-
1
-
-
0016279782
-
Studies on polynucleotides. The linkage of deoxyribonucleic templates to cellulose and its use in their replication
-
Panet A, Khorana HG. Studies on polynucleotides. The linkage of deoxyribonucleic templates to cellulose and its use in their replication. J Biol Chem. 249:1974;5213-5221.
-
(1974)
J Biol Chem
, vol.249
, pp. 5213-5221
-
-
Panet, A.1
Khorana, H.G.2
-
2
-
-
0015222688
-
Studies on polynucleotides. XCVI. Repair replication of short synthetic DNAs as catalyzed by DNA polymerases
-
Kleppe K, Ohstuka E, Kleppe R, Molineux L, Khorana HG. Studies on polynucleotides. XCVI. Repair replication of short synthetic DNAs as catalyzed by DNA polymerases. J Mol Biol. 56:1971;341-361.
-
(1971)
J Mol Biol
, vol.56
, pp. 341-361
-
-
Kleppe, K.1
Ohstuka, E.2
Kleppe, R.3
Molineux, L.4
Khorana, H.G.5
-
3
-
-
0022372670
-
Enzymatic amplification of β-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia
-
Saiki RK, Scharf S, Faloona F, Mullis KB, Horn GT, Erlich HA, Arnheim N. Enzymatic amplification of β-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia. Science. 230:1985;1350-1354.
-
(1985)
Science
, vol.230
, pp. 1350-1354
-
-
Saiki, R.K.1
Scharf, S.2
Faloona, F.3
Mullis, K.B.4
Horn, G.T.5
Erlich, H.A.6
Arnheim, N.7
-
4
-
-
0023242425
-
An improved method for prenatal diagnosis of genetic diseases by analysis of amplified DNA sequences
-
Kogan SC, Doherty M, Gitschier J. An improved method for prenatal diagnosis of genetic diseases by analysis of amplified DNA sequences. N Eng J Med. 317:1987;985-990.
-
(1987)
N Eng J Med
, vol.317
, pp. 985-990
-
-
Kogan, S.C.1
Doherty, M.2
Gitschier, J.3
-
5
-
-
0345329269
-
DNA extraction and PCR for the high school student [abstract]
-
Decker L, Allergy J. DNA extraction and PCR for the high school student [abstract]. Clin Immunol. 99:1997;3.
-
(1997)
Clin Immunol
, vol.99
, pp. 3
-
-
Decker, L.1
Allergy, J.2
-
6
-
-
0030021221
-
The challenges to PCR: A proliferation of chain reactions
-
Landegran U. The challenges to PCR: a proliferation of chain reactions. Curr Opin Biotechnol. 7:1996;95-97.
-
(1996)
Curr Opin Biotechnol
, vol.7
, pp. 95-97
-
-
Landegran, U.1
-
7
-
-
0028952526
-
The polymerase chain reaction: New variations on an old theme
-
Taylor GR, Logan WP. The polymerase chain reaction: new variations on an old theme. Curr Opin Biotechnol. 6:1995;24-29.
-
(1995)
Curr Opin Biotechnol
, vol.6
, pp. 24-29
-
-
Taylor, G.R.1
Logan, W.P.2
-
8
-
-
0030606548
-
Simplified hot start PCR
-
of special interest. This Nature product review describes the use of a Taq polymerase derivative (AmpliTaq gold) which is inactive at room temperature. A more elegant solution than the inclusion of anti-Taq antibodies, but yield not as high as with KlenTaq+ antibody. Some problems have been reported if AmpliTaq gold is used in non-standard buffer systems.
-
Birch DE. Simplified hot start PCR. of special interest Nature. 381:1996;445-446 This Nature product review describes the use of a Taq polymerase derivative (AmpliTaq gold) which is inactive at room temperature. A more elegant solution than the inclusion of anti-Taq antibodies, but yield not as high as with KlenTaq+ antibody. Some problems have been reported if AmpliTaq gold is used in non-standard buffer systems.
-
(1996)
Nature
, vol.381
, pp. 445-446
-
-
Birch, D.E.1
-
9
-
-
0030606308
-
Oligonucleotide inhibitors of Taq DNA polymerase facilitate detection of low copy number targets by PCR
-
Dang C, Jayasena SD. Oligonucleotide inhibitors of Taq DNA polymerase facilitate detection of low copy number targets by PCR. J Mol Biol. 264:1996;268-278.
-
(1996)
J Mol Biol
, vol.264
, pp. 268-278
-
-
Dang, C.1
Jayasena, S.D.2
-
10
-
-
0030851627
-
The elimination of primer-dimer accumulation in PCR
-
Brownie J, Shawcross S, Theaker J, Whitcombe D, Ferrie R, Newton C, Little S. The elimination of primer-dimer accumulation in PCR. Nucleic Acids Res. 25:1997;3235-3241.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 3235-3241
-
-
Brownie, J.1
Shawcross, S.2
Theaker, J.3
Whitcombe, D.4
Ferrie, R.5
Newton, C.6
Little, S.7
-
11
-
-
0030904035
-
Identification and sizing of the GAA trinucleotide repeat expansion of Friedreich's ataxia in 56 patients - Clinical and genetic correlates
-
of special interest. A number of genetic diseases are known to demonstrate genetic anticipation and often result from tri-nucleotide expansion with genes. This paper describes one such disease and the application of long-PCR to determine the length of these repeats.
-
Lamont PJ, Davis MB, Wood NW. Identification and sizing of the GAA trinucleotide repeat expansion of Friedreich's ataxia in 56 patients - clinical and genetic correlates. of special interest Brain. 120:1997;673-680 A number of genetic diseases are known to demonstrate genetic anticipation and often result from tri-nucleotide expansion with genes. This paper describes one such disease and the application of long-PCR to determine the length of these repeats.
-
(1997)
Brain
, vol.120
, pp. 673-680
-
-
Lamont, P.J.1
Davis, M.B.2
Wood, N.W.3
-
12
-
-
0031002374
-
Application of long PCR to detect t(8;14)(q24;q32) translocations in childhood Burkitt's lymphoma and B-ALL
-
of special interest. This paper is an example of how long PCR can be successfully used to map chromosomal translocations in purified genomic DNa samples. It is often possible to use large segments of DNA, such as YACs from YAC contigs, to identify the approximate regions associated with chromosomal translocations. Identification of small regions of DNA sequence every 10-20 base-pairs from these YACs would permit the identification of the region of the two chromosomal strands of DNA involved in the translocation. This approach would be particularly valuable if variability in the translocation breakpoints were observed. Employing classical PCR would not be useful in this regard because it would require a previous knowledge of the translocation breakpoint to design PCR primers close enough to the break-point for successful PCR amplification. The use of long PCR avoids this need.
