Abstract
DNA diagnostics is a new field that utilizes the techniques of molecular biology to identify and characterize the specific genetic material associated with genetic, neoplastic, and infectious diseases. DNA diagnostics grew out of the discoveries made possible using molecular cloning and DNA sequencing techniques beginning in the mid-1970s. Despite the availability of exquisitely specific reagents such as restriction endonucleases, synthetic oligonucleotides, and cloned DNA and cDNA probes, as well as technologies such as electrophoretic methods to fractionate DNA and novel DNA hybridization methods (Southern and Northern blots, dot blot, etc.), DNA diagnostic procedures were not immediately adopted by clinical laboratories. This failure was due in part to the long turnaround times, the lack of sensitivity, and the lack of reliable nonradioactive detection procedures.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Abravaya, K., Carrino, J. J., Muldoon, S., and Lee, H. H. (1995). Detection of point mutations with a modified ligase chain reaction (gap-LCR). Nucleic Acids Res. 23:675–682.
Balles, J., and Plfugfelder, G. O. (1994). Facilitated isolation of rare recombinants by ligase chain reaction: Selection for intragenic crossover events in the Drosophila optomotor-blind gene. Mol. Gen. Genet. 245:734–740.
Barany, F. (1991a). Genetic disease and DNA amplification using cloned thermostable ligase. Proc. Natl. Acad. Sci. USA 88:189–193.
Barany, F. (1991b). The ligase chain reaction in a PCR world. PCR Methods Appl. 1:5–16.
Barany, F., and Gelfand, D. H. (1991). Cloning, overexpression and nucleotide sequence of a thermostable DNA ligase-encoding gene. Gene 109:1–11.
Bassiri, M., Hu, H. Y., Domeika, M. A., Burczak, J., Svensson, L.-O., Lee, H. H. and Mardh, P.-A. (1995). Detection of Chlamydia trachomatis in urine specimens from women by ligase chain reaction. J. Clin. Microbiol. 33:898–900.
Batt, C. A., Wagner, P., Wiedmann, M., Luo, J., and Gilbert, R. (1994). Detection of bovine leukocyte adhesion deficiency by nonisotopic ligase chain reaction. Anim. Genet. 25:95–98.
Birkenmeyer, L., and Armstrong, A. S. (1992). Preliminary evaluation of the ligase chain reaction for specific detection of Neisseria gonorrhoeae. J. Clin. Microbiol. 30:3089–3094.
Chernesky, M. A., Jang, D., Lee, H., Burczak, J. D., Hu, H., Sellors, J., Tomazic-Allen, S. J., and Mahony, J. B. (1994a). Diagnosis of Chlamydia trachomatis infections in men and women by testing first-void urine by ligase chain reaction. J. Clin. Chem. 32:2682–2685.
Chemesky, M. A., Lee, H, Schachter, J., Burczak, J. D., Stamm, W. E., McCormack, W. M., and Quinn, T. C. (1994b). Diagnosis of Chlamydia trachomatis urethral infection in symptomatic and asymptomatic men by testing first-void urine in a ligase chain reaction assay. J. Infect. Dis. 170:1308–1311.
Chetverin, A. B., and Kramer, F. R. (1994). Oligonucleotide arrays: New concepts and possibilities. Bio/ Technology 12:1093–1099.
Delahunty, C. M., Ankener, W., Brainerd, S., Nickerson, D. A., and Monomen, I. T. (1995). Finnish-type aspartylglucosaminuria detected by oligonucleotide ligation assay. Clin. Chem. 41:59–61.
Dille, B. J., Butzen, C. C., and Birkenmeyer, L. G. (1993). Amplification of Chlamydia trachomatis DNA by ligase chain reaction. J. Clin. Microbiol. 31:729–731.
Eckert, K. A., and Kunkel, T. A. (1991). DNA polymerase fidelity and the polymerse chain reaction. PCR Methods Appl. 1:17–24.
Eggerding, F.fA., Iovannisci, D. M., Brinson, E., Grossman, P., and Winn-Deen, E. S. (1995). Fluorescence-based oligonucleotide ligation assay for analysis of cystic fibrosis transmembrane conductance regulator gene mutations. Hum. Mutat. 5:153–165.
