DNA hybridization : fundamental studies and applications in directed assembly

Programmed self-assembly using non-covalent DNA-DNA interactions is a promising technique for the creation of next-generation functional devices for electronic, optical, and magnetic applications. This thesis develops the ability to tailor surfaces for the DNA-driven assembly of molecular, nano-, and micron-sized objects. Specifically, DNA hybridization was employed to direct the regiospecific assembly of DNA molecules onto substrates and in the targeted assembly of supraparticulate structures from nanoparticles and microparticles that express DNA molecules on their surfaces. These studies provide fundamental information needed for deploying a programmable process for the 'bottom-up' assembly of smaller species into large aggregates. DNA-based assembly spans areas of molecular biology and nanotechnology. In the former area, DNA microarrays have become a standard tool for gene expression analysis. In spite of the large number of studies that employ DNA microarrays, fundamental aspects of DNA hybridization on these platforms have been largely unexplored. In this thesis, the effects of immobilized probe density on DNA hybridization were examined by employing a mixed silane chemistry to systematically control the density of immobilized probe DNA strands (0.2 x 10¹³ probes/cm² to 5.2 x 10¹³ probes/cm²) on glass surfaces. The surface density of the immobilized species was found to significantly affect the hybridization yields; the equilibrium dsDNA amounts being highest on surfaces with ss-DNA probe densities corresponding to average inter- strand distances of 18 [Angstroms]. The strong effects of surface probe density on hybridization performance indicate that it can be a useful parameter for improving the signal-to-noise ratios for assays performed on microarrays.

Department dc:contributor.department

Massachusetts Institute of Technology. Dept. of Chemical Engineering.

Grantor dc:publisher

Massachusetts Institute of Technology

Year dc:date.issued

2005

Author dc:creator

• Bajaj, Manish G. (Manish Gopal)

Advisor dc:contributor.advisor

• Paul E. Laibinis and Gregory Stephanopoulos.

• Chemical Engineering.

Statement dc:rights

• M.I.T. theses are protected by copyright. They may be viewed from this source for any purpose, but reproduction or distribution in any format is prohibited without written permission. See provided URL for inquiries about permission.

Licence dc:rights.uri

• http://dspace.mit.edu/handle/1721.1/7582

Language dc:language.iso

eng

Handle dc:identifier.uri

http://hdl.handle.net/1721.1/32327

OAI identifier oai:identifier

oai:dspace.mit.edu:1721.1/32327