-
zur Stadt U, Hoser G, Reiter A, Welte K, Sykora KW. Application of long PCR to detect t(8;14)(q24;q32) translocations in childhood Burkitt's lymphoma and B-ALL. of special interest Ann Oncol. 8:1997;31-35 This paper is an example of how long PCR can be successfully used to map chromosomal translocations in purified genomic DNa samples. It is often possible to use large segments of DNA, such as YACs from YAC contigs, to identify the approximate regions associated with chromosomal translocations. Identification of small regions of DNA sequence every 10-20 base-pairs from these YACs would permit the identification of the region of the two chromosomal strands of DNA involved in the translocation. This approach would be particularly valuable if variability in the translocation breakpoints were observed. Employing classical PCR would not be useful in this regard because it would require a previous knowledge of the translocation breakpoint to design PCR primers close enough to the break-point for successful PCR amplification. The use of long PCR avoids this need.
-
(1997)
Ann Oncol
, vol.8
, pp. 31-35
-
-
Zur Stadt, U.1
Hoser, G.2
Reiter, A.3
Welte, K.4
Sykora, K.W.5
-
13
-
-
0030917946
-
Biological characterization of human immunodeficiency virus type 1 clones derived from different organs of an AIDS patient by long-range PCR
-
of special interest. The sequence of virtually full-length variants of HIV proviruses were amplified using long-PCR from different tissues of one patient. These sequences were then used to construct replication-competent virus.
-
Dittmar MT, Simmons G, Donaldson Y, Simmonds P, Clapham PR, Schulz TF, Weiss RA. Biological characterization of human immunodeficiency virus type 1 clones derived from different organs of an AIDS patient by long-range PCR. of special interest J Virol. 71:1997;5140-5147 The sequence of virtually full-length variants of HIV proviruses were amplified using long-PCR from different tissues of one patient. These sequences were then used to construct replication-competent virus.
-
(1997)
J Virol
, vol.71
, pp. 5140-5147
-
-
Dittmar, M.T.1
Simmons, G.2
Donaldson, Y.3
Simmonds, P.4
Clapham, P.R.5
Schulz, T.F.6
Weiss, R.A.7
-
14
-
-
0030871022
-
An unusual pattern of mutation in the duplicated portion of PKD1 is revealed by use of a novel strategy for mutation detection
-
Watnick TJ, Piotnek KB, Cordal TM, Weber H, Gandolph MA, Oian F, Lens XM, Neumann HPH, Germino GG. An unusual pattern of mutation in the duplicated portion of PKD1 is revealed by use of a novel strategy for mutation detection. Hum Mol Genet. 6:1997;1473-1482.
-
(1997)
Hum Mol Genet
, vol.6
, pp. 1473-1482
-
-
Watnick, T.J.1
Piotnek, K.B.2
Cordal, T.M.3
Weber, H.4
Gandolph, M.A.5
Oian, F.6
Lens, X.M.7
Neumann, H.P.H.8
Germino, G.G.9
-
15
-
-
0029966662
-
Multiplex co-amplification of 24 retinoblastoma gene exons after pre-amplification by long-distance PCR
-
of special interest. The complexity of the multiplex gene target was reduced by pre-amplifying the entire gene by long distance PCR. Mutations were searched after exon amplification by 2D electrophoresis, size in one direction and then denaturing gradient gel electrophoresis in the other. This highlights the difficulty in analysing so many samples at once.
-
Li D, Vijg J. Multiplex co-amplification of 24 retinoblastoma gene exons after pre-amplification by long-distance PCR. of special interest Nucleic Acids Res. 24:1996;538-539 The complexity of the multiplex gene target was reduced by pre-amplifying the entire gene by long distance PCR. Mutations were searched after exon amplification by 2D electrophoresis, size in one direction and then denaturing gradient gel electrophoresis in the other. This highlights the difficulty in analysing so many samples at once.
-
(1996)
Nucleic Acids Res
, vol.24
, pp. 538-539
-
-
Li, D.1
Vijg, J.2
-
16
-
-
0029820375
-
Uniform amplification of a mixture of deoxyribonucleic acids with varying GC content
-
of special interest. The addition of Betaine, a cheap amino aid analogue, aided in the amplification of difficult templates.
-
Baskaran N, Kandpal RP, Bhargava AK, Glynn MW, Weissman SM. Uniform amplification of a mixture of deoxyribonucleic acids with varying GC content. of special interest Genome Res. 6:1996;633 The addition of Betaine, a cheap amino aid analogue, aided in the amplification of difficult templates.
-
(1996)
Genome Res
, vol.6
, pp. 633
-
-
Baskaran, N.1
Kandpal, R.P.2
Bhargava, A.K.3
Glynn, M.W.4
Weissman, S.M.5
-
17
-
-
0029915406
-
Cystic-fibrosis mutation detection by hybridization to light-generated DNA-probe arrays
-
Cronin MT, Fucini RV, Kim SM, Masino RS, Wespi RM, Miyada CG. Cystic-fibrosis mutation detection by hybridization to light-generated DNA-probe arrays. Hum Mut. 7:1996;244-255.
-
(1996)
Hum Mut
, vol.7
, pp. 244-255
-
-
Cronin, M.T.1
Fucini, R.V.2
Kim, S.M.3
Masino, R.S.4
Wespi, R.M.5
Miyada, C.G.6
-
18
-
-
10244219858
-
Accessing genetic information with high-density DNA arrays
-
note
-
Chee M, Yang R, Hubbell E, Berno A, Huang XC, Stem D, Winkler J, Lockhart DJ, Morris MS, Fodor SPA. Accessing genetic information with high-density DNA arrays. of outstanding interest Science. 274:1996;610-614 This paper is from the Affymetrix group which received substantial funding from the US advanced technology program to develop DNA genotyping using sequencing-by-hybridisation on DNA chips. It describes the analysis of the entire mitochondrial genome. Oligonucleotides are arrayed in rows of four, the top row being the perfect complement and the other three rows corresponding to a single base mismatch at position 10. One set of 20mers is used for each base position. These arrays were then queried using RNA fluorescent probes, either in a one colour or a two colour competitive format. The hi-tech aspect of this process is the ability to array oligonucleotides in a very small space by a process analogous to photo-etching. The signal-noise ratios are of the order of 10. Although not an elegant solution, it has the potential for parallel analysis. Industrial-scale operation could make it a low cost option for high-throughput screening; however, problems may occur when companies try to create a demand for genetic testing. At present the main focus is in collaborative ventures with the pharmaceutical industry.
