Genomics- The Science and Technology Behind the Human Genome Project. Charles R. Cantor, Cassandra L / genomics1-10 / 4

Figure 4.23

Example of the use of Q

to detect a target, HIV RNA, by ligation. Here two specific

RNA probes are designed to be complementary to adjacent target sequences. Each probe alone con-

tains insufficient secondary structure features to support Q

replicase amplification. Two additional

end-biotinylated DNA capture probes are used to allow a streptavidin-based solid phase purification

of the probe-target complexes and then release of these

complexes by digestion with RNAse H

which specifically cleaves RNA-DNA duplexes. The released complexes are treated with T4 DNA

ligase, which will work on a pure double-stranded

RNA substrate. Ligation produces an RNA that

is now recognized and amplified by Q

replicase. (Adapted from Kramer and Tyagi, 1996.

SOURCES

AND

ADDITIONAL READINGS

Abramson R. D., and Myers, T. W. 1993. Nucleic acid amplification technologies.

Current Biology

4:41–47.

Arnheim, N., and Erlich, H. 1992. Polymerase chain reaction strategy.

Annual Review of

Biochemistry

61:131–156.

Barany, F. 1991. Genetic disease detection and DNA amplification using cloned thermostable li-

gase.

Proceedings of the National Academy of Sciences USA

88:189–193.

SOURCES AND ADDITIONAL

READINGS

129

Barnes, W. 1994. PCR Amplification of up to 35-kb DNA with high fidelity and high yield from

bacteriophage templates.

Proceedings of the National Academy of Sciences USA

91:2216–2220.

Blanco, L., Lazaro, J. M., De Vega, M., Bonnin, A., and Salas, M. 1994. Terminal protein-primed

DNA amplification.

Proceedings of the National Academy of Sciences USA

91: 12198–12202.

Bloch, W. 1991. A biochemical perspective of the polymerase chain reaction.

Biochemistry

30:

2735–2747.

Caetano-Annolés, G. 1996. Scanning of nucleic acids by in vitro amplification: New developments

and applications.

Nature Biotechnology

14: 1668–1674.

Cheng, S., Fockler, C., Barnes, W. M., and Higuchi, R. 1994. Effective amplification of long targets

from cloned inserts and human genomic DNA.

Proceedings

of the

National Academy

of

Sciences USA

91: 5695–5699.

Cheung, V. G., and Nelson, S. F. 1996. Whole genome amplification using a degenerate oligonu-

cleotide primer allows hundreds of genotypes to be performed on less than one nanogram of ge-

nomic DNA.

Proceedings of the National Academy of Sciences USA

93: 14676–14679.

Chou, W., Russell, M., Birch, D. E., Raymond, J., and Block, W. 1992. Prevention of pre-PCR mis-

priming and primer dimerization improves low-copy-number amplifications.

Nucleic

Acids

Research

20: 1717–1723.

Cobb, B. D., and Clarkson, J. M. 1994. A Simple procedure for optimising the polymerase chain re-

action (PCR) using modified Taguchi methods.

Nucleic Acids Research

22: 3801–3805.

Diatchenko, L., Lau, Y. F., Campbell, A. P., Chenchik, A., Moqadam, F., Huang, B., Lukyanov, S.,

Lukyanov, K., Gurskaya, N., and Sverdlov, E. D. 1996. Suppression subtractive hybridization: A

method for generating differentially regulated or tissue-specific cDNA probes and libraries.

Proceedings of the National Academy of Sciences USA

93: 6025–6030.

Erlich, H. A., Gelfand, D., and Sninsky, J. J. 1991. Recent advances in the polymerase chain reac-

tion.

Science

252: 1643–1651.

Fahy, E., Kwoh, D. Y., and Gingeras, T. R. 1991. Self-sustained sequence replication (3SR): An

isothermal transcription-based amplification system alternative to PCR.

PCR

Methods

and

Applications

1: 25–33.

Fire, A., and Xu, S., 1995. Rolling replication of short DNA circles.

Proceedings of the

National

Academy of Sciences USA

92: 4641–4645.

Grothues, D., Cantor, C. R., and Smith, C. L. 1993. PCR amplification of megabase DNA with

tagged random primers (T-PCR).