Grimberg, J., Lin, C. P., Sheridan, K., Tackney, C., and Waksal, J. (1993). Detection of serum hepatitis B virus DNA sequence by the repair chain reaction DNA amplification system. Clin. Chem. 39:738.
Grossman, P. D., Bloch, W., Brinson, E., Chang, C. C., Eggerding, F. A., Fung, S., Iovannisci, D.A., Woo, S., and Winn-Deen, E. S. (1994). High-density multiplex detection of nucleic acid sequences: Oligonucleotide ligation assay and sequence-coded separation. Nucleic Acids Res. 22:4527–4534.
Higuchi, R., Fockler, C., Dollinger, G., and Watson, R. (1993). Kinetic PCR analysis: Real-time monitoring of DNA amplification reactions. Bio/Technology 11:1026–1030.
Jou, C., Rhoads, J., Bouma, S., Ching, S. F., Hoijer, J., Schroeder-Poliak, P., Zaun, P., Smith, S., Richards, S., Caskey, C. T., and Gordon, J. (1995). Deletion detection in the dystrophin gene by multiplex gap ligase chain reaction and immunochromatographic strip technology. Hum. Mutat. 5:86–93.
Kleppe, K., Ohtsuka, E., Kleppe, R., Molineux, I., and Khorana, H. G. (1971). Studies on polynucleotides. XCVI. Repair replication of short synthetic DNAs as catalyzed by DNA polymerases. J. Mol. Biol. 56:341–361.
Landegren, U., Kaiser, R., Sanders, J., and Hood, L. (1988). A ligase-mediated gene detection technique. Science 241:1077–1080.
Lawyer, F C., Stoffel, S., Saiki, R. K., Myambo, K., Drummond, R., and Gelfand, D. H. (1989). Isolation, characterization, and expression in E. coli of the DNA polymerase gene from the extreme thermophile, Thermus aquaticus. J. Biol. Chem. 264:6427–6437.
Leckie, G., Cao, J., Davis, A., Facey, I., Lin, B.-C, and Lee, H. (1994). Ligase chain reaction (LCR) DNA amplification for direct detection of Mycobacterium tuberculosis (MTB) in clinical specimens, in:Abstracts of the General Meeting of the American Society for Microbiology, 189.
Lee, H. H., Chernesky, M. A., Schachter, J., Burczak, J. D., Andrews, W. W, Muldoon, S., Leckie, G., and Stamm, W. E. (1995). Diagnosis of Chlamydia trachomatis genitourinary infection in women by ligase chain reaction assay of urine. Lancet 345:213–216.
Lin, C. P., Goldbard, S., Grills, G., Sheridan, K., Waksal, H. W, Tackney, C., and Segev. D. (1991). Amplification and nonradioactive detection of the human papilloma virus 16 DNA by the repair chain reaction, in Abstracts of the Annual San Diego Conference on Nucleic Acids..
Ling, L. L., Keohavong, P., Dias, C., and Thilly, W. G. (1991). Optimization of polymerase chain reaction with regard to fidelity: Modified T7, Taq and Vent DNA polymerases. PCR Methods Appl. 1:63–69.
Liu, M. S., Zang, J., Evangelista, R. A., Rampai, S., and Chen, F.-T. A. (1995). Double-stranded DNA analysis by capillary electrophoresis with laser-induced fluorescence using ethidium bromide as an intercalator. Bio-Techniques 18:316–323.
Livak, K. J., Marmaro, J., and Todd, J. A. (1995). Towards fully automated genome-wide polymorphism screening. Nature Genet. 9:341–342.
Marshall, R. L., Laffler, T. G., Cerney, M. B., Sustachek, J. C., Kratochvil, J. D., and Morgan, R. L. (1994). Detection of HCV RNA by the asymmetric gap ligase chain reaction. PCR Methods Appl. 4:80–84.
Mattila, P., Korpela, J., Tenkanen, T., and Pitkanen, K. (1991). Fidelity of DNA synthesis by the Thermococcus litoralis DNA polymerase—an extremely heat stable enzyme with proofreading activity. Nucleic Acids Res. 19:4967–4973.
Nakazawa, H., English, D., Randell, P. L., Nakazawa, K., Martel, N., Armstrong, B. K., and Yamasaki, H. (1994) UV and skin cancer: Specific p53 gene mutation in normal skin as a biologically relevant exposure measurement. Proc. Natl. Acad. Sci. USA 91:360–364.
