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  • DNA amplification fingerprinting (DAF)  (2)
  • 1
    Electronic Resource
    Electronic Resource
    Primer-template interactions during DNA amplification fingerprinting with single arbitrary oligonucleotides (1992)
    Springer
    Molecular genetics and genomics 235 (1992), S. 157-165 
    Details
    ISSN: 1617-4623
    Keywords: DNA amplification fingerprinting (DAF) ; PCR ; Primer-template interactions ; Single oligonucleotide primer
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary DNA amplification fingerprinting (DAF) is the enzymatic amplification of arbitrary stretches of DNA which is directed by very short oligonucleotide primers of arbitrary sequence to generate complex but characteristic DNA fingerprints. To determine the contribution of primer sequence and length to the fingerprint pattern and the effect of primer-template mismatches, DNA was amplified from several sources using sequence-related primers. Primers of varying length, constructed by removing nucleotides from the 5′ terminus, produced unique patterns only when primers were 8 nucleotides or fewer in length. Larger primers produced either identical or related fingerprints, depending on the sequence. Single base changes within this first 8-nucleotide region of the primer significantly altered the spectrum of amplification products, especially at the 3′ terminus. Increasing annealing temperatures from 15° to 70° C during amplification did not shift the boundary of the 8-nucleotide region, but reduced the amplification ability of shorter primers. Our observations define a 3′-terminal oligonucleotide domain that is at least 8 bases in length and largely conditions amplification, but that is modulated by sequences beyond it. Our results indicate that only a fraction of template annealing sites are efficiently amplified during DAF. A model is proposed in which a single primer preferentially amplifies certain products due to competition for annealing sites between primer and terminal hairpin loop structures of the template.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00279356
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  • 2
    Electronic Resource
    Electronic Resource
    Enhanced detection of polymorphic DNA by multiple arbitrary amplicon profiling of endonuclease-digested DNA: identification of markers tightly linked to the supernodulation locus in soybean (1993)
    Springer
    Molecular genetics and genomics 241 (1993), S. 57-64 
    Details
    ISSN: 1617-4623
    Keywords: Amplification fragment length polymorphism ; Arbitrary primers ; DNA amplification fingerprinting (DAF) ; Genetic polymorphism ; Nodulation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Multiple endonuclease digestion of template DNA or amplification products can increase significantly the detection of polymorphic DNA in fingerprints generated by multiple arbitrary amplicon profiling (MAAP). This coupling of endonuclease cleavage and amplification of arbitrary stretches of DNA, directed by short oligonucleotide primers, readily allowed distinction of closely related fungal and bacterial isolates and plant cultivars. MAAP analysis of cleaved template DNA enabled the identification of molecular markers linked to a developmental locus of soybean (Glycine max L. Merrill). Ethyl methane sulfonate (EMS)-induced supernodulating, near-isogenic lines altered in the nts locus, which controls nodule formation, could be distinguished from each other and from the parent cultivar by amplification of template pre-digested with 2–3 restriction enzymes. A total of 42 DNA polymorphisms were detected using only 19 octamer primers. In the absence of digestion, 25 primers failed to differentiate these soybean genotypes. Several polymorphic products co-segregated tightly with the nts locus in F2 families from crosses between the allelic mutants nts382 and nts1007 and the ancestral G. soja Sieb. & Succ. PI468.397. Our results suggest that EMS is capable of inducing extensive DNA alterations, probably around discrete mutational hot-spots. EMS-induced DNA polymorphisms may constitute sequence-tagged markers diagnostic of specific genomic regions.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00280201
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