1. Chemically Induced Hairpin Formation in DNA Monolayers
Emily A. Smith, Motoki Kyo, Hiroyuki Kumasawa, Kazuhiko Nakatani, Isao Saito, and Robert M. Corn* J. Am. Chem. Soc., 124 (24), (2002)
MEC Seminar
10/18/02
Summarized by Park, Ji-Yoon

2. Abstract A naphthyridine dimer binds specifically to G-G mismatches
Induce hairpin formation in oligonucleotides immobilized onto chemically modified gold surfaces
SPR imaging measurements
Binding of the naphthyridine dimer to G-G mismatches within the stem portion of an immobilized 42-mer oligonucleotide

3. Previous Study by Robert M.Corn
Surface Plasmon Resonance Imaging Measurements of DNA and RNA Hybridization Adsorption onto DNA Microarrays Anal. Chem. 73 (1), 1 -7(2001)
Surface plasmon resonance imaging measurements of ultrathin organic films Annu. Rev. Phys. Chem. 51, 41-63(2000)
The procedure used for constructing DNA microarrays on gold surfaces has been previously reported J. Am. Chem. Soc. 121, (1999)

4. Structure of the G-G Mismatch
Scheme 1. Structure of the G-G Mismatch Stabilizing Naphthyridine Dimer

5. Molecular Design of a Ligand(1-4) Nature Biotechnology 19, 51 - 55 (2001)
(A) Structures of naphthyridine dimers 1 and (green), and hydrogen-bonding pattern to guanine (red) (B) An illustration of duplex containing a G-G mismatch
(C) Hypothetical structure of the G-G mismatch regarded as two consecutive guanine bulges
(D) A proposed binding model for ligand 1 to the G-G mismatch (E) Molecular models of the simulated complex of ligand 1 and DNA containing the G-G mismatch viewed from the major groove side (left) and the minor groove side (right)

6. SPR Assay by a Sensor Chip(2) Nature Biotechnology 19, 51 - 55 (2001)
(A) The angle for a reflection of a polarized light would be changed as a binding of DNAs to the sensor surface.
(B) The change of the angle is computed to the change of response unit (RU) and plotted against time.

7. Tm of the mismatch-containing duplex(3)

8. Complete DNA Sequence Used in this study

9. Fig 1. SPR difference image of a four-complement DNA array
SPR difference image of a four-component DNA array
(a) Surface-bound 11-mer DNA sequence (b) SPR imaging measurement Each immobilized oligonucleotide differs by one base
- The image condition; M naphthyridine dimer with 1 uM DNA complement Perfect match & the G-G mismatch
Fig 1. SPR difference image of a four-complement DNA array

10. How “Chemically induced” Hairpins
Surface-bound DNA sequence (X , Y; 18 mers)
Complementary to the sequence of an 18-mer probe (Z)
Flanking regions - act as the stem of a hairpin
Sequence “ Y” forms a hairpin structure in the presence of Naphthyridine dimer
Scheme 2. Schematic representation of the oligonucleotides used in Fig 2

11. SPR difference images of a two-component DNA array
(a) In the absence of the dimer
- hybridization adsorption is observed to both X and Y - no hairpin formation in sequence Y
(b) Exposure to the naphthyridine dimer - Increase in reflectivity only for sequence Y - Hairpin formation
(c) After the subsequent exposure of the surface to the complement molecule Z - hybridization adsorption is only observed to the sequence X element
Fig 2. SPR difference images of a two-component DNA array obtained from the SPR image before and after