DNA Amplification Fingerprinting Using Very Short Arbitrary Oligonucleotide Primers

Caetano‐Anollés, Gustavo; Bassam, Brant J.; Gresshoff, Peter M.

doi:10.1038/nbt0691-553

Cited by 513 publications

(187 citation statements)

References 32 publications

Supporting

Mentioning

175

Contrasting

Unclassified

Order By: Relevance

“…AFLPs. Amplification fragment length polymorphisms (AFLPs) are DNA fragments with different nucleotide sequences (Caetano-Anolles et al 1991), of which millions of copies have been synthesized (i.e., amplified) via the polymerase chain reaction [(PCR), Mullis et al 1986;Erlich et al 1991]. Only the DNA sequence interval (several thousand nucleotides) between the sites where one or more base pairs (bp) of polynucleotide (15 to 35 bp) or oligonucleotide (2 to 10 bp) primers anneal to a DNA template is so amplified.…”

Section: Dnamentioning

confidence: 99%

Genetic Markers and Plant Genetic Resource Management

Bretting

Widrlechner

1995

Plant Breeding Reviews

137

View full text Add to dashboard Cite

Section: Dnamentioning

confidence: 99%

Genetic Markers and Plant Genetic Resource Management

Bretting

Widrlechner

1995

Plant Breeding Reviews

137

View full text Add to dashboard Cite

“…Gresshoff and colleagues have shown that primers as short as five bases could be used for PCR (2). However, short primers of 5 or 6 bases, while they would occur frequently in the list of interest, would also occur frequently in other RNAs and therefore might not generate any significant selectivity for the mRNAs in our list of interest.…”

Section: Program Design and Resultsmentioning

confidence: 99%

GeneUp: A Program to Select Short PCR Primer Pairs that Occur in Multiple Members of Sequence Lists

et al. 1998

View full text Add to dashboard Cite

A computer program is presented that selects a small set of short primer pairs for PCR to sample all the sequences in a user -specified list of mRNAs. Such primer pairs could be used to increase the probability of sampling mRNAs of particular interest in differential dis INTRODUCTIONThe polymerase chain reaction (PCR) uses specific DNA primers to amplify specific sequences from a complex source of nucleic acids (13). If arbitrarily selected primers are used instead, then a reproducible fingerprint of products can be generated under the appropriate conditions (8,20,21). Arbitrary primers initiate PCR from sites on the template with varying efficiencies depending on the quality of the overall match and with particular regard to the match at the 3 ′ end of the primer. Relatively efficient priming events within a few thousand base pairs and facing each other on opposite strands, lead to PCR-amplifiable products. Products that are the most efficiently primed and most efficiently amplified compete most effectively in the subsequent PCR amplification and are visualized as a fingerprint after gel electrophoresis.This method was first applied to detect polymorphisms among related genomes because differences in primer-binding sites result in differences in the resulting PCR products (21,26). Later, the method was applied to studying differential expression of arbitrarily sampled RNAs (8,20). Differences in a cDNA PCR product derived from two isogenic RNA samples reflected differences in the abundance of the mRNA between the populations.One of the features of the method that could be changed is the arbitrary nature of the sampling. The first efforts to direct PCR fingerprints to particular sequences were applied to genomic DNAs. For example, the rate of detection of polymorphisms in higher eukaryote nuclear DNA could be increased by using primers that target the more polymorphic simple repeats or hyper-mutable methylation sites (25). Primers can also be directed towards sequences that are more frequent in some bacterial genomes (12,22,24,27).PCR with pairs of degenerate primers derived from back translation of conserved amino acid motifs have been widely used for finding new members of gene families (e.g., Reference 3). Similarly, PCR fingerprinting with primers derived from conserved motifs sometimes enriches for genes of interest (4,18,28). Another approach to selecting primers for targeted fingerprinting is to determine which oligonucleotide sequences are common in the list of sequences of interest and determine which pairs of primers will give a significant number of PCR products from these sequences. With the addition of arbitrary 5 ′ tails, these primers can then be used at relatively high stringency to sample sequences from the family of interest; although, other mRNAs could also be sampled by the same primers (9).We present a program to effectively select perfectly matched primer pairs for all or most of the sequences in a list of interest. Primers that match hyper -abundant RNAs are excluded. RATIONALEPre...

show abstract

“…Native B. thuringiensis isolates, retrieved from different locations (Table 1), were subjected to randomly amplifi ed polymorphic DNA (RAPD) marker-based analysis for characterization of their genetic diversity. Recently, various techniques that rely on different nucleic acid pattern and discriminate at genetic level have been developed to gain information about the genetic diversity and genetic relationship between different organisms [5][6][7]. The RAPD markerbased analysis was found to be an easy, quick and reliable technique to assess the diversity of different types of organisms [8,9] and this technology was successfully applied to characterize the genetic diversity in various B. thuringiensis isolates [10].…”

Section: Introductionmentioning

confidence: 99%

Characterization of native Bacillus thuringiensis strains by PCR-RAPD based fingerprinting

2009

View full text Add to dashboard Cite

Seventy isolates of Bacillus thuringiensis were isolated from soil samples collected from cotton fi elds. These isolates were characterized by randomly amplifi ed poylmorphic DNA (RAPD) markers to determine their genetic diversity pattern based on their source of origin. Different random decamer primers were used for RAPD amplifi cation, which generated a total of 1935 fragments; of these 1865 were polymorphic and 68 monomorphic. The primers OPA03, OPA08, OPD14, OPD19, OPD20, OPE17 and OPD19 produced 100% polymorphic fragments, whereas primers OPC06, OPC20 and OPD17 produced 20, 31 and 17 monomorphic fragments, respectively. When the RAPD banding pattern data was subjected to dendrogram construction, the 70 isolates fell into two separate clusters, cluster I and cluster II, which includes 26 and 44 B. thuringiensis isolates, respectively. These two main clusters were further divided into four subclusters at Eucledian distance of 150 and 80% similarity index. All primers showed amplifi cation and indicated the good diversity of B. thuringiensis isolates. The RAPD pattern showed 4-10 bands per isolate, with MWt in the range of 0.4-3.5 Kb and an average of 193.5 fragments were produced per primer. The primer OPE17 was found to be the most discriminatory as it produced 286 polymorphic bands.

show abstract

DNA Amplification Fingerprinting Using Very Short Arbitrary Oligonucleotide Primers

Cited by 513 publications

References 32 publications

Genetic Markers and Plant Genetic Resource Management

Genetic Markers and Plant Genetic Resource Management

GeneUp: A Program to Select Short PCR Primer Pairs that Occur in Multiple Members of Sequence Lists

Characterization of native Bacillus thuringiensis strains by PCR-RAPD based fingerprinting

Contact Info

Product

Resources

About