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), 6810 -6811(2002) MEC Seminar 10/18/02 Summarized by Park, Ji-Yoon

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

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, 8044-8051(1999)

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

Molecular Design of a Ligand(1-4) Nature Biotechnology 19, 51 - 55 (2001) (A) Structures of naphthyridine dimers 1 and 2 (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)

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.

Tm of the mismatch-containing duplex(3)

Complete DNA Sequence Used in this study

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; 250 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

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

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