MagSNiPer: A new single nucleotide polymorphism typing method based on single base extension, magnetic separation, and chemiluminescence

Kakihara, Fumiko; Kurebayashi, Yukari; Tojo, Yuriko; Tajima, Hideji; Hasegawa, Setsuo; Yohda, Masafumi

doi:10.1016/j.ab.2005.03.015

Cited by 12 publications

(8 citation statements)

References 26 publications

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“…We recently developed a novel SNP typing method, namely MagSNiPer [24]. MagSNiPer is a method of typing SNPs based on SBE, magnetic separation and chemiluminescence.…”

Section: Resultsmentioning

confidence: 99%

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Quantitative discrimination of 16 S rRNA genes of Dehalococcoides species by MagSNiPer, a quantitative single‐nucleotide‐polymorphism genotyping method

Yohda¹,

Kobayashi²,

Ohishi³

et al. 2008

Biotech and App Biochem

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Previously we developed MagSNiPer, an SNP (single nucleotide polymorphism) genotyping method. In the present paper we show development of an automated system for MagSNiPer, namely MagSNiPer Station, and its application for quantitative discrimination of Dehalococcoides species, which perform anaerobic dechlorination of chloroethenes. MagSNiPer Station is equipped with a thermal cycler, a tip stand, a microtitre-plate automated stacker, an eight-channel tip dispenser, a magnetic separation unit for Magtration technology, and a chemiluminescence detector. It can automatically perform all processes required for SNP genotyping by MagSNiPer. A primer was designed for discriminating single nucleotide difference between 16 S rRNA genes of Dehalococcoides ethenogenes and Dehalococcoides BAV1. Chemiluminescence intensities for the 16 S rRNA genes obtained by MagSNiPer were proportional to their quantity. MagSNiPer analysis of 16 S rRNA genes amplified on the DNA purified from groundwater gave a ratio of these two 16 S rRNA genes similar to that obtained by cloning and sequencing. MagSNiPer is much easier, more rapid and more cost-effective than conventional sequencing. Compared with denaturing gradient-gel electrophoresis, MagSNiPer has the advantage of being quantitative. Therefore, by applying MagSNiPer at several sites where single base differences exist among Dehalococcoides species, it is possible to analyse Dehalococcoides consortia with ease, yielding useful information on anaerobic bioremediation of chloroethenes.

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“…We recently developed a novel SNP typing method, namely MagSNiPer [24]. MagSNiPer is a method of typing SNPs based on SBE, magnetic separation and chemiluminescence.…”

Section: Resultsmentioning

confidence: 99%

“…Previously we developed an SNP (single‐nucleotide polymorphism) genotyping method called ‘MagSNiPer’ [24]. MagSNiPer is based on SBE (single base extension), magnetic‐bead separation and chemiluminescence.…”

Section: Introductionmentioning

confidence: 99%

Quantitative discrimination of 16 S rRNA genes of Dehalococcoides species by MagSNiPer, a quantitative single‐nucleotide‐polymorphism genotyping method

Yohda¹,

Kobayashi²,

Ohishi³

et al. 2008

Biotech and App Biochem

Self Cite

View full text Add to dashboard Cite

show abstract

“…In such circumstances, the background fluorescence of unincorporated acceptors may hamper the straightforward evaluation of the pairs formed in the SBE reaction, and the excess of unincorporated ddNTPs can be removed from solution prior to evaluation of emission data (Kakiharaa et al, 2005;Pati et al, 2004;Vreeland et al, 2002).…”

Section: Coupling Spectral Codification To Single Base Extensionmentioning

confidence: 99%

Coupling single base extension to a spectral codification tool for increased throughput screening

Giestas

Lima

Baptista

2011

Journal of Biotechnology

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“…Alternatively, the detection primers were attached to a solid support covalently [15,16] or via biotin-avidin interactions [8] before the reaction. Haptenes were introduced as alternatives to radioisotopes for labelling ddNTPs, allowing colorimetric or chemiluminescent detection assays catalysed by alkaline phosphatase or peroxidase conjugated with the haptenebinding antibody [3,17,18].…”

Section: Labelling and Separationmentioning

confidence: 99%

The single-nucleotide primer extension (SNuPE) method for the multiplex detection of various DNA sequences: from detection of point mutations to microbial ecology

Nikolausz

Chatzinotas

Táncsics

et al. 2009

Biochemical Society Transactions

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Methods based on SNuPE (single-nucleotide primer extension) have become invaluable tools for the rapid and highly specific detection of point mutations and single-nucleotide polymorphisms in the field of human genetics. In the primer extension reaction, a DNA polymerase is used to label a specific primer hybridized to the target sequence by incorporating a single labelled ddNTP (dideoxynucleotide). This labelling provides not only information about the complementary nucleotide of interest in the opposite strand but also a semiquantitative analysis of the sequence targeted by the primer. Since several subdisciplines of microbiology increasingly require cultivation-independent molecular screening tools for elucidating differences between either strains or community structures based on sequence variations of marker genes, SNuPE offers a promising alternative to the existing tool box. The present review describes the method in detail and reports the state-of-the-art applications of this technique both in the field of nucleic acid detections in human genetics and in microbiology.

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MagSNiPer: A new single nucleotide polymorphism typing method based on single base extension, magnetic separation, and chemiluminescence

Cited by 12 publications

References 26 publications

Quantitative discrimination of 16 S rRNA genes of Dehalococcoides species by MagSNiPer, a quantitative single‐nucleotide‐polymorphism genotyping method

Quantitative discrimination of 16 S rRNA genes of Dehalococcoides species by MagSNiPer, a quantitative single‐nucleotide‐polymorphism genotyping method

Coupling single base extension to a spectral codification tool for increased throughput screening

The single-nucleotide primer extension (SNuPE) method for the multiplex detection of various DNA sequences: from detection of point mutations to microbial ecology

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