNA. Small deletions or insertion create bulge-type heteroduplexes which is stable and is verified by electron microscope. Single base substitutions creates more unstable heteroduplexes called bubble-type heteroduplexes, because of low stability it is difficult to visualize in electron microscopy. HDA is widely used for rapid screening of mutation of the 3 bp p.F508del deletion in the CFTR gene.

Flap endonucleases are a class of nucleolytic enzymes that act as both 5'-3' exonucleases and structure-specific endonucleases on specialised DNA structures that occur during the biological processes of DNA replication, DNA repair, and DNA recombination. Flap endonucleases have been identified in eukaryotes, prokaryotes, archaea, and some viruses. Organisms can have more than one FEN homologue; this redundancy may give an indication of the importance of these enzymes. In prokaryotes, the FEN enzyme is found as an N-terminal domain of DNA polymerase I, but some prokaryotes appear to encode a second homologue.

SNP genotyping is the measurement of genetic variations of single nucleotide polymorphisms (SNPs) between members of a species. It is a form of genotyping, which is the measurement of more general genetic variation. SNPs are one of the most common types of genetic variation. An SNP is a single base pair mutation at a specific locus, usually consisting of two alleles. SNPs are found to be involved in the etiology of many human diseases and are becoming of particular interest in pharmacogenetics. Because SNPs are conserved during evolution, they have been proposed as markers for use in quantitative trait loci (QTL) analysis and in association studies in place of microsatellites. The use of SNPs is being extended in the HapMap project, which aims to provide the minimal set of SNPs needed to genotype the human genome. SNPs can also provide a genetic fingerprint for use in identity testing. The increase of interest in SNPs has been reflected by the furious development of a diverse range of SNP genotyping methods.

An allele-specific oligonucleotide (ASO) is a short piece of synthetic DNA complementary to the sequence of a variable target DNA. It acts as a probe for the presence of the target in a Southern blot assay or, more commonly, in the simpler Dot blot assay. It is a common tool used in genetic testing, forensics, and Molecular Biology research.

<span class="mw-page-title-main">Nuclease S1</span> Class of enzymes

Nuclease S1 is an endonuclease enzyme that splits single-stranded DNA (ssDNA) and RNA into oligo- or mononucleotides. This enzyme catalyses the following chemical reaction

<span class="mw-page-title-main">Apoptotic DNA fragmentation</span> Cleavage of DNA into tiny pieces during apoptosis

Apoptotic DNA fragmentation is a key feature of apoptosis, a type of programmed cell death. Apoptosis is characterized by the activation of endogenous endonucleases, particularly the caspase-3 activated DNase (CAD), with subsequent cleavage of nuclear DNA into internucleosomal fragments of roughly 180 base pairs (bp) and multiples thereof (360, 540 etc.). The apoptotic DNA fragmentation is being used as a marker of apoptosis and for identification of apoptotic cells either via the DNA laddering assay, the TUNEL assay, or the by detection of cells with fractional DNA content ("sub G1 cells") on DNA content frequency histograms e.g. as in the Nicoletti assay.

<span class="mw-page-title-main">Oligomer restriction</span>

Oligomer Restriction is a procedure to detect an altered DNA sequence in a genome. A labeled oligonucleotide probe is hybridized to a target DNA, and then treated with a restriction enzyme. If the probe exactly matches the target, the restriction enzyme will cleave the probe, changing its size. If, however, the target DNA does not exactly match the probe, the restriction enzyme will have no effect on the length of the probe. The OR technique, now rarely performed, was closely associated with the development of the popular polymerase chain reaction (PCR) method.

Restriction Fragment Mass Polymorphism (RFMP) is a technology which digests DNA into oligonucleotide fragments, and detects variation of DNA sequences by molecular weight of the fragments. RFMP is a proprietary technology of GeneMatrix and can be utilized for genotyping viruses and microorganisms, and for human genome research. It is relatively restricted in usage due to the existence of many other genotyping products.

