Abstract
Denaturing high performance liquid chromatography (dHPLC) is a fast and reliable technique for the DNA variation screening (1,2).It can detect in minutes with close to 100% sensitivity and specificity single-base substitutions as well as small deletions and insertions in DNA fragments ranging from 80-1500 base pairs in size (3,4).In partially denaturing HPLC, typically 2–10 chromosomes are compared as a mixture of PCR products. Upon mixing, denaturing and reannealing of amplicons containing one or more mismatches, not only the original homoduplices are formed again but, simultaneously, the sense and anti-sense strands of either homoduplex form two heteroduplices. Heteroduplices denature more extensively at elevated column temperatures in the range of 48-67°C; they are retained less on the chromatographic separation matrix, allowing the separation of homo- and heteroduplex species by ion-pair reversed-phase HPLC (IP-RP-HPLC) (5). Characteristic peak patterns both for homozygous and heterozygous samples are obtained.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Oefner, P. J. and Underhill, P. A. (1995) Comparative DNA sequencing by denaturing high-performance liquid chromatography (dHPLC). Am. J. Hum. Genet. 57 (Suppl.), A266.
Xiao, W. and Oefner, P. J. (2001) Denaturing high performance liquid chromatography: a review. Human Mutat. 17, 439–474.
Jones, A. C., Austin, J., Hansen, N., Hoogendoorn, B., Oefner, P. J., Cheadle, J. P., and O’Donovan, M. C. (1999) Optimal temperature selection for mutation detection by denaturing HPLC and comparison to single-stranded conformation polymorphism and heteroduplex analysis. Clin. Chem. 45, 1133–1140.
Spiegelman, J. I., Mindrinos, M. N., and Oefner, P. J. (2000) High-accuracy DNA sequence variation screening by dHPLC. Biotechniques 29, 1084–1092.
Oefner, P. J. & Underhill, P. A. (1998) DNA mutation detection using denaturing high-performance liquid chromatography, in Current Protocols in Human Genetics (Dracopoli, N. C., Haines, J. L., Korf, B. R., et al., eds.), John Wiley & Sons, New York, NY, pp. 7.10.1–7.10.12.
Oefner, P. J. (2000) Allelic discrimination by denaturing high-performance liquid chromatography. J Chromatogr. B739, 345–355.
Huber, C. G., Premstaller, A., Xiao, W., Oberacher, H., Bonn, G. K., and Oefner, P. J. (2001) Mutation detection by capillary denaturing high-performance liquid chromatography using monolithic columns. J. Biochem. Biophys. Methods 47, 5–19.
Ishii, D. (1988) Introduction to Microscale High-Performance Liquid Chromatography.VCH, Weinheim.
Premstaller, A., Xiao, W., Oberacher, H., et al. (2001) Temperature-modulated arrary high-performance liquid chromatography. Genome Res. 11, 1944–1951.
Huber, C. G. and Krajete, A. (1999) Analysis of nucleic acids by capillary ion-pair reversed-phase HPLC coupled to negative ion-electrospray ionization mass spectrometry. Anal. Chem. 71, 3730–3739.
Oberacher, H., Oefner, P. J., Parson, W., Huber, C. G. (2001) On-line liquid chromatography-mass spectrometry: A useful tool for the detection of DNA sequence variation. Angew. Chem. Int. Ed. 40, 3828–3830.
Kheterpal, I., Scherer, J. R., Clark, S. M., Radhakrishnan, A., Ju, J., Ginther, C. L., et al. (1996) DNA sequencing using a four-color confocal fluorescence capillary array scanner. Electrophoresis 17, 1852–1859.
Huber, C. G., Oefner, P. J., and Bonn, G. K. (1993) High-resolution liquid chromatography of oligonucleotides on highly crosslinked poly(styrene-divinylbenzene) particles. Anal. Biochem. 212, 351–358.
Premstaller, A., Oberacher, H., and Huber, C. G. (2000) High-performance liquid chromatography-electrospray ionization mass spectrometry of single-and double stranded nucleic acids using monolithic capillary columns. Anal. Chem. 72, 4386–4393.
Huber, C. G., Oefner, P. J., and Bonn, G. K. (1995) Rapid and accurate sizing of DNA fragments by ion-pair reversed-phase chromatography on alkylated nonporous poly-styrene/divinylbenzene particles. Anal. Chem. 67, 578–585.
O’Donovan, M. C., Oefner, P. J., Roberts, C. S., Austin, J., Hoogendoorn, B., Guy, C., et al. (1998) Blind analysis of denaturing high-performance liquid chromatography as a tool for mutation detection. Genomics 52, 44–49.
Chervet, J. P. (1991) Micro flow processor. EP 0495255A1.
Chervet, J. P., Ursem, M., and Salzmann, J. P. (1996) Instrumental requirements for nanoscale liquid chromatography. Anal. Chem. 68, 1507–1512.
Oefner, P. J., Huber, C. G., Umlauft, F., Berti, G. N., Stimpfl, E., and Bonn, G. K. (1994) High-resolution liquid chromatography of fluorescent dye labeled nucleic acids. Anal. Biochem. 223, 39–46.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2003 Humana Press Inc.
About this protocol
Cite this protocol
Premstaller, A., Oefner, P.J. (2003). Denaturing High-Performance Liquid Chromatography. In: Kwok, PY. (eds) Single Nucleotide Polymorphisms. Methods in Molecular Biology™, vol 212. Springer, Totowa, NJ. https://doi.org/10.1385/1-59259-327-5:015
Download citation
DOI: https://doi.org/10.1385/1-59259-327-5:015
Publisher Name: Springer, Totowa, NJ
Print ISBN: 978-0-89603-968-1
Online ISBN: 978-1-59259-327-9
eBook Packages: Springer Protocols