Application of microarrays for single nucleotide polymorphims (SNPs) has a limited appeal currently due to low
reliability of experimental results. Theoretical and experimental studies of surface hybridization of heterozygous
samples allow us to identify two factors of observed instabilities. First, reactions may not reach thermodynamic
equilibrium in the course of the experiment and second, competitive displacement of low affinity species by
high affinity species is the mechanism defining specificity of molecular recognition. Here we describe a real time
optical detection arrangement that facilitated the detection of competitive displacement between a wild-type
target and a SNP target. Results show that even when the SNP is an order of magnitude lower in concentration
(100 pM) then the wild-type target, the kinetics of the SNP hybridization affects hybridization of the wild-type
target. Additionally, results show that observed binding kinetics can be altered by adjusting the concentration
of the SNP without changing the concentration of the wild-type target. These results have significance when
considering what needs to be accounted for when analyzing real time hybridization data.
Microarray analysis has become increasingly complex due to the growing size of arrays. In this work we explore the effects that temperature and SNP, mismatch, concentration have on the dynamic range of detection in a two component system. A finite element software is used to simulate the mass transport of DNA through a microfluidic chamber to the sensing surface where hybridization of DNA is modeled using the corresponding kinetic equation. We compare the theoretical maximum dynamic range with those from simulations when the match target is 90% of its equilibrium value. Results show that even though the maximum dyamic range decreases as temperature increases the observed dynamic range at 90% match equilibrium grows.
Microarray analysis has become increasingly complex due to the growing size of arrays. In this work we explore the effects of diffusion and convective fluxes on the time of hybridization and sensing specificity in a single component system. A .nite element software is used to simulate the diffusion of DNA through a microfluidic chamber to the sensing surface where hybridization of DNA is modeled using the corresponding kinetic equation. The differences between diffusion controlled and convection controlled mass transport are investigated as a function of concentration and hybridization time. Hybridization enhancement produced by microfluidics versus stationary diffusion is introduced as a useful metrics for quantitation of mass transport effects.
With the goal of a portable diagnostic system in mind, we have designed a disposable platform for DNA detection. Surface micromachining using the SwIFT process at Sandia National Laboratories was used to make the new device, combining a waveguide, grating optics, heating structures, on-chip pumping, and microfluidics in a disposable package. PDMS microfluidic channels are integrated with the surface micromachined device to enable higher flow rates and added fluid complexity. Work on DNA hybridization under flow is presented, as applies to the function of the sensor. A description of the platform covering heating of the waveguide surface, laser coupling into the waveguide using grating optics, attachment chemistry for the sensor surface, and sealing of the PDMS microfluidic system to the device is given.