COLD-PCR is a modified polymerase chain reaction (PCR) protocol that enriches variant alleles from a mixture of wildtype and mutation-containing DNA. The ability to preferentially amplify and identify minority alleles and low-level somatic DNA mutations in the presence of excess wildtype alleles is useful for the detection of mutations. Detection of mutations is important in the case of early cancer detection from tissue biopsies and body fluids such as blood plasma or serum, assessment of residual disease after surgery or chemotherapy, disease staging and molecular profiling for prognosis or tailoring therapy to individual patients, and monitoring of therapy outcome and cancer remission or relapse. Common PCR will amplify both the major (wildtype) and minor (mutant) alleles with the same efficiency, occluding the ability to easily detect the presence of low-level mutations. The capacity to detect a mutation in a mixture of variant/wildtype DNA is valuable because this mixture of variant DNAs can occur when provided with a heterogeneous sample – as is often the case with cancer biopsies. Currently, traditional PCR is used in tandem with a number of different downstream assays for genotyping or the detection of somatic mutations. These can include the use of amplified DNA for RFLP analysis, MALDI-TOF genotyping, or direct sequencing for detection of mutations by Sanger sequencing or pyrosequencing. Replacing traditional PCR with COLD-PCR for these downstream assays will increase the reliability in detecting mutations from mixed samples, including tumors and body fluids.

Meganucleases are endodeoxyribonucleases characterized by a large recognition site ; as a result this site generally occurs only once in any given genome. For example, the 18-base pair sequence recognized by the I-SceI meganuclease would on average require a genome twenty times the size of the human genome to be found once by chance. Meganucleases are therefore considered to be the most specific naturally occurring restriction enzymes.

No-SCAR genome editing is an editing method that is able to manipulate the Escherichia coli genome. The system relies on recombineering whereby DNA sequences are combined and manipulated through homologous recombination. No-SCAR is able to manipulate the E. coli genome without the use of the chromosomal markers detailed in previous recombineering methods. Instead, the λ-Red recombination system facilitates donor DNA integration while Cas9 cleaves double-stranded DNA to counter-select against wild-type cells. Although λ-Red and Cas9 genome editing are widely used technologies, the no-SCAR method is novel in combining the two functions; this technique is able to establish point mutations, gene deletions, and short sequence insertions in several genomic loci with increased efficiency and time sensitivity.

<span class="mw-page-title-main">GLAD-PCR assay</span>

Glal hydrolysis and Ligation Adapter Dependent PCR assay is the novel method to determine R(5mC)GY sites produced in the course of de novo DNA methylation with DNMTЗA and DNMTЗB DNA methyltransferases. GLAD-PCR assay do not require bisulfite treatment of the DNA.

<span class="mw-page-title-main">RNase H-dependent PCR</span> Laboratory technique

RNase H-dependent PCR (rhPCR) is a modification of the standard PCR technique. In rhPCR, the primers are designed with a removable amplification block on the 3’ end. Amplification of the blocked primer is dependent on the cleavage activity of a hyperthermophilic archaeal Type II RNase H enzyme during hybridization to the complementary target sequence. This RNase H enzyme possesses several useful characteristics that enhance the PCR. First, it has very little enzymatic activity at low temperature, enabling a “hot start PCR” without modifications to the DNA polymerase. Second, the cleavage efficiency of the enzyme is reduced in the presence of mismatches near the RNA residue. This allows for reduced primer dimer formation, detection of alternative splicing variants, ability to perform multiplex PCR with higher numbers of PCR primers, and the ability to detect single-nucleotide polymorphisms.

