Separation, Deposition, and Characterization of Single Stranded DNA on Polymer Coated Surfaces

Abstract

Stony Brook UniversityThe Graduate SchoolDoctoral Defense AnnouncementAbstractSeparation, Deposition, and Characterization of Single Stranded DNA on Polymer Coated SurfacesByEli HooryAnalysis of DNA structure and behavior, up to and including full sequencing of a genome's bases, and of biological processes such as replication, transcription and translation, is essential for an understanding of genetic variation, heritable diseases and the effects of environmental factors. Recently, single-molecule techniques have been developed to study DNA properties in unprecedented detail. For a number of these techniques, controlled adsorption of linearly stretched DNA molecules on surfaces is necessary. In experiments where hybridization of adsorbed molecules to labeled probes is used to determine DNA structure, single-stranded DNA is needed. Conventionally, for long DNA's (up to Mbp), double-stranded DNA is deposited on a surface and denatured in-situ. While successful, this method has several disadvantages. This thesis reports efforts to directly adsorb long single-stranded DNA's out of solution as an alternative strategy. It consists of three parts:1. The Establishment of a simple method using Acridine Orange (AO) staining dye to determine whether DNA's are ss or ds on the surface. The method allows for the assessment of the degree of renaturation during deposition. Incubation of surface-adsorbed DNA in solutions of AO dye in the concentration range of 10-15æM were found to be effective for discriminating between ss and ds DNA based on differences in the fluorescence emission spectra.2. Deposition of ss DNA produced by heat denaturation on polymer-coated surfaces. Lambda DNA (48502bp) was adsorbed by drop evaporation or dipping/extraction on surface out of a buffered solution. The efficiency of deposition was optimized with respect to DNA concentration, buffer type and pH.3. Separation of complimentary single strands of lambda, mono-cut digest and Hind III digest by gel electrophoresis. Using gels in concentrations ranging from 0.4% to 1.4% (weight/volume), electric fields in the range 1-4V/cm in 1x Tris-Acetate-EDTA (TAE) buffer, good strand separation could be obtained. Both DC and pulsed electric fields were used and compared. Following separation, sense and anti-sense strands of lambda DNA were extracted from gels and deposited separately onto surfaces, and length distributions of the isolated molecules were measured by fluorescence microscopy.