-
(1996)
Science
, vol.274
, pp. 610-614
-
-
Chee, M.1
Yang, R.2
Hubbell, E.3
Berno, A.4
Huang, X.C.5
Stem, D.6
Winkler, J.7
Lockhart, D.J.8
Morris, M.S.9
Fodor, S.P.A.10
-
19
-
-
0030834257
-
Whole genome analysis: Experimental access to all genome sequenced segments through larger-scale efficient oligonucleotide synthesis and PCR
-
Lashkari DA, McCusker JH, Davis RW. Whole genome analysis: experimental access to all genome sequenced segments through larger-scale efficient oligonucleotide synthesis and PCR. Proc Natl Acad Sci USA. 94:1997;8945-8947.
-
(1997)
Proc Natl Acad Sci USA
, vol.94
, pp. 8945-8947
-
-
Lashkari, D.A.1
McCusker, J.H.2
Davis, R.W.3
-
20
-
-
0030749872
-
Optimization of the performance of the polymerase chain reaction in silicon-based microstructures
-
Taylor TB, Winn-Deen ES, Picozza E, Woudenbergand TM, Albin M. Optimization of the performance of the polymerase chain reaction in silicon-based microstructures. Nucleic Acids Res. 25:1997;3164-3168.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 3164-3168
-
-
Taylor, T.B.1
Winn-Deen, E.S.2
Picozza, E.3
Woudenbergand, T.M.4
Albin, M.5
-
21
-
-
0029918709
-
Chip PCR I surface pasivation of microfabricated silicon-glass chips for PCR
-
of special interest. This study was undertaken to establish which microfabricated devices could be made PCR-friendly and thus serve as micro-reaction vessels. Untreated silicon and silicon nitride inhibited PCR; silanization and protein coating helped but was not reproducible. In contrast, silicon oxide coating was successful and is now standard manufacturing procedure. Further work is required for sample preparation and analysis en route to an integrated PCR analysis system.
-
Shoffner MA, Cheng J, Hvichia GE, Kricka LJ, Wilding. Chip PCR I surface pasivation of microfabricated silicon-glass chips for PCR. of special interest Nucleic Acids Res. 24:1996;375-379 This study was undertaken to establish which microfabricated devices could be made PCR-friendly and thus serve as micro-reaction vessels. Untreated silicon and silicon nitride inhibited PCR; silanization and protein coating helped but was not reproducible. In contrast, silicon oxide coating was successful and is now standard manufacturing procedure. Further work is required for sample preparation and analysis en route to an integrated PCR analysis system.
-
(1996)
Nucleic Acids Res
, vol.24
, pp. 375-379
-
-
Shoffner, M.A.1
Cheng, J.2
Hvichia, G.E.3
Kricka, L.J.4
Wilding5
-
22
-
-
0029939192
-
Chip PCR II Investigation of different PCR amplification systems in microfabricated silicon-glass chips
-
of special interest. The 12L reaction volume was within normal laboratory scale. PCR worked best using Taq start antibody. Direct use of purified lymphocytes was as good as DNA. Although it looked as hard to purify lymphocytes as to extract DNA, automated cell sorting could be used, which is probably more robust than automated DNA extractors.
-
Cheng J, Shoffner MA, Hvichia GE, Kricka LJ, Wilding. Chip PCR II Investigation of different PCR amplification systems in microfabricated silicon-glass chips. of special interest Nucleic Acids Res. 24:1996;380-385 The 12L reaction volume was within normal laboratory scale. PCR worked best using Taq start antibody. Direct use of purified lymphocytes was as good as DNA. Although it looked as hard to purify lymphocytes as to extract DNA, automated cell sorting could be used, which is probably more robust than automated DNA extractors.
-
(1996)
Nucleic Acids Res
, vol.24
, pp. 380-385
-
-
Cheng, J.1
Shoffner, M.A.2
Hvichia, G.E.3
Kricka, L.J.4
Wilding5
-
23
-
-
0031033829
-
Sequencing in nanofabricated arrays: A feasibility study
-
of special interest. The feasibility of using nanofabricated arrays as electrophoretic chambers for DNA sequencing is investigated. A specific array design, consisting of rows of closely spaced posts, separated by longer open spaces, is proposed. Molecules driven through the array by an electric field get hooked over obstacles at successive rows and their progress through the device is delayed as a consequence. The dependence of the delay time on molecular size is derived. Numerical evaluation indicates that a device of modest dimensions, operating at high fields, can rapidly resolve oligonucleotides containing several hundred bases.
-
Duke T, Monnelly G, Austin RH, Cox EC. Sequencing in nanofabricated arrays: a feasibility study. of special interest Electrophoresis. 18:1997;17-22 The feasibility of using nanofabricated arrays as electrophoretic chambers for DNA sequencing is investigated. A specific array design, consisting of rows of closely spaced posts, separated by longer open spaces, is proposed. Molecules driven through the array by an electric field get hooked over obstacles at successive rows and their progress through the device is delayed as a consequence. The dependence of the delay time on molecular size is derived. Numerical evaluation indicates that a device of modest dimensions, operating at high fields, can rapidly resolve oligonucleotides containing several hundred bases.
-
(1997)
Electrophoresis
, vol.18
, pp. 17-22
-
-
Duke, T.1
Monnelly, G.2
Austin, R.H.3
Cox, E.C.4
-
25
-
-
0029880002
-
PCR-mediated synthesis of exogenous competitors for quantitative
-
of special interest. An example of a simple procedure to generate exogenous competitor RNA for quantitative PCR
-
Schneeberger C, Zellinger R. PCR-mediated synthesis of exogenous competitors for quantitative. of special interest PCR Biotechniques. 20:1996;360-362 An example of a simple procedure to generate exogenous competitor RNA for quantitative PCR.