Off-target genome editing refers to nonspecific and unintended genetic modifications that can arise through the use of engineered nuclease technologies such as: clustered, regularly interspaced, short palindromic repeats (CRISPR)-Cas9, transcription activator-like effector nucleases (TALEN), meganucleases, and zinc finger nucleases (ZFN). These tools use different mechanisms to bind a predetermined sequence of DNA (“target”), which they cleave, creating a double-stranded chromosomal break (DSB) that summons the cell's DNA repair mechanisms and leads to site-specific modifications. If these complexes do not bind at the target, often a result of homologous sequences and/or mismatch tolerance, they will cleave off-target DSB and cause non-specific genetic modifications. Specifically, off-target effects consist of unintended point mutations, deletions, insertions inversions, and translocations.

References

  1. 1 2 3 4 Yang, B.; Wen, X.; Kodali, N. S.; Oleykowski, C. A.; Miller, C. G.; Kulinski, J.; Besack, D.; Yeung, J. A.; Kowalski, D. (2000-04-04). "Purification, cloning, and characterization of the CEL I nuclease". Biochemistry. 39 (13): 3533–3541. doi:10.1021/bi992376z. ISSN   0006-2960. PMID   10736152.
  2. 1 2 3 4 5 6 Qiu, Peter; Shandilya, Harini; D'Alessio, James M.; O'Connor, Kevin; Durocher, Jeffrey; Gerard, Gary F. (2004-04-01). "Mutation detection using Surveyor nuclease". BioTechniques. 36 (4): 702–707. doi: 10.2144/04364PF01 . ISSN   0736-6205. PMID   15088388.
  3. 1 2 3 4 Yeung, Anthony T.; Hattangadi, Deepali; Blakesley, Lauryn; Nicolas, Emmanuelle (2005-05-01). "Enzymatic mutation detection technologies". BioTechniques. 38 (5): 749–758. doi: 10.2144/05385rv01 . ISSN   0736-6205. PMID   15948293.
  4. ↑ Huang, Mo Chao; Cheong, Wai Chye; Lim, Li Shi; Li, Mo-Huang (2012-03-01). "A simple, high sensitivity mutation screening using Ampligase mediated T7 endonuclease I and Surveyor nuclease with microfluidic capillary electrophoresis". Electrophoresis. 33 (5): 788–796. doi:10.1002/elps.201100460. ISSN   1522-2683. PMID   22437793. S2CID   40764751.
  5. 1 2 3 Oleykowski, Catherine A.; Mullins, Colleen RB; Godwin, Andrew K; Yeung, Anthony T (1998). "Mutation detection using a novel plant endonuclease". Nucleic Acids Research. 26 (20): 4597–4602. doi:10.1093/nar/26.20.4597. PMC   147896 . PMID   9753726.
  6. ↑ Kulinski, J.; Besack, D.; Oleykowski, C. A.; Godwin, A. K.; Yeung, A. T. (2000-07-01). "CEL I enzymatic mutation detection assay". BioTechniques. 29 (1): 44–46, 48. doi: 10.2144/00291bm07 . ISSN   0736-6205. PMID   10907074.
  7. 1 2 Hung, Chia-Cheng; Su, Yi-Ning; Lin, Chia-Yun; Chang, Yin-Fei; Chang, Chien-Hui; Cheng, Wen-Fang; Chen, Chi-An; Lee, Chien-Nan; Lin, Win-Li (2008-01-01). "Comparison of the mismatch-specific endonuclease method and denaturing high-performance liquid chromatography for the identification of HBB gene mutations". BMC Biotechnology. 8: 62. doi:10.1186/1472-6750-8-62. ISSN   1472-6750. PMC   2525636 . PMID   18694524.
