Deoxyribonucleic acid hybridization : fundamental studies and applications in directed assembly

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 2005.Includes bibliographical references.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.(cont.) A target in nanotechnology is the generation of larger functional units from smaller nanoscale objects. Using a mixed silane chemistry, the DNA-directed assembly of gold nanoparticles was investigated on surfaces with different probe densities. Gold nanoparticles could be assembled at a dense coverage of [approx.] 28% corresponding to a density of [approx.] 1070 particles/[mu]m². As with DNA-DNA hybridization, particle coverage was reduced at high probe densities due to strong steric and electrostatic hindrances. Non-specific adsorption-crucial for the creation of defect-free assembled devices-was three orders of magnitude lower than the specific adsorption of nanoparticles demonstrating the effectiveness of the surface chemistry in blocking extraneous particle-substrate interactions. The effect of probe density on the thermodynamics of nanoparticle adsorption was found to be fundamentally different than that on the thermodynamics of molecular DNA adsorption due to the multivalent nature of nanoparticle attachment. Asymmetric building blocks can substantially broaden the creation of novel self- assembled devices because of their morphological and/or chemical asymmetry. In this thesis, DNA-based recognition was employed to achieve orthogonal self-assembly on asymmetric microspheres. Dual-functional microspheres with two different DNA sequences were made by a shadow deposition of gold onto silica microspheres in conjunction with DNA immobilization procedures using thiol and silane chemistries. The prepared microspheres were used as templates for the selective orthogonal assembly of fluorophore-tagged target oligonucleotides and for the regiospecific assembly of nanoparticles of two different sizes.(cont.) The selective attachment of nanoparticles and DNA molecules onto different specified regions of the building block was achieved solely by the sequence complementarity of the various components. Extending the shadow deposition technique a step further, tri-functional particles were formed by the shadow deposition of gold and aluminum. After functionalizing the silica and gold surfaces with two different DNA sequences and passivating the aluminum surface with stearic acid, an orthogonal assembly of DNA molecules was successfully performed within specified regions on these tri- functional particles. The flexibility for specifying the regio-selective attachment of DNA molecules and nanoparticles onto these building block objects will be important for the modular creation of a variety of novel self-assembled devices. In order to expand the assembly to other asymmetric structures and to understand the effect of shape on DNA-mediated attachment, microrods were selectively assembled via DNA- DNA interactions on complementary surfaces. Because of the weak nature of the DNA-DNA interactions, a large contact area between the building block and substrate-as made possible by the microrod geometry-was essential in ensuring robust assembly. Further, dual-functional microrods were prepared by a shadow deposition of gold and could be assembled on flat surfaces in an orientation-specific manner highlighting another advantage of DNA-directed assembly beyond regiospecificity.(cont.) In essence, employing DNA as the linker molecule and a robust chemistry for DNA attachment, asymmetric multi-functional particles were assembled into novel configurations, which would be difficult to realize using symmetrical building blocks. This programmable self-assembly approach exploits the multiplicity and specificity of DNA-DNA interactions and provides a powerful strategy for the generation of novel l-D, 2-D, and 3-D functional devices.by Manish G. Bajaj.Ph.D