Novel technology detects human DNA mutations

Rapid enzyme-free platform allows robust gene identification without gene amplification

Researchers at Nanosphere, Inc. today reported unprecedented benefits in the company’s technology for the medical analysis of human DNA.

Nanosphere’s nanoparticle-based technology allows for rapid, highly-sensitive and specific Single Nucleotide Polymorphism (SNP) genotyping, which is the direct detection of a particular gene and the extent to which it is normal or mutated. The technology, reported in the February 2005 (Volume 33, Number 2), issue of Nucleic Acids Research, allows detection of a SNP in an unknown genotype with a greater than 99 percent confidence threshold and can be used with human DNA obtained from samples as small as a drop of blood. Importantly, the technology eliminates the need for costly, time and labor intensive gene amplification or enzymatic interventions – two widespread methods currently used to perform such analyses.

“Nanosphere’s new SNP analysis methodology for whole genomic human DNA is a powerful example of the versatility of our proprietary ClearReadTM nanoparticle technology,” said William Moffitt, Nanosphere’s President and CEO. “This study and the use of nanoparticles to dramatically increase sensitivity in our other proprietary applications — such as bio-barcode for ultra sensitive detection of proteins — demonstrate the broad applicability of nanotechnology and its potential to markedly advance the state-of-the-art in nucleic acid and proteomic research and diagnostics.”

The analysis of whole human genomic DNA is extraordinarily complex as it requires sifting through the more than one billion base pairs of DNA to find a particular base pair of interest. Once that base pair is located, it is then necessary to determine if either of the bases is mutated (i.e., has SNPs). Nanosphere’s technology can rapidly, easily, and accurately interrogate both bases in the pair to determine if they are homozygous (i.e., both are mutant or normal) or heterozygous (i.e., one is mutant, one is normal) – the most critical step in correlating the SNP with a disease or drug sensitivity.

To do so, Nanosphere scientists employ a two-step process called ClearReadTM technology. This method sandwiches a target DNA SNP segment between two oligonucleotide sequences to greatly increase detection specificity and sensitivity. One segment identifies any mutations in the DNA and the probe, a highly sensitive gold nanoparticle, creates a strong signal accurately indicating the presence of a specific target SNP. Proof of principle, reproducibility, and the robust, simple and rapid characteristics of this technology were demonstrated with unamplified DNA samples representing all possible forms of three genes implicated in hypercoagulation disorders.