  8. ↑ Yen, Hsiu-Chuan; Li, Shiue-Li; Hsu, Wei-Chien; Tang, Petrus (2014-01-01). "Interference of Co-amplified nuclear mitochondrial DNA sequences on the determination of human mtDNA heteroplasmy by Using the SURVEYOR nuclease and the WAVE HS system". PLOS ONE. 9 (3): e92817. Bibcode:2014PLoSO...992817Y. doi: 10.1371/journal.pone.0092817 . ISSN   1932-6203. PMC   3963942 . PMID   24664244.
  9. ↑ Guschin, Dmitry Y.; Waite, Adam J.; Katibah, George E.; Miller, Jeffrey C.; Holmes, Michael C.; Rebar, Edward J. (2010-01-01). A rapid and general assay for monitoring endogenous gene modification. Methods in Molecular Biology. Vol. 649. pp. 247–256. doi:10.1007/978-1-60761-753-2_15. ISBN   978-1-60761-752-5. ISSN   1940-6029. PMID   20680839.
  10. ↑ Ran, F. Ann; Hsu, Patrick D.; Lin, Chie-Yu; Gootenberg, Jonathan S.; Konermann, Silvana; Trevino, Alexandro E.; Scott, David A.; Inoue, Azusa; Matoba, Shogo (2013-09-12). "Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity". Cell. 154 (6): 1380–1389. doi:10.1016/j.cell.2013.08.021. ISSN   1097-4172. PMC   3856256 . PMID   23992846.
  11. ↑ Wang, Haoyi; Yang, Hui; Shivalila, Chikdu S.; Dawlaty, Meelad M.; Cheng, Albert W.; Zhang, Feng; Jaenisch, Rudolf (2013-05-09). "One-step generation of mice carrying mutations in multiple genes by CRISPR/Cas-mediated genome engineering". Cell. 153 (4): 910–918. doi:10.1016/j.cell.2013.04.025. ISSN   1097-4172. PMC   3969854 . PMID   23643243.
  12. ↑ Wada, Takahito; Fukushima, Yoshimitsu; Saitoh, Shinji (2006-07-15). "A new detection method for ATRX gene mutations using a mismatch-specific endonuclease". American Journal of Medical Genetics Part A. 140 (14): 1519–1523. doi:10.1002/ajmg.a.31310. ISSN   1552-4825. PMID   16763962. S2CID   6803312.
  13. ↑ Bannwarth, Sylvie; Procaccio, Vincent; Paquis-Flucklinger, Veronique (2005-06-01). "Surveyor Nuclease: a new strategy for a rapid identification of heteroplasmic mitochondrial DNA mutations in patients with respiratory chain defects". Human Mutation. 25 (6): 575–582. doi: 10.1002/humu.20177 . ISSN   1098-1004. PMID   15880407. S2CID   9919530.
  14. ↑ Tan, Ying-Cai; Blumenfeld, Jon D.; Anghel, Raluca; Donahue, Stephanie; Belenkaya, Rimma; Balina, Marina; Parker, Thomas; Levine, Daniel; Leonard, Debra G. B. (2009-02-01). "Novel method for genomic analysis of PKD1 and PKD2 mutations in autosomal dominant polycystic kidney disease". Human Mutation. 30 (2): 264–273. doi: 10.1002/humu.20842 . ISSN   1098-1004. PMID   18837007. S2CID   5419679.
  15. ↑ Voskarides, Konstantinos; Deltas, Constantinos (2009-07-01). "Screening for mutations in kidney-related genes using SURVEYOR nuclease for cleavage at heteroduplex mismatches". The Journal of Molecular Diagnostics. 11 (4): 311–318. doi:10.2353/jmoldx.2009.080144. ISSN   1943-7811. PMC   2710707 . PMID   19525337.
  16. 1 2 Engelman, Jeffrey A.; Mukohara, Toru; Zejnullahu, Kreshnik; Lifshits, Eugene; Borrás, Ana M.; Gale, Christopher-Michael; Naumov, George N.; Yeap, Beow Y.; Jarrell, Emily (2006-10-01). "Allelic dilution obscures detection of a biologically significant resistance mutation in EGFR-amplified lung cancer". The Journal of Clinical Investigation. 116 (10): 2695–2706. doi:10.1172/JCI28656. ISSN   0021-9738. PMC   1570180 . PMID   16906227.
