DIRECT-DETECTION OF NUCLEIC-ACID HYBRIDIZATION ON THE SURFACE OF A CHARGE-COUPLED-DEVICE

A method is described for the detection of DNA hybrids formed on a sol id support, based upon the pairing of oligonucleotide chemistry and th e technologies of electronic microdevice design. Surface matrices have been created in which oligonucleotide probes are covalently linked to a thin SiO2 film. P-32 labeled target nucleic acid is then hybridized to this probe matrix under conditions of high stringency. The salient feature of the method is that to achieve the highest possible collect ion efficiency, the hybridization matrix is placed directly on the sur face of a charge coupled device (CCD), which is used to detect P-32 de cay from hybridized target molecules (1, Eggers, M.D., Hogan, M.E., Re ich, R.K., Lamture, J.B., Beattie, K.L., Hollis, M.A., Ehrilich, D.J., Kosicki, B.B., Shumaker, J.M., Varma, R.S., Burke, B.E., Murphy, A., and Rathman, D.D., (1993), Advances in DNA Sequencing Technology, Proc . SPIE, 1891, 13-26). Two implementations of the technology have been employed. The first involves direct attachment of the matrix to the su rface of a CCD. The second involves attachment of the matrix to a disp osible SiO2 coated chip, which is then placed face to face upon the CC D surface. As can be predicted from this favorable collection geometry and the known characteristics of a CCD, it is found that as measured by the time required to obtain equivalent signal to noise ratios, P-32 detection speed by the direct CCD approach is at least 10 fold greate r than can be obtained with a commercial gas phase array detector, and at least 100 fold greater than when X-ray film is used for P-32 detec tion. Thus, it is shown that excellent quality hybridization signals c an be obtained from a standard hybridization reaction, after only 1 se cond of CCD data acquisition.