Investigation of silver nanoparticle assembly following hybridization with different lengths of DNA

Assays involving the controlled assembly of oligonucleotide-functionalised nanoparticles have been widely investigated for the detection of short, specific sequences of DNA. The surface plasmon resonance changes that result from the near-field coupling of the nanoparticles provide a means for investigating formation of these assemblies. For these assays to be effective in practice, there needs to be rapid and efficient hybridisation of the functionalised nanoparticles with target DNA. However, it is known that the hybridisation rate is adversely affected by increased numbers of non-hybridising bases on the target DNA strand. This study investigates the DNA-directed assembly of oligonucleotide-functionalised silver nanoparticles, with the aim of identifying the parameters that will maximise hybridisation efficiency with long target sequences. The study shows that increasing the length of probes from 12 to 24 bases, and orientating them in a tail-to-tail rather than a head-to-tail configuration, results in significantly enhanced hybridisation with a long target sequence. The use of a volume excluding polymer such as dextran sulphate in the buffer also markedly improves hybridisation. This information will prove useful for researchers involved in the design of DNA-mediated nanoparticle assembly assays, particularly for the detection of long sequences of DNA.