Oligonucleotide-based Theorem Proving by Cross-Linking Gold Nanoparticle Assembly 2004. 3. 23 Park, Ji-Yoon.

Slides:



Advertisements
Similar presentations
Introduction to perl programming: the minimum to know! Bioinformatic and Comparative Genome Analysis Course HKU-Pasteur Research Centre - Hong Kong, China.
Advertisements

Uses of Cloned Genes sequencing reagents (eg, probes) protein production insufficient natural quantities modify/mutagenesis library screening Expression.
The genetic code.
Center for Biological Sequence Analysis Prokaryotic gene finding Marie Skovgaard Ph.D. student
 -GLOBIN MUTATIONS AND SICKLE CELL DISORDER (SCD) - RESTRICTION FRAGMENT LENGTH POLYMORPHISMS (RFLP)
ATG GAG GAA GAA GAT GAA GAG ATC TTA TCG TCT TCC GAT TGC GAC GAT TCC AGC GAT AGT TAC AAG GAT GAT TCT CAA GAT TCT GAA GGA GAA AAC GAT AAC CCT GAG TGC GAA.
Supplementary Fig.1: oligonucleotide primer sequences.
Gene Mutations Worksheet
Transcription & Translation Worksheet
Crick’s early Hypothesis Revisited. Or The Existence of a Universal Coding Frame Axel Bernal UPenn Center for Bioinformatics Jean-Louis Lassez Coastal.
1 Essential Computing for Bioinformatics Bienvenido Vélez UPR Mayaguez Lecture 5 High-level Programming with Python Part II: Container Objects Reference:
Today… Genome 351, 8 April 2013, Lecture 3 The information in DNA is converted to protein through an RNA intermediate (transcription) The information in.
UALR Biosciences Core Facility High Throughput DNA Sequencing Fragment Analyses Real Time PCR In situ Hybridization Proteomics.
Dictionaries.
GENE MUTATIONS aka point mutations. DNA sequence ↓ mRNA sequence ↓ Polypeptide Gene mutations which affect only one gene Transcription Translation © 2010.
C HAPTER 11: DNA AND G ENES 11-1 – DNA: The Molecule of Heredity.
IGEM Arsenic Bioremediation Possibly finished biobrick for ArsR by adding a RBS and terminator. Will send for sequencing today or Monday.
Nature and Action of the Gene
Synthesis of metallic Ag and semiconducting ZnS nanoparticles in self-assembled polyelectrolyte templates M.Logar, B.Jančar and D.Suvorov Institute Jožef.
Math 15 Introduction to Scientific Data Analysis Lecture 10 Python Programming – Part 4 University of California, Merced Today – We have A Quiz!
More on translation. How DNA codes proteins The primary structure of each protein (the sequence of amino acids in the polypeptide chains that make up.
Undifferentiated Differentiated (4 d) Supplemental Figure S1.
Supplemental Table S1 For Site Directed Mutagenesis and cloning of constructs P9GF:5’ GAC GCT ACT TCA CTA TAG ATA GGA AGT TCA TTT C 3’ P9GR:5’ GAA ATG.
Other Detection System of Theorem Proving Park, Ji-Yoon.
Lecture 10, CS5671 Neural Network Applications Problems Input transformation Network Architectures Assessing Performance.
Polyamine Oxidase is the Source of Hydrogen Peroxide in Plants
Fig. S1 siControl E2 G1: 45.7% S: 26.9% G2-M: 27.4% siER  E2 G1: 70.9% S: 9.9% G2-M: 19.2% G1: 57.1% S: 12.0% G2-M: 30.9% siRNF31 E2 A B siRNF31 siControl.
PART 1 - DNA REPLICATION PART 2 - TRANSCRIPTION AND TRANSLATION.
TRANSLATION: information transfer from RNA to protein the nucleotide sequence of the mRNA strand is translated into an amino acid sequence. This is accomplished.
Antibiotic Resistance and Strategies to Develop New Antibiotics D. J. Kalita Associate Professor Department of Veterinary Biochemistry Faculty of Veterinary.
Top-Down Meets Bottom-Up: Dip-Pen Nanolithography and DNA-Directed Assembly of Nanoscale Electrical Circuits Student: Xu Zhang Chad A. Mirkin et al. Small.
NSCI 314 LIFE IN THE COSMOS 4 - The Biochemistry of Life on Earth Dr. Karen Kolehmainen Department of Physics CSUSB
The 3 rd Research on Theorem Proving MEC Meeting Hanyang University Proteome Research Lab Park, Ji-Yoon.
Prodigiosin Production in E. Coli Brian Hovey and Stephanie Vondrak.
Passing Genetic Notes in Class CC106 / Discussion D by John R. Finnerty.
Supplementary materials
Dictionaries. A “Good morning” dictionary English: Good morning Spanish: Buenas días Swedish: God morgon German: Guten morgen Venda: Ndi matscheloni Afrikaans:
Transcription and Translation Activity 1.You will work with the person sitting next to you. 2.One of you will take the role of RNA polymerase and transcribe.
The 3 rd Research on Theorem Proving MEC Meeting Hanyang University Proteome Research Lab Hanyang University Proteome Research Lab Park, Ji-Yoon.
Suppl. Figure 1 APP23 + X Terc +/- Terc +/-, APP23 + X Terc +/- G1Terc -/-, APP23 + X G1Terc -/- G2Terc -/-, APP23 + X G2Terc -/- G3Terc -/-, APP23 + and.
GENE EXPRESSION. Transcription 1. RNA polymerase unwinds DNA 2. RNA polymerase adds RNA nucleotides (A ↔ U, G ↔ C) 3. mRNA is formed! DNA reforms a double.
RA(4kb)- Atggagtccgaaatgctgcaatcgcctcttctgggcctgggggaggaagatgaggc……………………………………………….. ……………………………………………. ……………………….,……. …tactacatctccgtgtactcggtggagaagcgtgtcagatag.
Example 1 DNA Triplet mRNA Codon tRNA anticodon A U A T A U G C G
Topic: Replication of DNA Standard: Explain the role of DNA in storing and transmitting cellular information.
DNA, RNA and Protein.
THE ROLES OF DNA.
Ji-Yoon Park Nanoparticle-Based Theorem Proving.
Protein Synthesis Worksheet Answer Key
Nanoparticle-based Theorem Proving
Protein Synthesis DNA RNA Protein.
Modelling Proteomes.
Supplementary information Table-S1 (Xiao)
Sequence – 5’ to 3’ Tm ˚C Genome Position HV68 TMER7 Δ mt. Forward
DNA – Review Unit 4.
Python.
Supplemental Table 3. Oligonucleotides for qPCR
GENE MUTATIONS aka point mutations © 2016 Paul Billiet ODWS.
Supplementary Figure 1 – cDNA analysis reveals that three splice site alterations generate multiple RNA isoforms. (A) c.430-1G>C (IVS 6) results in 3.
Huntington Disease (HD)
DNA By: Mr. Kauffman.
Tissue-Specific Reduction in Splicing Efficiency of IKBKAP Due to the Major Mutation Associated with Familial Dysautonomia  Math P. Cuajungco, Maire Leyne,
Protein Synthesis Review Answers
DNA and RNA.
Gene architecture and sequence annotation
More on translation.
Molecular engineering of photoresponsive three-dimensional DNA
Fundamentals of Protein Structure
Python.
Station 2 Protein Synethsis.
Presentation transcript:

Oligonucleotide-based Theorem Proving by Cross-Linking Gold Nanoparticle Assembly Park, Ji-Yoon

March 23, 2004 APRL 2 Colloidal Gold  Diameter: 5-20 nm  SPR (Surface plasmon resonance): 520 nm optical obsorption peak  Aggregation (>520 nm: shift the absorption peak)  Cross-linking mechanism by target DNA between the gold particle  Application: DNA, lectin, heavy metal ion, potassium ion, protein A

March 23, 2004 APRL 3 The DNA-based Nanoparticle Assembly Strategy 15 mer 45 mer

March 23, 2004 APRL 4 Purpose In this paper, we purpose to assembly of DNA-functionalized gold nanoparticles as optical detection approach. Oligonucleotides offer several advantages over non-biological-based linker molecules. –Various sizes of gold nanoparticles are readily available at low cost, surface modification with probe DNA is easier, and the temperature control for the formation of nanoparticles is not necessary.

March 23, 2004 APRL 5 The Target Problem R is true !! nil, add R as

March 23, 2004 APRL 6 Experimental Section Preparation of Au Nanoparticles Synthesis and Purification of (Alkanethiol)-Modified Oligonucleotides Preparation of 3'- or 5'-(Alkanethiol)oligonucleotide-Modified Au Nanoparticles Preparation and Characterization of Linker DNA Preparation and Characterization of DNA-Linked Au Nanoparticle Aggregates Transmission Electron Microscopy (TEM) Calculations of UV-vis Exinction Spectra

March 23, 2004 APRL 7 PrimerSequence(5’ → 3’)LengthModification GC Content ( % ) ST¬Q AAG CAG TAG CGA CCA ATT GAC GCA AAT TGA CGT ACG TAC GCT GAA 45 merNone46.7 ¬RPQ CAT ACA ATG AAC GCA GTC AAC GCA AGG CAG TTC AGC GTA CGT ACG 45 merNone51.1 ¬P CTG CCT TGC GTT GAC 15 mer 5’-phosphate60.0 R TGC GTT CAT TGT ATG 15 mer 3’-thiol40.0 ¬S TGG TCG CTA CTT 15 mer 3’-thiol53.3 ¬T TCA ATT TGC GTC AAT 15 mer 5’-phosphate33.3 The Sequence Information

March 23, 2004 APRL nm Comparison between Before and After Hybridization

March 23, 2004 APRL 9 (A) The UV-vis spectrum of oligonucleotide-modified 10-nm particles before (red line) and after (blue line) DNA-induced assembly (B) Solutions of 10-nm-diameter Au particles before (cuvette A) and after (cuvette B) DNA-induced assembly (C) Aqueous solution of 10-nm-diameter Au particles before (red) and after (blue) the addition of NaCl. This is an irreversible process (A)(B)(C)

March 23, 2004 APRL 10 Concentration Variation of 10 nm Colloidal Gold

March 23, 2004 APRL 11 Conclusions A new “programmed assembly” strategy for organizing nanoparticles into periodic functional materials The strategy utilize nanoparticle building blocks modified with alkanethiol- capped oligonucleotides and complementary linker oligonucleotide strands to form extended structures with control over particle chemical composition, periodicity, and aggregated thermal stability Highly selective diagnostic method relies on the distance-dependent optical properties of gold particles