Nickerson, D. A., Kaiser, R., Lappin, S., Stewart, J., Hood, L., and Landegren, U. (1990). Automated DNA diagnostics using an EUSA-based oligonucleotide ligation assay. Proc. Natl. Acad. Sci. USA 87:8923–8927.
Pfeffer, M., Meyer, H., and Wiedmann, M. (1994). A ligase chain reaction targeting two adjacent nucleotides allows the differentiation of cowpox virus from other Orthopoxvirus species. J. Virol. Methods 49:353–360.
Saiki, R. K., Gelfand, D. H., Stoffel, S., Scharf, F. J., Higuchi, R., Horn, G. T., Mullis, K. B., and Ehrlich, H. A. (1988). Primer-directed enzymatic amplification of cDNA with a thermal stable DNA polymerase. Science 239:487–491.
Schachter, J., Stamm, W. E., Quinn, T. C., Andrews, W. W., Burzak, J. D., and Lee, H. H. (1994). Ligase chain reaction to detect Chlamydia trachomatis infection of the cervix. J. Clin. Microbiol. 32:2540–2543.
Schwartz, H. E., and Ulfelder, K. J. (1992). Capillary electrophoresis with laser-induced fluorescence detection of PCR fragments using thiazole orange. Anal. Chem. 64:1737–1740.
Segev, D. (1992). Amplification of nucleic acid sequence by the repair chain reaction, in:Nonradioactive Labeling and Detection of Biomolecules (C. Kessler, ed.), Springer-Verlag, Berlin, pp. 212–218.
Takahashi, M., Yamaguchi, E., and Uchida, T. (1984). Thermophilic DNA ligase—Purification and properties of the enzyme from Thermus thermophilus HB8. J. Biol. Chem. 259:10041–10047.
Tavormina, P. L., Shiang, R., Thompson, L. M., Zhu, Y.-Z., Wilkin, D. J., Lachman, R. S., Wilcox, W. R., Rimoin, D. L., Cohn, D. H., and Wasmuth, J. J. (1995). Thanatophoric dysplasia (types I and II) caused by distinct mutations in fibroblast growth factor receptor 3. Nature Genet. 9:321–328.
Ugozzoli, L., and Wallace, R. B. (1991). Allele specific polymerase chain reaction. Methods: A Companion to Methods in Enzymology 2:42–48.
Wallace, R. B., Ugozzoli, L., Lowery, J., and Reyes, A. A. (1994). The application of LCR to neonatal testing of variant hemoglobin genes. Proceedings, 10th National Neonatal Screening Symposium, Seattle, Washington, pp. 127–130.
Ward, L. J., Brown, J. C., and Davey, G. P. (1994). Application of the ligase chain reaction to the detection of nisinZ genes in Lactococcus lactis ssp. lactis. FEMS Microbiol. Lett. 117:29–34.
Wiedmann, M., Wilson, W. J., Czajka, J., Luo, J., Barany, F., and Batt, C. A. (1994). Ligase chain reaction (LCR)—Overview and applications. PCR Methods Appl. 3:S51–S64.
Wu, D. Y., and Wallace, R. B. (1989a). The ligation amplification reaction (LAR)—Amplification of specific DNA sequences using sequential rounds of template-dependent ligation. Genomics 4:560–569.
Wu, D. Y., and Wallace, R. B. (1989b). Specificity of the nick-closing activity of bacteriophage T4 DNA ligase. Gene 76:245–254.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 1996 Springer Science+Business Media New York
About this chapter
Cite this chapter
Wallace, R.B., Lin, CI.P., Reyes, A.A., Lowery, J.D., Ugozzoli, L. (1996). Ligase Chain Reaction for the Detection of Specific DNA Sequences and Point Mutations. In: Pfeifer, G.P. (eds) Technologies for Detection of DNA Damage and Mutations. Springer, Boston, MA. https://doi.org/10.1007/978-1-4899-0301-3_23
Download citation
DOI: https://doi.org/10.1007/978-1-4899-0301-3_23
Publisher Name: Springer, Boston, MA
Print ISBN: 978-1-4899-0303-7
Online ISBN: 978-1-4899-0301-3
eBook Packages: Springer Book Archive