  17. ↑ Jackman, David M.; Holmes, Alison J.; Lindeman, Neal; Wen, Patrick Y.; Kesari, Santosh; Borras, Ana M.; Bailey, Christopher; de Jong, Francisca; Jänne, Pasi A. (2006-09-20). "Response and resistance in a non-small-cell lung cancer patient with an epidermal growth factor receptor mutation and leptomeningeal metastases treated with high-dose gefitinib". Journal of Clinical Oncology. 24 (27): 4517–4520. doi: 10.1200/JCO.2006.06.6126 . ISSN   1527-7755. PMID   16983123.
  18. ↑ Jackman, David M.; Yeap, Beow Y.; Sequist, Lecia V.; Lindeman, Neal; Holmes, Alison J.; Joshi, Victoria A.; Bell, Daphne W.; Huberman, Mark S.; Halmos, Balazs (2006-07-01). "Exon 19 deletion mutations of epidermal growth factor receptor are associated with prolonged survival in non-small cell lung cancer patients treated with gefitinib or erlotinib". Clinical Cancer Research. 12 (13): 3908–3914. doi: 10.1158/1078-0432.CCR-06-0462 . ISSN   1078-0432. PMID   16818686.
  19. ↑ Jänne, Pasi A.; Borras, Ana M.; Kuang, Yanan; Rogers, Andrew M.; Joshi, Victoria A.; Liyanage, Hema; Lindeman, Neal; Lee, Jeffrey C.; Halmos, Balazs (2006-02-01). "A rapid and sensitive enzymatic method for epidermal growth factor receptor mutation screening". Clinical Cancer Research. 12 (3 Pt 1): 751–758. doi: 10.1158/1078-0432.CCR-05-2047 . ISSN   1078-0432. PMID   16467085.
  20. ↑ Jamieson, Catriona H. M.; Gotlib, Jason; Durocher, Jeffrey A.; Chao, Mark P.; Mariappan, M. Rajan; Lay, Marla; Jones, Carol; Zehnder, James L.; Lilleberg, Stan L. (2006-04-18). "The JAK2 V617F mutation occurs in hematopoietic stem cells in polycythemia vera and predisposes toward erythroid differentiation". Proceedings of the National Academy of Sciences of the United States of America. 103 (16): 6224–6229. Bibcode:2006PNAS..103.6224J. doi: 10.1073/pnas.0601462103 . ISSN   0027-8424. PMC   1434515 . PMID   16603627.
  21. ↑ Sattler, Martin; Walz, Christoph; Crowley, Brian J.; Lengfelder, Eva; Jänne, Pasi A.; Rogers, Andrew M.; Kuang, Yanan; Distel, Robert J.; Reiter, Andreas (2006-02-01). "A sensitive high-throughput method to detect activating mutations of Jak2 in peripheral-blood samples". Blood. 107 (3): 1237–1238. doi:10.1182/blood-2005-07-2899. ISSN   0006-4971. PMC   1895916 . PMID   16434495.
  22. ↑ Mitani, Noriaki; Niwa, Yoshimasa; Okamoto, Yasuyuki (2007-11-01). "Surveyor nuclease-based detection of p53 gene mutations in haematological malignancy". Annals of Clinical Biochemistry. 44 (Pt 6): 557–559. doi:10.1258/000456307782268174. ISSN   0004-5632. PMID   17961311. S2CID   22933002.
  23. ↑ Shi, Ruiru; Otomo, Koji; Yamada, Hiroyuki; Tatsumi, Taiga; Sugawara, Isamu (2006-01-01). "Temperature-mediated heteroduplex analysis for the detection of drug-resistant gene mutations in clinical isolates of Mycobacterium tuberculosis by denaturing HPLC, SURVEYOR nuclease". Microbes and Infection / Institut Pasteur. 8 (1): 128–135. doi:10.1016/j.micinf.2005.06.008. ISSN   1286-4579. PMID   16182590.
This page is based on this Wikipedia article
Text is available under the CC BY-SA 4.0 license; additional terms may apply.
Images, videos and audio are available under their respective licenses.