-
(1996)
PCR Biotechniques
, vol.20
, pp. 360-362
-
-
Schneeberger, C.1
Zellinger, R.2
-
26
-
-
0029778731
-
Technical aspects of quantitative competitive PCR
-
of special interest. An excellent review article outlining in detail the practical aspects that should be considered when attempting to use quantitative PCR for the first time.
-
Zimmermann K, Mannhalter JW. Technical aspects of quantitative competitive PCR. of special interest Biotechniques. 21:1996;268-279 An excellent review article outlining in detail the practical aspects that should be considered when attempting to use quantitative PCR for the first time.
-
(1996)
Biotechniques
, vol.21
, pp. 268-279
-
-
Zimmermann, K.1
Mannhalter, J.W.2
-
27
-
-
0031045298
-
Rapid detection of trisomy 21 by homologous gene quantitative PCR
-
note
-
Lee H-H, Chong JG, Lin SP, Choo HT, Yang ML, Ng HT. Rapid detection of trisomy 21 by homologous gene quantitative PCR. of outstanding interest Hum Genet. 99:1997;364-367 The authors describe an internally controlled semi-quantitative PCR for trisomy 21. A rapid, low-cost alternative to cytogenetics, which could potentially be automated. Quantitative PCR for Down syndrome (DS) must be able to detect a 50% increase in gene dosage. This has been tackled by PCR methods using either microsatellites to detect an extra allele and/or a dosage effect, or by semi-quantitative PCR using heterologous templates, for example, CFTR (chromosome 7) or IGF1 (chromosome 12) and something on chromosome 21 (e.g. SOD1). Neither of these two methods have been entirely satisfactory, and as far as I know are not in routine use. Here a method which uses a homologous target is described. The human liver phosphofructokinase gene (PFKL-CH21) is located at 21q22.3 and is thought to be involved in the DS phenotype. Two other isoenzymes exist: muscle-type (PFKM-CH1) one chromosome 1 and platelet-type (PFKP-CH10) on chromosome 10. PFKL-CH21 has 68% and 63% sequence homology with hose two genes, respectively. This study reports the use of one set of primers to amplify PFKL-CH21 and PFKM-CH1 products. The method has two big advantages over previous PCR methods; it has an internal control (although the robustness of that control must be established): and the probe can detect unbalanced transactions. Automated fluorescent detection might be more accurate. Although this method looks promising, it has not gone far enough in terms of quantitation. Do both genes amplify with equal efficiency? Clearly this would affect the product ratio if they do not. An automated approach to molecular screening for the most common annueploidy could have significant public health implications.
-
(1997)
Hum Genet
, vol.99
, pp. 364-367
-
-
Lee H-H1
Chong, J.G.2
Lin, S.P.3
Choo, H.T.4
Yang, M.L.5
Ng, H.T.6
-
29
-
-
0029670262
-
Molecular beacons - Probes that fluoresce upon hybridization
-
of outstanding interest. Novel nucleic acid probes were developed that recognize and report the presence of specific nucleic acids in homogeneous solutions. These probes undergo a spontaneous fluorogenic conformational change when they hybridize to their targets. Only perfectly complementary targets elicit this response, as hybridization does not occur when the target contains a mismatched nucleotide or a deletion. The probes are particularly suited for monitoring the synthesis of specific nucleic acids in real time. When used in nucleic acid amplification assays, gene detection is homogeneous and sensitive, and can be carried out in a sealed tube. When introduced into living cells, these probes should enable the origin, movement, and fate of specific mRNAs to be traced.
-
Tyagi S, Kramer FR. Molecular beacons - probes that fluoresce upon hybridization. of outstanding interest Nat Biotechnol. 14:1996;303-308 Novel nucleic acid probes were developed that recognize and report the presence of specific nucleic acids in homogeneous solutions. These probes undergo a spontaneous fluorogenic conformational change when they hybridize to their targets. Only perfectly complementary targets elicit this response, as hybridization does not occur when the target contains a mismatched nucleotide or a deletion. The probes are particularly suited for monitoring the synthesis of specific nucleic acids in real time. When used in nucleic acid amplification assays, gene detection is homogeneous and sensitive, and can be carried out in a sealed tube. When introduced into living cells, these probes should enable the origin, movement, and fate of specific mRNAs to be traced.
-
(1996)
Nat Biotechnol
, vol.14
, pp. 303-308
-
-
Tyagi, S.1
Kramer, F.R.2
-
30
-
-
0029803735
-
Molecular haplotyping of genetic makers 10 kb apart by allele-specific long range PCR
-
Michalatos-Beloin S, Tishkoff SA, Bentley KA, Kidd KK, Ruano G. Molecular haplotyping of genetic makers 10 kb apart by allele-specific long range PCR. Nucleic Acids Res. 24:1996;4841-4843.
-
(1996)
Nucleic Acids Res
, vol.24
, pp. 4841-4843
-
-
Michalatos-Beloin, S.1
Tishkoff, S.A.2
Bentley, K.A.3
Kidd, K.K.4
Ruano, G.5
-
31
-
-
0027493961
-
Protein truncation test (PTT) for rapid detection of translation terminating mutations
-
Roest PAM, Roberts RG, Sugino S, van Ommen GJB, den Dunnen JT. Protein truncation test (PTT) for rapid detection of translation terminating mutations. Hum Mol Genet. 2:1993;665-669.
-
(1993)
Hum Mol Genet
, vol.2
, pp. 665-669
-
-
Roest, P.A.M.1
Roberts, R.G.2
Sugino, S.3
Van Ommen, G.J.B.4
Den Dunnen, J.T.5
-
32
-
-
12644303219
-
Detection of heterozygous truncating mutations in the BRCA1 and APC genes by using a rapid screening assay in yeast
-
of outstanding interest. This paper describes a general method for identifying protein-truncating mutations in any gene. Large segments of coding sequence (BRCA1 or APC) are amplified by RT-PCR (RNA) or PCR (genomic DNA). These fragments are introduced into yeast stains by homologous recombination into a yeast URA3 in fusion protein. Enzyme activity is not produced in sequences coding for a stop codon. The presence of a truncating mutation can, therefore, be detected by the ability of the yeast to grow on selectable medium. The numbers of colonies produced from wild-type gene are compared with those produced with the test gene. The presence of a wild-type and mutated allele will result in half the number of colonies compared to that obtained with two wild-type alleles.
