Sensitive and Selective Detection of DNA Fragments Associated with Ganoderma Boninense by DNA-Nanoparticle Conjugate Hybridisation

Abstract

<jats:p>&lt;u&gt;&lt;strong&gt; &lt;/strong&gt;&lt;/u&gt;&lt;p&gt;A colorimetric assay for the detection of DNA fragments associated with the oil palm pathogen Ganoderma boninense is reported, which is based on the aggregation of DNA-nanoparticle conjugated in the presence of complementary DNA from the pathogen. Here, various designs of DNA-nanoparticle conjugates were evaluated, and it was found that the best design gave a visually observable colour change with as little as 2 pmol of double-stranded DNA analyte even in the presence of a large excess of a mixture of non-complementary DNA. The assay was also able to differentiate analyte sequences with three or more single nucleotide mismatches. Overall, this label-free system is rapid, sensitive, selective, simple in design and easy to carry out. It does not require specialist equipment or specialist training for the interpretation of the results and therefore has the potential to be deployed of agricultural diagnostics in the field.&lt;/p&gt;&lt;u&gt;&lt;strong&gt;&lt;/strong&gt;&lt;/u&gt;</jats:p>

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“…The slight difference among M n sequences may result from the mismatch locations and the direct hybridization mechanism. [29] Careful examination shows that monitoring the hybridization kinetics at room temperature can distinguish the SBP mismatch from the positive control sequence without mutations ( Figure 3F ) and provides a potential way to further detect SBP mismatch.…”

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