Nucleic Acids Research

21:1321–1322.

Heid, C. A., Stevens, J., Livak, K. J., and Williams, P. M. 1996.

Real time

quantitative PCR.

Genome Research

6: 986–994.

Hendrickson, E. R., Hatfield-Truby, T. M., Joerger, R. D., Majarian, W. R., and Ebersole, R. C.

1995. High sensitivity multianalyte immunoassay using covalent DNA-labeled antibodies and

polymerase chain reaction.

Nucleic Acids Research

23: 522–529.

Lagerström, M., Parik, J., Malmgren, H., Stewart, J., Pettersson, U., and Landegren, U. 1991.

Capture PCR: Efficient amplification of DNA fragments adjacent to a known sequence in human

and YAC DNA.

PCR Methods and Applications

1: 111–119.

Landegren, U. 1992. DNA probes and automation.

Current Opinion in Biotechnology

3: 12–17.

Lizardi, P. M., Guerra, C. E., Lomeli, H., Tussie-Luna, I., and Kramer, F. R. 1988. Exponential am-

plification of recombinant-RNA hybridization probes.

Biotechnology

6: 1197–1202.

Mikheeva, S., and Jarrell, K. A. 1996. Use of engineered ribozymes to catalyze chimeric gene as-

sembly.

Proceedings of the National Academy of Sciences USA

93: 7486–7490.

Nickerson, D. A., Kaiser, R., Lappin, S., Stewart, J., Hood, L., and Landegren, U. 1990. Automated

DNA diagnostics using an ELISA-based oligonucleotide ligation assay.

Proceedings of

the

National Academy of Sciences USA

87: 8923–8927.

Sano, T., and Cantor, C. R. 1991. A streptavidin-protein A chimera that allows one-step production

of a variety of specific antibody conjugates.

Bio/Technology

9: 1378–1381.

130

METHODS FOR IN VITRO DNA AMPLIFICATION

Sano, T., Smith, C. L., and Cantor, C. R. 1992. Immuno-PCR: Very sensitive antigen detection by

means of specific antibody-DNA conjugates.

Science

258: 120–122.

Siebert, P. D., Chenchik, A., Kellogg, D. E., Lukyanov, K. A., and Lukyanov, S. A. 1995. An im-

proved PCR method for walking in uncloned genomic DNA.

Nucleic

Acids Research

23:

1087–1088.

Stemmer, W. P. C. 1994. Rapid evolution of a protein

in

vitro by DNA shuffling.

Nature

370:

389–391.

Telenius, H., Carter, N. P., Bebb, C. E., Nordenskjöld, M., Ponder, B. A. J., and Tunnacliffe, A.

1992. Degenerate oligonucleotide-primed PCR: General amplification of target DNA by a single

degenerate primer.

Genomics

13: 718–725.

Telenius, H., Pelmear, A., Tunnacliffe, A., Carter, N. P., Behmel, A., Ferguson-Smith, M. A.,

Nordenskjöld, M., Pfragner, R., and Ponder, B. A. J. 1992. Cytogenetic analysis by chromosome

painting using DOP-PCR amplified flow-sorted chromosomes.

Genes,

Chromosomes and

Cancer

4: 257–263.

Tyagi, S., and Kramer, F. R. 1996. Molecular beacons: Probes that fluoresce upon hybridization.

Nature Biotechnology

14: 303–308.

Tyagi, S., Landedren, U., Tazi, M., Lizardi, P. M., and Kramer, F. R. 1996. Extremely sensitive,

background-free gene detection using binary probes and Q

replicase.

Proceedings

of the

National Academy of Sciences USA

93: 5395–5400.

Walker, G. T., Little, M., Nadeau, J. G., and Shank, D. D. 1992. Isothermal in vitro amplification of

DNA by a restriction enzyme/DNA polymerase system.

Proceedings of the National Academy of

Sciences USA

89: 392–396.

White, T. J. 1996. The future of PCR technology: diversification of technologies and applications.

Trends in Biotechnology

14: 478–483.

Wittwer, C. T., Herrmann, M. G., Moss, A. A., and Rasmussen, R. P. 1997. Continuous fluorescence

monitoring of rapid cycle DNA amplification.

BioTechniques

22: 130–138.