We have been exploring the use of light scattering as a means to detect the binding of nucleic acids to high density DNA probe arrays. Initial work has concentrated on the use of 100 nanometer gold particles conjugated to monoclonal antibodies. A probe array scanner that utilizes an arc lamp source and a `photocopier grade' linear CCD detector has been developed. The optical configuration of the scanner maximizes dynamic range and minimizes optical backgrounds. Initial development of light scattering detection for the p53 cancer gene application shows that functional performance may be obtained that is essentially equivalent to existing fluorescence detection methodology.
We have been exploiting high density oligonucleotide arrays to carry out sequence analysis of genetic material from diverse sources. The method utilizes the hybridization of fluorophore labelled nucleic acids to the array and interpretation of the resulting spatial pattern of fluorescence. Our ability to obtain sequence information from the array is governed by the interplay of the synthesis and hybridization chemistry, the photophysics of the fluorophores and background interferences, and the performance of the fluorescence imaging system. The high photolithographic resolution and large usable area of the synthesis process and the presence of submonolayer coverages of fluorophores dictate that the fluorescence detection system meet several potentially conflicting performance criteria. High spatial resolution, high sensitivity, large field of view, low chromaticity and image distortion, and high dynamic range are required simultaneously. Suitable nucleic acid-fluorophore conjugates should have high absorption cross sections and emission quantum yields, low photobleaching quantum yields, and resistance to transient saturation under intense illumination. Our approaches to the design and photophysical characterization of the detection process will be discussed within the context of improving the volume of sequence information and detection limits.