Chemically Induced Hairpin Chemically Induced Hairpin Formation in DNA MonolayersFormation in DNA Monolayers

MEC Seminar

10/18/02

Summarized by Park, Ji-Yoon

Emily A. Smith,Emily A. Smith, Motoki Kyo,Motoki Kyo, Hiroyuki Kumasawa,Hiroyuki Kumasawa, Kazuhiko Nakatani,Kazuhiko Nakatani, Isao Saito, and Robert M. Corn*Isao Saito, and Robert M. Corn*

J. Am. Chem. Soc., J. Am. Chem. Soc., 124 (24),124 (24), 6810 -6811(2002)6810 -6811(2002)

Abstract

A naphthyridine dimer binds specifically to G-G A naphthyridine dimer binds specifically to G-G mismatchesmismatches Induce hairpin formation in oligonucleotides immobilized onto

chemically modified gold surfaces

SPR imaging measurementsSPR 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 Surface Plasmon Resonance Imaging Measurements of DNA and

RNA Hybridization Adsorption onto DNA MicroarraysRNA Hybridization Adsorption onto DNA Microarrays - Anal. Chem.Anal. Chem. 73 (1), 1 -7(2001 73 (1), 1 -7(2001)

Surface plasmon resonance imaging measurements of ultrathin organic Surface plasmon resonance imaging measurements of ultrathin organic filmsfilms - - Annu. Rev. Phys. Chem.Annu. Rev. Phys. Chem. 51, 41-63(2000) 51, 41-63(2000)

The procedure used for constructing DNA microarrays on gold The procedure used for constructing DNA microarrays on gold surfaces has been previously reportedsurfaces has been previously reported - - J. Am. Chem. Soc.J. Am. Chem. Soc. 121, 8044-8051(1999) 121, 8044-8051(1999)

Structure of the G-G Mismatch

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

Molecular Design of a Ligand(1-4)Nature BiotechnologyNature Biotechnology 19, 51 - 55 (2001) 19, 51 - 55 (2001)

(A) Structures of naphthyridine dimers(A) Structures of naphthyridine dimers 1 and 21 and 2 (green), and hydrogen-bonding pattern to hydrogen-bonding pattern to guanine guanine (red)

(B) An illustration of duplex containing a G-G duplex containing a G-G mismatch mismatch

(C) Hypothetical structure of the G-G mismatchHypothetical 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 Molecular models of the simulated complex of ligand 1 and DNA containing the G-G of ligand 1 and DNA containing the G-G mismatch mismatch viewed from the major groove side (left) and the minor groove side (right)

SPR Assay by a Sensor Chip(2)Nature BiotechnologyNature Biotechnology 19, 51 - 55 (2001) 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

SPR difference image of a four-component DNA array

(a) Surface-bound 11-mer DNA sequence(a) Surface-bound 11-mer DNA sequence

(b) SPR imaging measurement (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 mismatchFig 1. SPR difference image of aFig 1. SPR difference image of a

four-complement DNA array 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 Scheme 2. Schematic representation of the oligonucleotides used in Fig 2 the oligonucleotides used in Fig 2

SPR difference images of a two-component DNA array

(a) In the absence of the dimer(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(b) Exposure to the naphthyridine dimer - Increase in reflectivity only for sequence Y - Hairpin formation

(c) After the subsequent exposure of the (c) After the subsequent exposure of the surface to the complement molecule Zsurface to the complement molecule Z - hybridization adsorption is only observed to the sequence X element Fig 2. SPR difference images of a two-Fig 2. SPR difference images of a two-

component DNA array obtained from the component DNA array obtained from the SPR image before and after SPR image before and after