Targeted gene walking polymerase chain reaction

Parker, Jay D.; Rabinovitch, Peter S.; Burmer, Glenna C.

doi:10.1093/nar/19.11.3055

Cited by 167 publications

(93 citation statements)

References 13 publications

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“…By attaching to ubiquitous genomic sequences, this nonspecific walking primer could support the first primer in generating fragments within a 5 kb size range, a strategy that was first applied in targeted gene walking PCR. 86 Although we did not demonstrate that the generated PCR products are within genes or that the PCR products generated, e.g., with the TATA primer indeed encompass TATA boxes, other groups have shown that PCR with degenerate primers that encode conserved amino acid sequences can be used to screen animal genomes reliably for likely gene family members. 87 In this way, we think that we increased the possibility of amplifying these regions.…”

Section: Resultscontrasting

confidence: 55%

Assessment of genomic instability in breast cancer and uveal melanoma by random amplified polymorphic DNA analysis

Papadopoulos

Benter

Anastassiou

et al. 2002

Intl Journal of Cancer

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Some types of cancer have been associated with abnormal DNA fingerprinting. We used random amplified polymorphic DNA (RAPD) to generate fingerprints that detect genomic alterations in human breast cancer. Primers were designed by choosing sequences involved in the development of DNA mutations. Seventeen primers in 44 different combinations were used to screen a total of 6 breast cancer DNA/normal DNA pairs and 6 uveal melanoma DNA/normal DNA pairs. Forty-five percent of these combinations reliably detected quantitative differences in the breast cancer pairs, while only 18% of these combinations detected differences in the uveal melanoma pairs. Fourteen (32%) and 12 (27%) primers generated a smear or did not produce any band patterns in the first and second cases, respectively. Taking into account the ability of RAPD to screen the whole genome, our results suggest that the genomic damage in breast cancer is significantly higher than in uveal melanoma. Our study confirms other reports that the molecular karyotypes produced with random priming, called amplotypes, are very useful for assessing genomic damage in cancer. Genomic instability is a hallmark of neoplastic transformation and a herald of genomic damage. The existence of an additional type of genomic instability has been described, the microsatellite mutator phenotype pathway. Progress in molecular cancer genetics has facilitated the detection of these mutations. In the last decade, representation differential analysis and comparative genomic hybridization (CGH) were added to methods like flow cytometry, restriction fragment length polymorphisms of polymorphic minisatellite loci and allelotyping, a PCR amplification of informative microsatellite loci.Another promising approach has been introduced, arbitrarily primed PCR 1 combined with random amplified polymorphic DNA (RAPD). 2 Both PCR-based techniques, called amplotyping, use fingerprinting to quantitatively and qualitatively evaluate band alterations. 3 This random priming method allows comparison of normal and tumor tissues at a minimum of 20 -40 genome sites in a single PCR, though evidence suggests that the number of compared loci runs into the hundreds if we take into account that a gel band consists of many comigrating fragments. 4,5 It also includes internal controls and detects moderate gains of chromosomal sequences (trisomy/tetrasomy) that would otherwise escape detection.Previously, we addressed the problems of reproducibility and contamination in random priming. In the present work, we used RAPD fingerprinting to assess the genomic damage present in breast cancer and in uveal melanoma cells. For this task, we designed primers based on sequences that are supposed to play an important role in the mechanisms leading to DNA alterations. Human gene mutations appear to be caused by multiple mechanisms whose relative importance is probably governed by local primary and secondary DNA structure. 7 We have searched for consensus sequences located in the immediate vicinity of gene mutations and for "hot s...

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Section: Resultscontrasting

confidence: 55%

Assessment of genomic instability in breast cancer and uveal melanoma by random amplified polymorphic DNA analysis

Papadopoulos

Benter

Anastassiou

et al. 2002

Intl Journal of Cancer

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“…This lysate was used to transduce strain JE3777 to tetracycline resistance. Arbitrary primer PCR was used to identify a DNA sequence flanking the linked insertion (37,38). Chromosomal DNA of strain JE3845 was prepared using the MasterPure TM genomic DNA isolation kit (Epicentre, Madison, WI).…”

Section: Mapping the Glta Gtg Mutationmentioning

confidence: 99%

Studies of Propionate Toxicity in Salmonella enterica Identify 2-Methylcitrate as a Potent Inhibitor of Cell Growth

