The researchers from Northwestern University, US used DNA-modified gold nanoparticles to develop the microarray assay that can discriminate between strong, intermediate and weak duplex and triplex DNA binders in a high-throughput manner.

The device, described in an early view article in the journal Analytical Chemistry , measures the change in melting temperature of the DNA strands immobilised on the gold nanoparticles upon binding on duplex or triplex DNA binding molecules.

The 'melting temperature' of a DNA duplex is defined as the temperature at which half of the double strands are separated into single strands.

Many anticancer drugs, doxorubicine, daunorubicin and amsacrine are known to intercalate between the two strands of DNA and stop the enzyme topoisomerase II from unwinding the DNA prior to transcription, preventing the DNA replication process and the formation of new cancerous cells.

"Triplex binders are also promising drug candidates… [and] in conjunction with triplex forming oligonucleotides could potentially be used to achieve control of gene expression by interfering with transcription factors that bind to DNA," write the authors.

DNA functionalised gold nanoparticles exhibit intense optical properties that can be used to monitor the melting temperature of the immobilised DNA and this has been used in a variety of applications.

"Since DNA-functionalised gold nanoparticles have such an intense optical signature, one can work at higher ratios of potential binder : probe DNA, which leads to larger absolute changes in the DNA melting temperature compared with conventional UV-vis approaches," write the authors.

The researchers first took a glass chip and arrayed it with synthetic alkylamine-functionalised oligonucleotides to which the gold nanoparticles, functionalised with a complimentary DNA sequence are hybridised.

A sample holder containing aqueous solutions of different potential binders is then placed on the chip to allow the binders to hybridise with the DNA.

The probes are then developed with a silver enhancement solution to increase the size and light scattering of the nanoparticles which is then measured using a Nanosphere Verigene ID scanner.

To determine how strong the binders are, the incubation process is carried out under a range of conditions that require the DNA binders to increase the hybridisation strength and keep the gold nanoparticles attached to the chip.

According to the authors, the dehybridisation of the nanoparticles from the chip directly correlates with a reduction of signal after silver enhancement allowing the measurement of the relative duplex (or triplex) binding strengths of various binding molecules.

"Generally, the strength of binding between drug and target molecule correlates with the drug's biological activity, and therefore, it is important to obtain a quantitative measure of the difference in binding capabilities of the molecules that make up a particular library," the authors write.