Thin film micro arrays with immobilized DNA for hybridization analysis

Covalent immobilization of DNA and hybridization on microchips by microsecond electric field pulses

Single square voltage pulses were used to enhance by 7 and 9 orders of magnitude the rate of covalent immobilization and hybridization, respectively, of single stranded DNA probes on a chemically functionalized thin film surface (silicon dioxide) using 2 mm size electrodes. These electrodes were scaled down to 20 μm. Photolithography was used to define the electrode voltage line, ground line, and functionalized thin-film area on a plastic substrate (polyimide). At all electrode dimensions, electric field-assisted DNA immobilization and hybridization can be achieved in the microsecond time scale, far faster than the 2 hr or 16 hr needed for immobilization and hybridization, respectively, without the electric field. Pulse conditions optimized with the large-size electrodes (2 mm) were used in the microelectrodes.

Single base mismatch detection by microsecond voltage pulses

A single square voltage pulse applied to metal electrodes underneath a silicon dioxide film upon which DNA probes are immobilized allows the discrimination of DNA targets with a single base mismatch during hybridization. Pulse duration, magnitude and slew rate of the voltage pulse are all key factors controlling the rates of electric field assisted hybridization. Although pulses with 1 V, lasting less than 1 ms and with a rise/fall times of 4.5 ns led to maximum hybridization of fully complementary strands, lack of stringency did not allow the discrimination of single base mismatches. However, by choosing pulse conditions that are slightly off the optimum, the selectivity for discriminating single base mismatches could be improved up to a factor approximately 5 when the mismatch was in the middle of the strand and up to approximately 1.5 when the mismatch was on the 5'-end and. These results demonstrate that hybridization with the appropriate electric field pulse provides a new, site-specific, approach to the discrimination of single nucleotide polymorphisms in the sub-millisecond time scale, for addressable DNA microarrays.

Electric-field assisted immobilization and hybridization of DNA oligomers on thin-film microchips

Single, square voltage pulses in the microsecond timescale result in selective 5'-end covalent bonding (immobilization) of thiolated single-stranded (ss) DNA probes to a modified silicon dioxide flat surface and in specific hybridization of ssDNA targets to the immobilized probe. Immobilization and hybridization rates using microsecond voltage pulses at or below 1 V are at least 10(8) times faster than in the passive control reactions performed without electric field (E), and can be achieved with at least three differently functionalized thin-film surfaces on plastic or glass substrates. The systematic study of the effect of DNA probe and target concentrations, of DNA probe and target length, and the application of asymmetric pulses on E-assisted DNA immobilization and hybridization showed that: (1) the rapidly rising edge of the pulse is most critical to the E-assisted processes, but the duration of the pulse is also important; (2) E-assisted immobilization and hybridization can be performed with micrometre-sized pixels, proving the potential for use on microelectronic length scales, and the applied voltage can be scaled down together with the electrode spacing to as low as 25 mV; and (3) longer DNA chains reduce the yield in the E-assisted immobilization and hybridization because the density of physisorbed single-stranded DNA is reduced. The results show that the E-induced reactions can be used as a general method in DNA microarrays to produce high-density DNA chips (E-immobilization) and speed the microarray-based analysis (E-hybridization).

Immobilization and hybridization by single sub-millisecond electric field pulses, for pixel-addressed DNA microarrays

Single square voltage pulses applied to buried electrodes result in dramatic rate increases for (1) selective covalent bonding (immobilization) of single-stranded DNA (ssDNA) probes to a functionalized thin film SiO(2) surface on a plastic substrate and (2) hybridization of ssDNA to the immobilized probe. DNA immobilization and hybridization times are 100 ns and 10 micros, respectively, about 10(9) times faster than the corresponding passive reactions without electric field. Surface coverage is comparable. Duration, magnitude and slew rate of the voltage pulse are all key factors controlling the rates of ssDNA immobilization and hybridization. With rise times of 4.5 ns, pulses shorter than 1 ms and voltages below 1V are effective. The ssDNA adsorbed on the surface is reoriented by the rapidly changing electric field. This reduces steric barriers and speeds the immobilization and hybridization reactions. These results open the way for pixel-addressed microarrays driven by silicon microelectronics circuits.