1. 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

2. APRL http://gene.hanyang.ac.kr APRL http://gene.hanyang.ac.kr 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

3. APRL http://gene.hanyang.ac.kr APRL http://gene.hanyang.ac.kr June 23, 2003 Snowflakes and Dendrimers

4. APRL http://gene.hanyang.ac.kr APRL http://gene.hanyang.ac.kr June 23, 2003 Dendrimers  Dendrimers have a branchlike structure  Highly branched molecules that combine the properties of polymers as well as small discrete molecules

5. APRL http://gene.hanyang.ac.kr APRL http://gene.hanyang.ac.kr 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.

6. APRL http://gene.hanyang.ac.kr APRL http://gene.hanyang.ac.kr 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.

7. APRL http://gene.hanyang.ac.kr APRL http://gene.hanyang.ac.kr June 23, 2003 Control of interaction by dendrimer branching

8. APRL http://gene.hanyang.ac.kr APRL http://gene.hanyang.ac.kr 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

9. APRL http://gene.hanyang.ac.kr APRL http://gene.hanyang.ac.kr 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

10. APRL http://gene.hanyang.ac.kr APRL http://gene.hanyang.ac.kr 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

11. APRL http://gene.hanyang.ac.kr APRL http://gene.hanyang.ac.kr 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

12. APRL http://gene.hanyang.ac.kr APRL http://gene.hanyang.ac.kr 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

13. APRL http://gene.hanyang.ac.kr APRL http://gene.hanyang.ac.kr 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