Rapid, high fidelity analysis of simple sequence repeats on an electronically active DNA microchip

Abstract

We describe a method for the discrimination of short tandem repeat (STR) alleles based on active microarray hybridization. An essential factor in this method is electronic hybridization of the target DNA, at high stringency, in <5 min. High stringency is critical to avoid slippage of hybrids along repeat tracts at allelespecific test sites in the array. These conditions are attainable only with hybridization kinetics realized by electronic concentration of DNA. A sandwich hybrid is assembled, in which proper base stacking of juxtaposed terminal nucleotides results in a thermodynamically favored complex. The increased stability of this complex relative to non-stacked termini and/or base pair mismatches is used to determine the identification of STR alleles. This method is capable of simultaneous and precise identification of alleles containing different numbers of repeats, as well as mutations within these repeats. Given the throughput capabilities of microarrays our system has the potential to enhance the use of microsatellites in forensic criminology, diagnostics and genetic mapping.

Detection of Biological Toxins on an Active Electronic Microchip

“…We are interested in developing methods and instrumentation that facilitate the analysis of molecular biological and biochemical samples in both research and diagnostic settings, based on our NanoChip technology. This technology applies free-space electrophoresis to move chemical species around with high efficiency on an active electronic microchip for biomolecule analysis (1,4,6,15,16,(21)(22)(23)(24).…”

Antimicrobial Resistance and Bacterial Identification Utilizing a Microelectronic Chip Array

“…Achieving amplification of and discrimination between very similar DNA targets is difficult to accomplish with a single-platform assay. We took advantage of base-stacking energy transfer techniques to assist in reporter discrimination of SNPs (14,17,23). Amplification primers were designed sur-FIG.…”

“…Base-stacking reporters were used such that the 5Ј end of the labeled reporter would base stack alongside a longer stabilizer oligonucleotide (14,17,23). If the amplified target presented a perfect match to the labeled reporter, then the base-stacking energies between the stabilizer oligonucleotide and the labeled reporter would be favorable, allowing the shorter reporter to remain hybridized to the amplified target at elevated temperatures.…”

Electrophoresis of DNA in human genetic diagnostics – state‐of‐the‐art, alternatives and future prospects

“…Therefore, efficient protocols using sometimes complex chemical and/or thermal conditions to promote highstringency hybridization are needed. Further advanced methods are used to overcome these problems by applying active electronic hybridization of the target DNA [56]. Yet, such approaches have so far not found their way into routine diagnostics in most laboratories.…”