Investigations on the compatibility of chemically oxidized silicon (SiOx)-surfaces for applications towards chip-based polymerase chain reaction

Several designs of micro-fabricated PCR-chips made in silicon have been developed. Upon miniaturization the surface-to-volume ratio (SVR) increases and therefore, effects related to the non-specific adsorption of Taq DNA polymerase and template DNA to chip-surfaces become significant. To repress the surface-mediated inhibition of these biological macro-molecules: (1) the PCR-compatibility of SiOx-surfaces, (2) the combination of silanization and dynamic coating with BSA on SiOx-surfaces on the PCR-efficiency, and (3) the stability of these surface-passivating films during PCR were investigated off-chip. (4) Finally, on-chip PCR-experiments were carried out under optimized reaction conditions. (CH3)(3)SiCl, (CH2)(2)SiCl2, [(CH3)(3)Si-2]NH and CH3(CH2)(2)SiCl3 were used to passivate SiOx-surfaces. The PCR was performed according to published procedures and the yield of the PCR-products was determined by get electrophoresis analysis. To follow the degradation of the surface-passivating films contact angles were measured. It could be demonstrated that: (1) SiOx-surfaces were an inhibitor of the PCR; (2) the PCR-efficiency of silanized SiOx-surfaces was in the order: CH3(CH2)(2)SiCl3 approximate to (CH3)(2)SiCl2 > CH3SiCl3 > [(CH3)(3)Si-2]NH and the amount of PCR-products was reduced from run to run; (3) the stability of the surface-passivating films resembled the same trend and none of these surfaces were stable for more than three consecutive PCR runs; (4) the specificity and product yield of the on-chip PCR was found to be equivalent to a conventional one, using a (CH3)(2)SiCl2-modified PCR-chip with a power consumption of 2.7 W, heating (cooling) rates of up to 50 K s(-1) (4) and reaction volumes in the range of 1-4 mul. Based on this test configuration the silanization of SiOx-surfaces alone will not be suited for multiple or long-term applications due to the degradation of the surface-passivating films. (C) 2004 Elsevier B.V. All rights reserved.