-
Ishioka C, Suzuki T, FitzGerald M, Krainer M, Shimodaira H, Shimada A, Nomizu T, Isselbacher KJ, Haber D, Kanamaru R. Detection of heterozygous truncating mutations in the BRCA1 and APC genes by using a rapid screening assay in yeast. of outstanding interest Proc Natl Acad Sci USA. 94:1997;2449-2453 This paper describes a general method for identifying protein-truncating mutations in any gene. Large segments of coding sequence (BRCA1 or APC) are amplified by RT-PCR (RNA) or PCR (genomic DNA). These fragments are introduced into yeast stains by homologous recombination into a yeast URA3 in fusion protein. Enzyme activity is not produced in sequences coding for a stop codon. The presence of a truncating mutation can, therefore, be detected by the ability of the yeast to grow on selectable medium. The numbers of colonies produced from wild-type gene are compared with those produced with the test gene. The presence of a wild-type and mutated allele will result in half the number of colonies compared to that obtained with two wild-type alleles.
-
(1997)
Proc Natl Acad Sci USA
, vol.94
, pp. 2449-2453
-
-
Ishioka, C.1
Suzuki, T.2
Fitzgerald, M.3
Krainer, M.4
Shimodaira, H.5
Shimada, A.6
Nomizu, T.7
Isselbacher, K.J.8
Haber, D.9
Kanamaru, R.10
-
33
-
-
0027430658
-
Screening patients for heterozygous p53 mutations using a functional assay in yeast
-
Ishioka C, Frebourg T, Yan Y-X, Vidal M, Friend SH, Schmidt S, Iggo RD. Screening patients for heterozygous p53 mutations using a functional assay in yeast. Nat Genet. 5:1993;124-129.
-
(1993)
Nat Genet
, vol.5
, pp. 124-129
-
-
Ishioka, C.1
Frebourg, T.2
Yan Y-X3
Vidal, M.4
Friend, S.H.5
Schmidt, S.6
Iggo, R.D.7
-
34
-
-
0030791118
-
Potassium permanganate and tetraethylammonium chloride are a safe and effective substitute for osmium tetroxide in solid-phase fluorescent chemical cleavage of mismatch
-
Roberts E, Deeble VJ, Woods GC, Taylor GR. Potassium permanganate and tetraethylammonium chloride are a safe and effective substitute for osmium tetroxide in solid-phase fluorescent chemical cleavage of mismatch. Nucleic Acids Res. 25:1997;3377-3378.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 3377-3378
-
-
Roberts, E.1
Deeble, V.J.2
Woods, G.C.3
Taylor, G.R.4
-
35
-
-
0029913452
-
Mutation detection with MutH, MutL, and MutS mismatch repair proteins
-
of special interest. E coli methyl directed mismatch repair is initiated by MutS, MutL, and ATP-dependent activation of MutH endonuclease, which cleaves at d(GATC) sites in the vicinity of a mismatch. This reaction provides an efficient method for detection of mismatches in heteroduplexes produced by hybridization of genetically distinct sequences after PCR amplification. Multiple examples of transition and transversion mutations, as well as one, two, and three nucleotide insertion/deletion mutants, were detected in PCR heteroduplexes ranging in size from 400bp to 2.5kb. Background cleavage of homoduplexes is largely due to polymerase errors that occur during amplification, and the MutHLS reaction provides an estimate of the incidence of mutant sequences that arise during PCR.
-
Smith J, Modrich P. Mutation detection with MutH, MutL, and MutS mismatch repair proteins. of special interest Proc Natl Acad Sci USA. 93:1996;4374-4379 E coli methyl directed mismatch repair is initiated by MutS, MutL, and ATP-dependent activation of MutH endonuclease, which cleaves at d(GATC) sites in the vicinity of a mismatch. This reaction provides an efficient method for detection of mismatches in heteroduplexes produced by hybridization of genetically distinct sequences after PCR amplification. Multiple examples of transition and transversion mutations, as well as one, two, and three nucleotide insertion/deletion mutants, were detected in PCR heteroduplexes ranging in size from 400bp to 2.5kb. Background cleavage of homoduplexes is largely due to polymerase errors that occur during amplification, and the MutHLS reaction provides an estimate of the incidence of mutant sequences that arise during PCR.
-
(1996)
Proc Natl Acad Sci USA
, vol.93
, pp. 4374-4379
-
-
Smith, J.1
Modrich, P.2
-
36
-
-
0029565778
-
A novel in vivo method to detect DNA sequence variation
-
of special interest. If a synthetic hemimethylated plasmid with a five base insertion in the β-gal gene has a mismatched template cloned into it, the five base insertion is coincidentally repaired along with the mismatch by the MutHLS system, restoring β-gal function, detectable by a blue-white colony assay on X-gal. The only problem is that PCR induced mismatches give false positives, and the authors to into great detail about reducing this by clean-up procedures which might make the technique too cumbersome for practical use. If the method could be simplified it could enable a new approach to mutation screening.
-
Faham M, Cox DR. A novel in vivo method to detect DNA sequence variation. of special interest Genome Res. 6:1996;474-482 If a synthetic hemimethylated plasmid with a five base insertion in the β-gal gene has a mismatched template cloned into it, the five base insertion is coincidentally repaired along with the mismatch by the MutHLS system, restoring β-gal function, detectable by a blue-white colony assay on X-gal. The only problem is that PCR induced mismatches give false positives, and the authors to into great detail about reducing this by clean-up procedures which might make the technique too cumbersome for practical use. If the method could be simplified it could enable a new approach to mutation screening.
-
(1996)
Genome Res
, vol.6
, pp. 474-482
-
-
Faham, M.1
Cox, D.R.2
-
37
-
-
0030941659
-
Evaluation of MutS as a tool for direct measurement of point mutations in genomic DNA
-
of special interest. The MutEx assay is a technique that was developed to detect and map mutations. This assay takes advantage of the Escherichia coli mismatch binding protein MutS, which binds and protects mismatched heteroduplex DNA from subsequent exonuclease digestion. The plausibility of using the MutEx assay as part of a genotypic selection scheme was investigated. The MutEx assay was able to enrich the mutant sequence approximately 1000-fold and, therefore, has considerable potential as a tool for mutation detection.
