Typing of multiple single-nucleotide polymorphisms using ribonuclease cleavage of DNA/RNA chimeric single-base extension primers and detection by MALDI-TOF mass spectrometry

Research output: Contribution to journal › Journal article › Research › peer-review

Standard

Typing of multiple single-nucleotide polymorphisms using ribonuclease cleavage of DNA/RNA chimeric single-base extension primers and detection by MALDI-TOF mass spectrometry. / Mengel-From, Jonas; Sanchez Sanchez, Juan Jose; Børsting, Claus; Kirpekar, Finn; Morling, Niels.

In: Analytical Chemistry, Vol. 77, No. 16, 2005, p. 5229-35.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Mengel-From, J, Sanchez Sanchez, JJ, Børsting, C, Kirpekar, F & Morling, N 2005, 'Typing of multiple single-nucleotide polymorphisms using ribonuclease cleavage of DNA/RNA chimeric single-base extension primers and detection by MALDI-TOF mass spectrometry', Analytical Chemistry, vol. 77, no. 16, pp. 5229-35. https://doi.org/10.1021/ac0502044

APA

Mengel-From, J., Sanchez Sanchez, J. J., Børsting, C., Kirpekar, F., & Morling, N. (2005). Typing of multiple single-nucleotide polymorphisms using ribonuclease cleavage of DNA/RNA chimeric single-base extension primers and detection by MALDI-TOF mass spectrometry. Analytical Chemistry, 77(16), 5229-35. https://doi.org/10.1021/ac0502044

Vancouver

Mengel-From J, Sanchez Sanchez JJ, Børsting C, Kirpekar F, Morling N. Typing of multiple single-nucleotide polymorphisms using ribonuclease cleavage of DNA/RNA chimeric single-base extension primers and detection by MALDI-TOF mass spectrometry. Analytical Chemistry. 2005;77(16):5229-35. https://doi.org/10.1021/ac0502044

Author

Mengel-From, Jonas ; Sanchez Sanchez, Juan Jose ; Børsting, Claus ; Kirpekar, Finn ; Morling, Niels. / Typing of multiple single-nucleotide polymorphisms using ribonuclease cleavage of DNA/RNA chimeric single-base extension primers and detection by MALDI-TOF mass spectrometry. In: Analytical Chemistry. 2005 ; Vol. 77, No. 16. pp. 5229-35.

Bibtex

@article{da6f09a097ad11de8bc9000ea68e967b,
title = "Typing of multiple single-nucleotide polymorphisms using ribonuclease cleavage of DNA/RNA chimeric single-base extension primers and detection by MALDI-TOF mass spectrometry",
abstract = "A novel single-base extension (SBE) assay using cleavable and noncleavable SBE primers in the same reaction mix is described. The cleavable SBE primers consisted of deoxyribonucleotides and one ribonucleotide (hereafter denoted chimeric primers), whereas the noncleavable SBE primers consisted of only deoxyribonucleotides (hereafter denoted standard primers). Biotin-labeled ddNTPs were used in the SBE reaction, and the SBE products were purified using the monomeric avidin triethylamine purification protocol, ensuring that only primers extended with a biotin-ddNTP in the 3'-end were isolated. A ribonuclease mix was developed to specifically cleave the chimeric primers, irrespective of the base of the ribonucleotide, whereas standard primers without a ribonucleotide were unaffected by the ribonuclease treatment. The SBE products were analyzed in linear mode using a matrix-assisted laser desorption/ionization time-of-flight mass spectrometer. The cleaved SBE products were detected in the 2000-5500 m/z range, and the noncleaved SBE products were detected in the 5500-10 000 m/z range. The method was validated by typing 17 Y chromosome single-nucleotide polymorphisms in 100 males with a 17-plex SBE package containing 9 chimeric primers and 8 standard primers.",
author = "Jonas Mengel-From and {Sanchez Sanchez}, {Juan Jose} and Claus B{\o}rsting and Finn Kirpekar and Niels Morling",
note = "Keywords: Base Sequence; DNA Primers; Molecular Sequence Data; Polymorphism, Single Nucleotide; RNA; Ribonucleases; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization",
year = "2005",
doi = "10.1021/ac0502044",
language = "English",
volume = "77",
pages = "5229--35",
journal = "Industrial And Engineering Chemistry Analytical Edition",
issn = "0003-2700",
publisher = "American Chemical Society",
number = "16",

}

RIS

TY - JOUR

T1 - Typing of multiple single-nucleotide polymorphisms using ribonuclease cleavage of DNA/RNA chimeric single-base extension primers and detection by MALDI-TOF mass spectrometry

AU - Mengel-From, Jonas

AU - Sanchez Sanchez, Juan Jose

AU - Børsting, Claus

AU - Kirpekar, Finn

AU - Morling, Niels

N1 - Keywords: Base Sequence; DNA Primers; Molecular Sequence Data; Polymorphism, Single Nucleotide; RNA; Ribonucleases; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization

PY - 2005

Y1 - 2005

N2 - A novel single-base extension (SBE) assay using cleavable and noncleavable SBE primers in the same reaction mix is described. The cleavable SBE primers consisted of deoxyribonucleotides and one ribonucleotide (hereafter denoted chimeric primers), whereas the noncleavable SBE primers consisted of only deoxyribonucleotides (hereafter denoted standard primers). Biotin-labeled ddNTPs were used in the SBE reaction, and the SBE products were purified using the monomeric avidin triethylamine purification protocol, ensuring that only primers extended with a biotin-ddNTP in the 3'-end were isolated. A ribonuclease mix was developed to specifically cleave the chimeric primers, irrespective of the base of the ribonucleotide, whereas standard primers without a ribonucleotide were unaffected by the ribonuclease treatment. The SBE products were analyzed in linear mode using a matrix-assisted laser desorption/ionization time-of-flight mass spectrometer. The cleaved SBE products were detected in the 2000-5500 m/z range, and the noncleaved SBE products were detected in the 5500-10 000 m/z range. The method was validated by typing 17 Y chromosome single-nucleotide polymorphisms in 100 males with a 17-plex SBE package containing 9 chimeric primers and 8 standard primers.

AB - A novel single-base extension (SBE) assay using cleavable and noncleavable SBE primers in the same reaction mix is described. The cleavable SBE primers consisted of deoxyribonucleotides and one ribonucleotide (hereafter denoted chimeric primers), whereas the noncleavable SBE primers consisted of only deoxyribonucleotides (hereafter denoted standard primers). Biotin-labeled ddNTPs were used in the SBE reaction, and the SBE products were purified using the monomeric avidin triethylamine purification protocol, ensuring that only primers extended with a biotin-ddNTP in the 3'-end were isolated. A ribonuclease mix was developed to specifically cleave the chimeric primers, irrespective of the base of the ribonucleotide, whereas standard primers without a ribonucleotide were unaffected by the ribonuclease treatment. The SBE products were analyzed in linear mode using a matrix-assisted laser desorption/ionization time-of-flight mass spectrometer. The cleaved SBE products were detected in the 2000-5500 m/z range, and the noncleaved SBE products were detected in the 5500-10 000 m/z range. The method was validated by typing 17 Y chromosome single-nucleotide polymorphisms in 100 males with a 17-plex SBE package containing 9 chimeric primers and 8 standard primers.

U2 - 10.1021/ac0502044

DO - 10.1021/ac0502044

M3 - Journal article

C2 - 16097763

VL - 77

SP - 5229

EP - 5235

JO - Industrial And Engineering Chemistry Analytical Edition

JF - Industrial And Engineering Chemistry Analytical Edition

SN - 0003-2700

IS - 16

ER -

ID: 14145124