Mutation detection using a novel plant endonuclease

Oleykowski, Catherine A.; Mullins, Colleen R. Bronson; Godwin, Andrew K.; Yeung, Anthony T.

doi:10.1093/nar/26.20.4597

Cited by 323 publications

(264 citation statements)

References 12 publications

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“…CEL I nuclease can cleave all of these mismatches. However, CEL I does demonstrate some substrate preference, as C/C was cleaved the most, T/T was cleaved least, and other mismatches were cleaved intermediately [64]. On the other hand, T7 endonuclease I is also said to cleave all type of mismatches; however, its properties have not been well studied [58,62].…”

Section: Discussionmentioning

confidence: 99%

“…Also, this EMC method is possible to apply to fluorescence automated sequencer [64,65,87] and CE platform [73] according to your laboratory equipments. We have established an ideal mutation screening system which is available to most any researcher.…”

Section: Discussionmentioning

confidence: 99%

“…Recently, there are several reports of EMC using different kinds of enzymes [56][57][58][59][60][61][62][63]. Among them CEL nuclease is potentially the most effective enzyme for EMC reported recently [64][65][66][67][68][69][70] and is now commercially available as SURVEYOR Nuclease S from Transgenomic (Omaha, NE, USA) [71][72][73].…”

Section: Introductionmentioning

confidence: 99%

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Development of a simple and highly sensitive mutation screening system by enzyme mismatch cleavage with optimized conditions for standard laboratories

Tsuji

Niida

2008

Electrophoresis

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Efficient screening of unknown DNA variations is one of the substantive matters of molecular biology even today. Historically, single-strand conformation polymorphism (SSCP) and heteroduplex analysis (HA) are the most commonly used methods for detecting DNA variations everywhere in the world because of their simplicity. However, the sensitivity of these methods is not satisfactory for screening purpose. Recently, several new PCR based mutation screening methods have been developed, but most of them require special instruments and adjustment of conditions for each DNA sequence to attain the maximum sensitivity, eventually becoming as inconvenient as old methods. Enzyme mismatch cleavage (EMC) is potentially an ideal screening method. With high performance nucleases and once experimental conditions are optimized, it requires only conventional staff and conditions remain the same for each PCR product. In this study we tested four commercially available endonucleases for EMC and optimized the electrophoresis and developing conditions. We prepared 25 known DNA variations consisting of 18 single base substitutions (8 transitions and 10 transversions, including all possible sets of mismatches) and 7 small deletions or insertions. The combination of CEL nuclease, 12% polyacrylamide gel electrophoresis and rapid silver staining can detect all types of mutations and achieved 100% sensitivity.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Development of a simple and highly sensitive mutation screening system by enzyme mismatch cleavage with optimized conditions for standard laboratories

Tsuji

Niida

2008

Electrophoresis

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“…[6][7][8][9][10] However, many of these methods are not suitable for routine diagnostic use because they are too insensitive or labor-intensive, involve toxic reagents, or require extensive optimization or special instrumentation. In addition, many are suitable only for DNA fragments shorter than 400 bp, and do not distinguish between a polymorphism and functional mutation occurring together within the same amplicon.…”

Section: Introductionmentioning

confidence: 99%

A novel detection method for heteroduplex DNA using carbodiimide-induced interrupted primer extension

Tabone¹,

Cotton²,

Mathew³

et al. 2010

J Nucleic Acids Invest

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Direct sequencing may be problematic in demonstrating mutations where inherited disease results from multiple different heterozygous variants in large genes. We describe here a novel mutation screening method based on the ability of carbodiimide to bind mismatched DNA and interrupt primer extension thereby identifying both a heterozygous variant and its location. This assay detected all four classes of DNA mismatch in 550 bp engineered plasmid fragments and in two dominantly inherited renal diseases. In patients with thin basement membrane nephropathy, the method demonstrated multiple variants within a single amplicon including some close to the primer binding site. This method also detected a complex mutation in medullary cystic kidney disease type 2 (c.278-289 del/insCCGGCTCCT) as multiple termination events and, furthermore, correctly identified five affected and 28 unaffected family members. Carbodiimide-induced interrupted primer extension identifies heterozygous variants in large or multiexonic genes, where the variants differ in each family, their locations are unknown, and even if there are multiple known non-pathogenic variants within the same amplicon. This assay incorporates a "universal" protocol that detects all types of mutations without the need for further optimization, and potentially detects mutations where the proportion of heteroduplex is less than 50%.

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“…The general approach is to screen large numbers of samples taken from chemically mutagenized individuals for mutations in genes of interest using PCRbased mutation detection strategies such as denaturing HPLC or heteroduplex cleavage by CEL I endonuclease [9]. Upon identification of a mutation, the corresponding individual is recovered and used as a founder for establishing a mutant line.…”

mentioning

confidence: 99%

Mouse splice mutant generation from ENU-treated ES cells—A gene-driven approach

2005

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Mutant mice are important for elucidating mammalian gene functions and for modeling human disease phenotypes. In recent years, chemical mutagenesis has become an increasingly popular method to disrupt gene functions due to its high efficiency of inducing mutations throughout the genome. Mutagenesis of embryonic stem (ES) cells offers the possibility of gene-driven approaches, which, however, require efficient mutation detection procedures to screen archives of mutated samples for lesions in particular genes. We have developed an approach that focuses on the detection of splice mutations in highly pooled cDNA samples using exon-skipping PCR primers. As a proof of concept, splice mutants for the Kit gene were isolated from a library comprising approximately 40,000 ES cell clones treated with N-ethyl-Nnitrosourea followed by transmission through the mouse germ-line. The approach will be useful for the production of mouse models for human disease-related splice mutations and as a general gene disruption strategy. D

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Mutation detection using a novel plant endonuclease

Cited by 323 publications

References 12 publications

Development of a simple and highly sensitive mutation screening system by enzyme mismatch cleavage with optimized conditions for standard laboratories

Development of a simple and highly sensitive mutation screening system by enzyme mismatch cleavage with optimized conditions for standard laboratories

A novel detection method for heteroduplex DNA using carbodiimide-induced interrupted primer extension

Mouse splice mutant generation from ENU-treated ES cells—A gene-driven approach

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