*** PhD defense for Marc Glazer - this Friday, 1:00 **

Marc Irving Glazer mglazer at stanford.edu
Mon Feb 25 16:18:13 PST 2002

"Colloidal Silica Films for High-Capacity DNA arrays"

PhD defense for Marc Glazer -
Stanford depts. of Materials Science and Chemical Engineering
in collaboration with Affymetrix, Inc.

will be held in *** CISX auditorium, Friday, March 1st, 1pm***


Colloidal Silica Films for High-Capacity DNA Arrays

The human genome project has greatly expanded the amount of genetic
information available to researchers, but before this vast new source of
data can be fully utilized, techniques for rapid, large-scale analysis of
DNA and RNA must continue to develop.  DNA arrays have emerged as a
powerful new technology for analyzing genomic samples in a highly parallel
format.  The detection sensitivity of these arrays depends on the quantity
and density of immobilized probe molecules, as well as on the
thermodynamics and kinetics of nucleic acid hybridization.  We have
prepared and investigated substrates with a porous, "three-dimensional"
surface layer as a means of increasing the surface area available for the
synthesis of oligonucleotide probes, thereby increasing the number of
available probes and the amount of detectable bound target per unit area.

Porous films were created by two techniques.  In the first approach, films
were deposited by spin-coating silica colloid suspensions onto flat glass
substrates, with the pores being formed by the natural voids between the
solid particles.  The resulting films have relatively small pores (23nm)
and low porosity (35%).  In the second approach, latex particles were
co-deposited with the silica and then pyrolyzed, creating films with
larger pores (36nm), higher porosity (65%), and higher surface area.  For
0.3 micron films, a 10-fold enhancement was achieved with the pure silica
films, and 15-fold with the films "templated" with polymer latex.

Having demonstrated the effectiveness of the high-capacity films, we next
investigated the kinetics of hybridization on these substrates.
Adsorption of DNA onto the high-capacity films is controlled by
traditional adsorption (ka) and desorption (kd) coefficients, as well as
morphology factors and transient binding interactions between the target
and the probes.  To describe these effects, we have developed a model
analogous to diffusion of a reactant in a porous catalyst.  We show that
the strength of the transient probe/target binding interactions are on the
order of 5-7 DNA base pairs, which suggests the formation of nucleation or
other metastable complexes, rather than fully-zippered duplexes.

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