-
Parsons BL, Heflich RH. Evaluation of MutS as a tool for direct measurement of point mutations in genomic DNA. of special interest Mut Res Fundam Mol Mechm Mutagen. 374:1997;277-285 The MutEx assay is a technique that was developed to detect and map mutations. This assay takes advantage of the Escherichia coli mismatch binding protein MutS, which binds and protects mismatched heteroduplex DNA from subsequent exonuclease digestion. The plausibility of using the MutEx assay as part of a genotypic selection scheme was investigated. The MutEx assay was able to enrich the mutant sequence approximately 1000-fold and, therefore, has considerable potential as a tool for mutation detection.
-
(1997)
Mut Res Fundam Mol Mechm Mutagen
, vol.374
, pp. 277-285
-
-
Parsons, B.L.1
Heflich, R.H.2
-
38
-
-
0029611353
-
Improved strategy for mutation detection - A modification to the enzyme mismatch cleavage method
-
Babon JJ, Youil R, Cotton RGH. Improved strategy for mutation detection - a modification to the enzyme mismatch cleavage method. Nucleic Acids Res. 23:1995;5082-5084.
-
(1995)
Nucleic Acids Res
, vol.23
, pp. 5082-5084
-
-
Babon, J.J.1
Youil, R.2
Cotton, R.G.H.3
-
40
-
-
0029843950
-
Methylation-specific PCR: A novel PCR assay for methylation status of CpG islands
-
note
-
Herman JG, Graff JR, Myohanen S, Nelkin BD, Baylin SB. Methylation-specific PCR: A novel PCR assay for methylation status of CpG islands. of outstanding interest Proc Natl Acad Sci USA. 93:1996;9821-9826 CpG island methylation is fundamental to gene expression, imprinting and chromosome X inactivation. Tools to investigate this are likely to be of diagnostic use. This paper examines methylation in p16, p15, E-cadherin and the VHL tumour suppressor genes. This PCR-based method uses primers to amplify either methylated or unmethylated cytosine residues. This is achieved using bisulfite modification of DNA, which converts unmodifed cytosine, but not 5-methyl-cytosine, to uracil. This method was developed by M Frommer and S Clarke, but the authors claim that their modifications make the technique simpler and more sensitive. Essentially, it relies on the use of primers designed to amplify DNA either before or after it has been modified. Methylated DNA should always amplify using normal primers, whereas unmethylated DNA would be modified and could, in principle, be amplified by two alternative sets of specific primers (one set for each strand since the strands are no longer complementary). Initial studies with the CpG island from p16 showed correlation with Southern blotting experiments using methylation-sensitive restriction enzymes. Sequence of modified unmethylated DNA showed that all C bases has moved into the T track. The method is safe and easy and could be used for female cell-line clonality studies, imprinting and X inactivation.
-
(1996)
Proc Natl Acad Sci USA
, vol.93
, pp. 9821-9826
-
-
Herman, J.G.1
Graff, J.R.2
Myohanen, S.3
Nelkin, B.D.4
Baylin, S.B.5
-
41
-
-
0030916936
-
A single-tube PCR test for the diagnosis of Angelman and Prader-Will syndrome based on allelic methylation differences at the SNRPN locus
-
of special interest. This study describes a single-tube PCR test based on sodium bisulfite treatment of DNA, which converts unmethylated, but not methylated, cytosine residues to uracil, and PCR primers specific for the maternal and the paternal allele. The method was validated in a blinded retrospective study on 87 DNA samples from normal controls and patients. Prospective studies by independent laboratories will be needed before this assay can replace Southern blot analysis in routine diagnostic procedures.
-
Zeschnigk M, Lich C, Buiting K, Doerfler W, Horsthemke B. A single-tube PCR test for the diagnosis of Angelman and Prader-Will syndrome based on allelic methylation differences at the SNRPN locus. of special interest Eur J Hum Genet. 5:1997;94-98 This study describes a single-tube PCR test based on sodium bisulfite treatment of DNA, which converts unmethylated, but not methylated, cytosine residues to uracil, and PCR primers specific for the maternal and the paternal allele. The method was validated in a blinded retrospective study on 87 DNA samples from normal controls and patients. Prospective studies by independent laboratories will be needed before this assay can replace Southern blot analysis in routine diagnostic procedures.
-
(1997)
Eur J Hum Genet
, vol.5
, pp. 94-98
-
-
Zeschnigk, M.1
Lich, C.2
Buiting, K.3
Doerfler, W.4
Horsthemke, B.5
-
42
-
-
0030751457
-
Identification of the human chromosomal region containing the iridogoniodysgenesis anamoly locus by genomic-mismatch scanning
-
Mirzayans F, Mears AJ, Guo S-W, Pearce WG, Walter MA. Identification of the human chromosomal region containing the iridogoniodysgenesis anamoly locus by genomic-mismatch scanning. Am J Hum Genet. 61:1997;111-119.
-
(1997)
Am J Hum Genet
, vol.61
, pp. 111-119
-
-
Mirzayans, F.1
Mears, A.J.2
Guo S-W3
Pearce, W.G.4
Walter, M.A.5
-
43
-
-
0029916529
-
A rat genetic map constructed by representation difference analysis markers with suitability for large-scale typing
-
note
-
2 hybrids were also selected that were different only at a specific region of chromosome 1 (genetically directed RDA). Four polymorphic clones for that region were generated. RDA, therefore, appears to be an efficient way to isolate polymorphic clones from inbred animal strains. It is technically simple and has many other potential applications.
-
(1996)
Proc Natl Acad Sci USA
, vol.93
, pp. 3914-3919
-
-
Toyota, M.1
Canzian, F.2
Ushijima, T.3
Hosoya, Y.4
Kuramoto, T.5
Serikawa, T.6
Imai, K.7
Sugimura, T.8
Nagao, M.9
-
45
-
-
0003995672
-
-
of special interest. P. Liang, Pardee A.B. Humana Press, Totowa, New Jeresy, A compilation of many of the methodologies and applications of DDRT-PCR highlighting problems that are associated with the procedure and protocols to overcome them
-
Liang P, Pardee AB. . of special interest Liang P, Pardee AB. Differential display methods and protocols. 1997;Humana Press, Totowa, New Jeresy, A compilation of many of the methodologies and applications of DDRT-PCR highlighting problems that are associated with the procedure and protocols to overcome them.
