Certain chemical pollutants can imitate hormones produced naturally in the body; bisphenol-A, for example, can mimic estrogen. Because estrogen can pass directly through cell walls to influence the transfer of genetic information, measuring changes in hormone activity with DNA-level accuracy is critically important.
Xiaodi Su from the Institute of Material Research and Engineering, Edison Liu from the Genome Institute of Singapore and co-workers from these A*STAR institutes in Singapore have now developed an assay that instantly measures binding interactions between estrogen receptor proteins and specific DNA sequences. This approach can detect single mutations in DNA strands as distinct color changes thanks to the optical capabilities of gold nanoparticles.
When hormone receptor proteins capture estrogen molecules that have entered the cell, the receptors move to the nucleus and regulate gene expression by binding to DNA sequences called estrogen response elements. Small changes in the nucleotide composition of these DNA strands can greatly affect transcription rates, but detecting sequence-dependent interactions currently requires time-consuming labeling and separation techniques, or complex instrumentation.
The method developed by Su and her co-workers uses the well-known aggregation behavior of gold nanoparticles to allow rapid identification of estrogen protein–DNA interactions by the naked eye. Gold nanoparticles have a rich supply of electrons oscillating at their surfaces, and when clustered together they appear differently colored than when dispersed in solution. Mixing biomolecules into gold nanoparticle solutions can strongly influence aggregation, factors the researchers exploited to create their assay.
Initially, the researchers’ gold nanoparticles were coated with charged molecules that prevented aggregation through electrostatic forces. Each component of the hormonal system — receptor proteins, DNA response elements and the protein–DNA complex — triggered a unique color change, from red to purple to blue, when added to the nanoparticles in the presence of a salt (Fig. 1). Every biomolecule caused different degrees of nanoparticle association; aggregation was most obstructed by the bulky receptor–response complex, while small DNA chains had little effect on clustering.
This assay proved to be sensitive enough to distinguish single base substitutions in the DNA receptor elements as different colors. The researchers attribute this finding to slight changes in stability for complexes between receptor proteins and mutant DNA; the resulting concentration differences modify the amount of nanoparticle aggregation.
The high-throughput potential and simplicity of this sensing technique should enable accurate analysis of numerous biomolecular systems, according to Su. “This concept can be adopted to study interactions between transcription factors and DNA, and to detect a wider range of transcription factors and other nontranscription proteins,” she says.