Self-Assembling DNA Nanostructures as Platforms for Placement of Fluorophores On Silicon [100]

In this work, chemically modified DNA tiles and self-assembled DNA raft are prepared and studied. The ultimate goal of this work is a chemical derivatization of pyrene and Tamra-dT tagged deoxyuridine and development of fluorescent labeled oligonucleotides, DNA tile, and 4-tile DNA raft. Understanding characteristics and structure of fluorescent labeled DNA raft will accelerate a study of DNA raft modification. DNA tile consists of 4 oligonucleotides and each of 3 oligonucleotides contains 1 fluorescent labeled deoxyuridines respectively. Each 4 DNA tiles are designed to contain 2 sticky ends, which make it possible to connect each other constructing 4-tile DNA raft. The size of modified DNA raft is 8ÌÄ' 37ÌÄ' 2nm and it is verified by tapping mode AFM imaging on mica. Comparing with bare mica, the fluorescence of modified DNA raft was highly intensed enough to be checked by the Fluorescent Microscope. Before annealing the DNA raft, purities of oligonucleotides and the DNA tile were checked by Agarose and Polyacrylamide gel electrophoresis respectively. To prepare fluorescent labeled deoxyuridines, pyrene moiety is coupled to 5-Iodo-2Ì¢‰âÂå_-deoxyuridine using sonogashira reactions and click chemistry. After an attachment of DMT (dimethoxytrityl) protecting group on 5' hydroxyl position of deoxyuridine, phosphoramidite group is attached to 3' hydroxyl group. Tamra-dT labeled oligonucleotides were purchased from Midland Certified Reagent Company Inc. to compare the properties of Tamra-dT modified DNA raft with pyrene attached DNA raft. This comparative study is useful to understand two fluorophores, which have different ranges of excitation wavelength. Pyrene has 330nm and Tamra-dT has 580nm of emission wavelength. 0.001mM of DNA tile is prepared from 4 oligonucleotides by thermal controller, which was programmed to increase the temperature to 90Ìâå¡C rapidly and to drop 1Ìâå¡C every 6 minutes until it reaches to 20Ìâå¡C. After annealing DNA tile and raft, DNA structure possibly denatured at a certain temperature, which is melting point. Therefore, DNA melting point experiment is required to keep the desirable structure for the DNA tile and raft from high temperature. Melting point experiment and a FRET (Fluorescence Resonance Energy Transfer) study was also conducted for better understanding of fluorescent tagged DNA raft.