-
(1997)
Differential Display Methods and Protocols
-
-
Liang, P.1
Pardee, A.B.2
-
46
-
-
0030825337
-
Automated differential display using a fluorescently-labelled universal primer
-
of special interest. The use of a universal, fluorescently-labelled primer for all the PCRs eliminates many of the problems associated with DDRT-PCR. The fluorescently labelled universal primer is a constant feature in every PCR reaction, artefacts that result from arbitrary-10mer to arbitrary-10mer primer amplifications are not observed and sample throughput and ease of data handling are increased.
-
Smith NR, Aldersley M, Li A, High AS, Moynihan TP, Markham AF, Robinson PA. Automated differential display using a fluorescently-labelled universal primer. of special interest Biotechniques. 23:1997;274-279 The use of a universal, fluorescently-labelled primer for all the PCRs eliminates many of the problems associated with DDRT-PCR. The fluorescently labelled universal primer is a constant feature in every PCR reaction, artefacts that result from arbitrary-10mer to arbitrary-10mer primer amplifications are not observed and sample throughput and ease of data handling are increased.
-
(1997)
Biotechniques
, vol.23
, pp. 274-279
-
-
Smith, N.R.1
Aldersley, M.2
Li, A.3
High, A.S.4
Moynihan, T.P.5
Markham, A.F.6
Robinson, P.A.7
-
47
-
-
0030753426
-
An mRNA differential display strategy for cloning genes expressed during mouse gonad development
-
of special interest. An example of the successful application of DDRT-PCR for the identification of differentially transcribed genes from very small quantities of tissue employing minor modifications to improve the reliability of the procedure.
-
Nordqvist K, Tohonen V. An mRNA differential display strategy for cloning genes expressed during mouse gonad development. of special interest Int J Dev Biol. 41:1997;627-638 An example of the successful application of DDRT-PCR for the identification of differentially transcribed genes from very small quantities of tissue employing minor modifications to improve the reliability of the procedure.
-
(1997)
Int J Dev Biol
, vol.41
, pp. 627-638
-
-
Nordqvist, K.1
Tohonen, V.2
-
48
-
-
0030855424
-
Isolation of rare transcripts by representational difference analysis
-
of special interest. The major argument against techniques such as representational difference analysis is the number of false positives isolated. This short paper describes the representational difference analysis protocol in detail and highlights precautions that should be undertaken to avoid false positives.
-
O'Neill MJ, Sinclair AH. Isolation of rare transcripts by representational difference analysis. of special interest Nucleic Acids Res. 25:1997;2681-2682 The major argument against techniques such as representational difference analysis is the number of false positives isolated. This short paper describes the representational difference analysis protocol in detail and highlights precautions that should be undertaken to avoid false positives.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 2681-2682
-
-
O'Neill, M.J.1
Sinclair, A.H.2
-
50
-
-
0030930366
-
A model for p53-induced apoptosis
-
of special interest. SAGE analysis was used to identify transcripts activated early in p53 induced apoptosis.
-
Polyak K, Xia Y, Zweier JL, Kinzler KW, Vogelstein B. A model for p53-induced apoptosis. of special interest Nature. 389:1997;300-305 SAGE analysis was used to identify transcripts activated early in p53 induced apoptosis.
-
(1997)
Nature
, vol.389
, pp. 300-305
-
-
Polyak, K.1
Xia, Y.2
Zweier, J.L.3
Kinzler, K.W.4
Vogelstein, B.5
-
51
-
-
0029748326
-
Parallel human genome analysis: Microarray-based expression monitoring of 1000 genes
-
2. Not as small scale as Affymatrix, this approach is to array expressed sequence tags (ESTs) and interrogate them with cDNA from different issues to profile their tissue distribution. The ability to array and then scan high density arrays looks set be become standard technology for YAC and EST screening. Equivalent information from SAGE but micro arrays may be more amenable to automation for high-throughput applications.
-
2. Not as small scale as Affymatrix, this approach is to array expressed sequence tags (ESTs) and interrogate them with cDNA from different issues to profile their tissue distribution. The ability to array and then scan high density arrays looks set be become standard technology for YAC and EST screening. Equivalent information from SAGE but micro arrays may be more amenable to automation for high-throughput applications.
-
(1996)
Proc Natl Acad Sci USA
, vol.93
, pp. 10614-10619
-
-
Schena, M.1
Shalon, D.2
Heller, R.3
Chai, A.4
O'Brown, P.5
Davis, R.W.6
-
52
-
-
0029738953
-
Cloning of 559 potential exons of genes of human-chromosome-21 by exon trapping
-
of special interest. An example of the application of exon trapping for the purposes of identifying multiple transcripts from a single chromosome is being employed more frequently to generate transcript maps of chromosomal loci.
-
Chen H, Chrast R, Rossier C, Morris MA, Lalioti MD, Antonarakis SE. Cloning of 559 potential exons of genes of human-chromosome-21 by exon trapping. of special interest Genome Res. 6:1996;747-760 An example of the application of exon trapping for the purposes of identifying multiple transcripts from a single chromosome is being employed more frequently to generate transcript maps of chromosomal loci.
-
(1996)
Genome Res
, vol.6
, pp. 747-760
-
-
Chen, H.1
Chrast, R.2
Rossier, C.3
Morris, M.A.4
Lalioti, M.D.5
Antonarakis, S.E.6
-
53
-
-
0029939504
-
A transcription map of the DiGeorge and Velo-cardio-facial syndrome minimal critical 22q11
-
of special interest. In addition to other approaches, such as direct sequencing, DNA selection was employed to generate a transcription map of 250 kb of the minimal DiGeorge critical region.
-
Gong WK, Emanuel BS, Collins J, Kim DH, Wang ZL, Chen F, Zhang GZ, Roe B, Budarf ML. A transcription map of the DiGeorge and Velo-cardio-facial syndrome minimal critical 22q11. of special interest Hum Mol Genet. 5:1996;789-800 In addition to other approaches, such as direct sequencing, DNA selection was employed to generate a transcription map of 250 kb of the minimal DiGeorge critical region.
