nanoparticle-based theorem proving
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Nanoparticle-basedNanoparticle-based Theorem Theorem ProvingProving
April 27, 2004 April 27, 2004 APRL http://gene.hanyang.ac.krAPRL http://gene.hanyang.ac.kr 22
The Target Problem
R is true !!R is true !! nilnil
, add R as, add R as
April 27, 2004 April 27, 2004 APRL http://gene.hanyang.ac.krAPRL http://gene.hanyang.ac.kr 33
Experimental Section
Preparation of Au nanoparticles
Synthesis & Purification of (alkanethiol)-modified oligonucleotides
Preparation of 3'- or 5'-(Alkanethiol)oligonucleotide-modified Au nanoparticles
Preparation and Characterization of Linker DNA
Characterization of DNA-Linked Au Nanoparticle Assembly
Transmission Electron Microscopy (TEM)
Calculations of UV-vis Spectra
April 27, 2004 April 27, 2004 APRL http://gene.hanyang.ac.krAPRL http://gene.hanyang.ac.kr 44
Primer Sequence(5’→3’) Length ModificationGC Content
( % )
ST¬QAAG CAG TAG CGA CCA ATT GAC
GCA AAT TGA CGT ACG TAC GCT GAA
45 mer None 46.7
¬RPQCAT ACA ATG AAC GCA GTC AAC
GCA AGG CAG TTC AGC GTA CGT ACG
45 mer None 51.1
¬P CTG CCT TGC GTT GAC 15 mer 5’-phosphate 60.0
R TGC GTT CAT TGT ATG 15 mer 3’-thiol 40.0
¬S TGG TCG CTA CTT 15 mer 3’-thiol 53.3
¬T TCA ATT TGC GTC AAT 15 mer 5’-phosphate 33.3
The Oligomer Sequence
April 27, 2004 April 27, 2004 APRL http://gene.hanyang.ac.krAPRL http://gene.hanyang.ac.kr 55
UV-vis Spectrum of DNA Linked Au Nanoparticle
(A)(A) (B)(B) (C)(C)
DNA-linked nanoparticle DNA-linked nanoparticle Assembly Assembly
April 27, 2004 April 27, 2004 APRL http://gene.hanyang.ac.krAPRL http://gene.hanyang.ac.kr 66
Further Work
15 mer15 mer 15 mer15 mer 45 mer45 mer
Assembly Assembly
S1 Nuclease Digestion S1 Nuclease Digestion
Selectivity Test Selectivity Test
Surface-basedSurface-based Theorem Proving Theorem Proving
April 27, 2004 April 27, 2004 APRL http://gene.hanyang.ac.krAPRL http://gene.hanyang.ac.kr 88
Surfaced-based Theorem Proving
15 mer15 mer15 mer15 mer 45 mer45 mer
April 27, 2004 April 27, 2004 APRL http://gene.hanyang.ac.krAPRL http://gene.hanyang.ac.kr 99
¬RPQ
¬RPQ
¬RPQ
¬T
¬T
¬T
¬S
¬S
¬S
P.C
P.C
P.C
N.C
N.C
N.C
R
¬RPQ
¬RPQ
¬RPQ
¬T
¬T
¬T
¬S
¬S
¬S
P.C
P.C
P.C
N.C
N.C
N.C
¬P
ST ¬Q
(a)
(b)
The schematic diagram of theorem proving before (a) and after (b) hybridization. (a) The immobilized probe DNA sequences on aldehyde-coated slide glass. (b) Molecular recognition properties by the target molecules between the probe sequences.
April 27, 2004 April 27, 2004 APRL http://gene.hanyang.ac.krAPRL http://gene.hanyang.ac.kr 1010
Experimental Section
Preparation of probe DNA
Preparation of Target DNA
Hybridization probe & Target DNA
Washing
Confocal microscope detectionConfocal microscope detection
April 27, 2004 April 27, 2004 APRL http://gene.hanyang.ac.krAPRL http://gene.hanyang.ac.kr 1111
100 pmol
ST¬QST¬Q
50 pmolTemp. 50°C Constant
Temp. 60°C Constant
¬RPQ¬RPQ ¬T¬T ¬S ¬S P.CP.C N.C N.C
R
¬¬P
ST¬ST¬Q
ST¬QST¬Q
April 27, 2004 April 27, 2004 APRL http://gene.hanyang.ac.krAPRL http://gene.hanyang.ac.kr 1212
100 pmol
¬¬P
50 pmolTemp. 50°C Constant
Temp. 60°C Constant
¬RPQ¬RPQ ¬T¬T ¬S ¬S P.CP.C N.C N.C
R
¬¬P
ST¬ST¬Q
¬¬P
April 27, 2004 April 27, 2004 APRL http://gene.hanyang.ac.krAPRL http://gene.hanyang.ac.kr 1313
100 pmol
RR
50 pmolTemp. 50°C Constant
Temp. 60°C Constant
¬RPQ¬RPQ ¬T¬T ¬S ¬S P.CP.C N.C N.C
R
¬¬P
ST¬ST¬Q
RR
April 27, 2004 April 27, 2004 APRL http://gene.hanyang.ac.krAPRL http://gene.hanyang.ac.kr 1414
Discussion
• Confocal microscope 457~633 nm Detection range dye & Non-overlapping emission wavelength Eqipment condition is break down now Microarray scanner (futher exp.)
• False positive signal ¬¬P and ¬¬S: non-complementary sequence Why (?)
GC ratio
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