Synthesis and Characterization of DNA- Dendrimer Building Blocks for the Creation of DNA-based Nanostructures Shiping Fang, Hye Jin Lee, Ming Li, Richard M. Crooks and Robert M. Corn June 23, 2003 Summarized by Ji-Yoon Park Synthesis and Characterization of DNA- Dendrimer Building Blocks for the Creation of DNA-based Nanostructures Shiping Fang, Hye Jin Lee, Ming Li, Richard M. Crooks and Robert M. Corn June 23, 2003 Summarized by Ji-Yoon Park

APRL APRL June 23, 2003 n Goal: Directed assembly of surface nanostructure n 2 DNA-dendrimer conjugates and the adsorption of DNA-based building blocks onto chemically modified gold surface n 2 Type of poly dendrimer: n 2 Type of poly dendrimer: PAMAM-NH 2, PAMAM-COOH n SPR(Surface Plasma Resonance) Imaging n by hybridization onto ssDNA microarray on gold film n To monitor the formation of DNA-dendrimer monolayer by hybridization onto ssDNA microarray on gold film n DNA-dendrimer conjugate: 4~7 times higher signal than oligomer n For the creation of 2-D and 3-D DNA-based nanostructures by programmable self-assembly process Abstract

APRL APRL June 23, 2003 Snowflakes and Dendrimers

APRL APRL June 23, 2003 Dendrimers  Dendrimers have a branchlike structure  Highly branched molecules that combine the properties of polymers as well as small discrete molecules

APRL APRL June 23, 2003 Convergent dendrimer synthesis Jean Frechet Science 263, 1710 (1994) The generation 1 fragments (G-1) react with the OH groups on the monomer that are directly attached to the aromatic ring. This creates a G-2 fragment. The OH group is replaced with Br so that the G-2 fragments can be attached to another monomer to make G-3. After G-3 is made, the process is repeated to make G-4.

APRL APRL June 23, 2003 Finishing the dendrimer A complete dendrimer is made by attaching fragments that have a reactive focal point. The two fragments do not have to be the same. For example, a fragment with a hydrophilic surface can be attached to a fragment with a hydrophobic surface to make an amphiphilic dendrimer that will be oriented at a water-oil interface.

APRL APRL June 23, 2003 Control of interaction by dendrimer branching

APRL APRL June 23, 2003 n Synthesis of DNA-PAMAM-NH conjugates n Synthesis of DNA-PAMAM-NH 2 conjugates n Ninhydrin & Ellman’s test n Characterization of the amount of DNA attached to the PAMAM-NH 2 n Synthesis of DNA-PAMAM-COOH n DNA array fabrication n SPR imaging Experimental Procedure

APRL APRL June 23, 2003 The Attachment of ssDNA on PAMAM-NH 2 PAMAM-NH 2 + ester group of SSMCC (Fig. 1) → maleimide + thiol-modified DNA → covalent link n n The amount of DNA attached to the PAMAM-NH 2 n Ninhydrin & Ellman’s test n Different ratio of SSMCC to dendrimer; 30: 1 n The number of DNA attached to each dendrimer

APRL APRL June 23, 2003 Monitoring of DNA-PAMAM-NH 2 Adsorption n SPR difference image (Fig. 2) n n Complementary 31mer DNA n n DNA-PAMAM-NH 2 n Hybridize to the two-component DNA array - DNA 1: complementary seq of ssDNA-dendrimer - DNA 2: 8-base mismatch to DNA 1 seq n n SPR signal n DNA-dendrimer(> 7 times higher) > complem. DNA

APRL APRL June 23, 2003 Electrostatic interaction between DNA and dendrimer n UV-vis absorption spectrum (Fig. 3) n n PAMAM-NH2, DNA, and mixed DNA & dendrimer (Fig. 3a) n n Mixed solution n Strong electrostatic interaction n n PAMAM-COOH, DNA, and mixed DNA & dendrimer (Fig. 3b) n n No electrostatic attraction n COOH-terminated dendrimer n Less elctrostatic interation near neutral pH

APRL APRL June 23, 2003 Monitoring of DNA-PAMAM-COOH Adsorption n SPR difference image (Fig. 4) n n Complementary 31mer DNA n n DNA-PAMAM-COOH n Hybridize to the two-component DNA array - DNA 1: complementary seq of ssDNA-dendrimer - DNA 2: control DNA n n SPR signal n DNA-dendrimer(> 4 times higher) > complem. DNA n n Much lower nonspecific adsorption on the control DNA array compared to DNA-PAMAM-NH 2 conjugate

APRL APRL June 23, 2003 Dendrimer: Summary Dendrimer: Summary Highly branched molecules-like snowflakes Surface defines processing Molecular “lego” Synthetic route for DNA-dendrimer conjugates by covalent linking