-
(1996)
Hum Mol Genet
, vol.5
, pp. 789-800
-
-
Gong, W.K.1
Emanuel, B.S.2
Collins, J.3
Kim, D.H.4
Wang, Z.L.5
Chen, F.6
Zhang, G.Z.7
Roe, B.8
Budarf, M.L.9
-
54
-
-
15444340362
-
A 1.1-mb transcript map of the hereditary hemochromatosis locus
-
of special interest. A combination of cDNA selection, exon trapping and sample sequencing were used to prepare a transcript map of this region of human chromosome 6.
-
Ruddy DA, Kronmal GS, Lee VK, Mintier GA, Quintana L, Domingo R, Meyer NC, Irrinki A, McClelland EE, Fullan A, et al. A 1.1-mb transcript map of the hereditary hemochromatosis locus. of special interest Genome Res. 7:1997;441-456 A combination of cDNA selection, exon trapping and sample sequencing were used to prepare a transcript map of this region of human chromosome 6.
-
(1997)
Genome Res
, vol.7
, pp. 441-456
-
-
Ruddy, D.A.1
Kronmal, G.S.2
Lee, V.K.3
Mintier, G.A.4
Quintana, L.5
Domingo, R.6
Meyer, N.C.7
Irrinki, A.8
McClelland, E.E.9
Fullan, A.10
-
55
-
-
0029978835
-
Construction of a 600-kilobase cosmid clone contig and generation of a transcriptional map surrounding the lung-cancer tumor-suppressor gene (TSG) locus on human-chromosome 3p21.3 - Progress toward the isolation of a lung-cancer TSG
-
of special interest. One of the major tumor suppressor genes yet to be characterised lies at chromosome 3p21.3. This manuscript describes the application of cDNA selection in order to generate a transcription map from a contig of 23 cosmids and one P1 comprising 700 kb of sequence mapping to this region of chromosome 3.
-
Wei MH, Latif F, Bader S, Kashuba V, Chen JY, Duh FM, Sekido Y, Lee CC, Geil L, Kuzmin I, et al. Construction of a 600-kilobase cosmid clone contig and generation of a transcriptional map surrounding the lung-cancer tumor-suppressor gene (TSG) locus on human-chromosome 3p21.3 - progress toward the isolation of a lung-cancer TSG. of special interest Cancer Res. 56:1996;1487-1492 One of the major tumor suppressor genes yet to be characterised lies at chromosome 3p21.3. This manuscript describes the application of cDNA selection in order to generate a transcription map from a contig of 23 cosmids and one P1 comprising 700 kb of sequence mapping to this region of chromosome 3.
-
(1996)
Cancer Res
, vol.56
, pp. 1487-1492
-
-
Wei, M.H.1
Latif, F.2
Bader, S.3
Kashuba, V.4
Chen, J.Y.5
Duh, F.M.6
Sekido, Y.7
Lee, C.C.8
Geil, L.9
Kuzmin, I.10
-
56
-
-
9044240048
-
A radiation hybrid map of the human genome
-
of outstanding interest. The screening of a panel of DNA samples prepared by whole-genome radiation hybrids now permit the reliable sub-localisation of any gene of interest so long as PCR primers are available which will specifically amplify the gene under investigation.
-
Gyapay G, Schmitt K, Fizames C, Jones H, Vega-Czarny N, Spillett D, Muselet D, Prud-Homme J-F, Dib C, Auffray C, et al. A radiation hybrid map of the human genome. of outstanding interest Hum Mol Genet. 5:1996;339-346 The screening of a panel of DNA samples prepared by whole-genome radiation hybrids now permit the reliable sub-localisation of any gene of interest so long as PCR primers are available which will specifically amplify the gene under investigation.
-
(1996)
Hum Mol Genet
, vol.5
, pp. 339-346
-
-
Gyapay, G.1
Schmitt, K.2
Fizames, C.3
Jones, H.4
Vega-Czarny, N.5
Spillett, D.6
Muselet, D.7
Prud-Homme J-F8
Dib, C.9
Auffray, C.10
-
57
-
-
0030980842
-
Human BAC library: Construction and rapid screening
-
Asakawa S, Abe I, Kudoh Y, Kishi N, Wang YM, Kubota R, Kudoh J, Kawasaki K, Minoshima S, Shimizu N. Human BAC library: construction and rapid screening. Gene. 191:1997;69-79.
-
(1997)
Gene
, vol.191
, pp. 69-79
-
-
Asakawa, S.1
Abe, I.2
Kudoh, Y.3
Kishi, N.4
Wang, Y.M.5
Kubota, R.6
Kudoh, J.7
Kawasaki, K.8
Minoshima, S.9
Shimizu, N.10
-
58
-
-
0025339588
-
A novel, rapid method for the isolation of terminal sequences from yeast artificial chromosomes
-
Riley J, Butler R, Ogilvie D, Finniear R, Jenner D, Powell S, Anand R, Smith JC, Markham AF. A novel, rapid method for the isolation of terminal sequences from yeast artificial chromosomes. Nucleic Acids Res. 18:1990;2887-2890.
-
(1990)
Nucleic Acids Res
, vol.18
, pp. 2887-2890
-
-
Riley, J.1
Butler, R.2
Ogilvie, D.3
Finniear, R.4
Jenner, D.5
Powell, S.6
Anand, R.7
Smith, J.C.8
Markham, A.F.9
-
59
-
-
0029805198
-
Genomic analysis of human multigene families using chromosomes-specific vectorette PCR
-
Moynihan TP, Markham AF, Robinson PA. Genomic analysis of human multigene families using chromosomes-specific vectorette PCR. Nucleic Acids Res. 24:1996;4094-4095.
-
(1996)
Nucleic Acids Res
, vol.24
, pp. 4094-4095
-
-
Moynihan, T.P.1
Markham, A.F.2
Robinson, P.A.3
-
60
-
-
0030461352
-
Structure of the human alpha(2) subunit gene of the glycine receptor - Use of vectorette and Alu-exon PCR
-
Monani U, Burghes AHM. Structure of the human alpha(2) subunit gene of the glycine receptor - use of vectorette and Alu-exon PCR. Genome Res. 6:1996;1200-1206.
-
(1996)
Genome Res
, vol.6
, pp. 1200-1206
-
-
Monani, U.1
Burghes, A.H.M.2
-
61
-
-
0030920610
-
Sequence mapping by electronic PCR
-
Schuler GD. Sequence mapping by electronic PCR. Genome Res. 7:1997;541-550.
-
(1997)
Genome Res
, vol.7
, pp. 541-550
-
-
Schuler, G.D.1
|