Horswill¹,

Dudding

Escalante‐Semerena

2001

Journal of Biological Chemistry

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Salmonella enterica serovar Typhimurium LT2 showed increased sensitivity to propionate when the 2-methylcitric acid cycle was blocked. A derivative of a prpC mutant (which lacked 2-methylcitrate synthase activity) resistant to propionate was isolated, and the mutation responsible for the newly acquired resistance to propionate was mapped to the citrate synthase (gltA) gene. These results suggested that citrate synthase activity was the source of the increased sensitivity to propionate observed in the absence of the 2-methylcitric acid cycle. DNA sequencing of the wild-type and mutant gltA alleles revealed that the ATG start codon of the wild-type gene was converted to the rare GTG start codon in the revertant strain. This result suggested that lower levels of this enzyme were present in the mutant. Consistent with this change, cell-free extracts of the propionate-resistant strain contained 12-fold less citrate synthase activity. This was interpreted to mean that, in the wild-type strain, high levels of citrate synthase activity were the source of a toxic metabolite. In vitro experiments performed with homogeneous citrate synthase enzyme indicated that this enzyme was capable of synthesizing 2-methylcitrate from propionyl-CoA and oxaloacetate. This result lent further support to the in vivo data, which suggested that citrate synthase was the source of a toxic metabolite.

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“…These primers amplify a fragment approximately 1600 bp in size. By using an additional set of four primer pairs (Table 1), 'targeted gene-walking PCR ' (Parker et al, 1991;Chang et al, 2001) was used to amplify further viral RT-PCR products. The general conditions for RT-PCR have been described previously (Liu & Kong, 2004).…”

mentioning

confidence: 99%

Isolation of avian infectious bronchitis coronavirus from domestic peafowl (Pavo cristatus) and teal (Anas)

Liu

Chen

et al. 2005

Journal of General Virology

131

132

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Coronavirus-like viruses, designated peafowl/China/LKQ3/2003 (pf/CH/LKQ3/03) and teal/China/LDT3/2003 (tl/CH/LDT3/03), were isolated from a peafowl and a teal during virological surveillance in Guangdong province, China. Partial genomic sequence analysis showed that these isolates had the S-3-M-5-N gene order that is typical of avian coronaviruses. The spike, membrane and nucleocapsid protein genes of pf/CH/LKQ3/03 had >99 % identity to those of the avian infectious bronchitis coronavirus H120 vaccine strain (Massachusetts serotype) and other Massachusetts serotype isolates. Furthermore, when pf/CH/LKQ3/03 was inoculated experimentally into chickens (specific-pathogen-free), no disease signs were apparent. tl/CH/LDT3/03 had a spike protein gene with 95 % identity to that of a Chinese infectious bronchitis virus (IBV) isolate, although more extensive sequencing revealed the possibility that this strain may have undergone recombination. When inoculated into chickens, tl/CH/LDT3/03 resulted in the death of birds from nephritis. Taken together, this information suggests that pf/CH/LKQ3/03 might be a revertant, attenuated vaccine IBV strain, whereas tl/CH/LDT3/03 is a nephropathogenic field IBV strain, generated through recombination. The replication and non-pathogenic nature of IBV in domestic peafowl and teal under field conditions raises questions as to the role of these hosts as carriers of IBV and the potential that they may have to transmit virus to susceptible chicken populations. INTRODUCTIONCoronaviruses (family Coronaviridae) belong to the order Nidovirales and contain a positive-stranded RNA genome that ranges from 27 to 31 kb in size (Cavanagh, 1997). Members of the family Coronaviridae infect a wide range of hosts and have been classified into three groups on the basis of antigenicity, genome organization and sequence similarity. Usually, coronaviruses infect only their normal target host species. It has, however, been reported that some strains of canine coronavirus and human coronavirus 229E can infect other, non-target species without causing disease (Barlough et al., 1984(Barlough et al., , 1985. The recent emergence of severe acute respiratory syndrome coronavirus (SARSCoV), which has been classified tentatively into group 2, has focused a great deal of interest on this virus family (Holmes, 2003). It was reported that SARS-CoV-like viruses were isolated from Himalayan palm civets (Guan et al., 2003) and ferrets (Mustela furo). Moreover, domestic cats (Felis domesticus) are susceptible to infection by SARSCoV, suggesting that the reservoir for this pathogen might involve a range of animal species (Martina et al., 2003).Infectious bronchitis virus (IBV), together with genetically related coronaviruses of turkey and pheasant, belongs to the group 3 coronaviruses. IBV is a pleomorphic, enveloped virus with club-shaped surface projections (spikes) and a single-stranded, positive-sense RNA genome of >27 kb in length (Boursnell et al., 1987). Upon virus entry into cells, a 39-coterminal nested set of six ...

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Targeted gene walking polymerase chain reaction

Cited by 167 publications

References 13 publications

Assessment of genomic instability in breast cancer and uveal melanoma by random amplified polymorphic DNA analysis

Assessment of genomic instability in breast cancer and uveal melanoma by random amplified polymorphic DNA analysis

Studies of Propionate Toxicity in Salmonella enterica Identify 2-Methylcitrate as a Potent Inhibitor of Cell Growth

Isolation of avian infectious bronchitis coronavirus from domestic peafowl (Pavo cristatus) and teal (Anas)

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