Summarized by In-Hee Lee

Slides:

Advertisements

Similar presentations

Research Techniques Made Simple: Polymerase Chain Reaction

Advertisements

The Biological Preparation of Shotgun DNA Mapping By Anthony Presents : I made this… …and this.

Structure of DNA. Polymerase Chain Reaction - PCR PCR amplifies DNA –Makes lots and lots of copies of a few copies of DNA –Can copy different lengths.

Molecular Computation : RNA solutions to chess problems Dirk Faulhammer, Anthony R. Cukras, Richard J. Lipton, and Laura F. Landweber PNAS 2000; vol. 97:

1 DNA Computation: The Secret of Life as Non-Living Technology Russell Deaton Professor Comp. Science & Engineering The University of Arkansas Fayetteville,

Additional Powerful Molecular Techniques Synthesis of cDNA (complimentary DNA) Polymerase Chain Reaction (PCR) Microarray analysis Link to Gene Therapy.

PCR - Polymerase Chain Reaction PCR is an in vitro technique for the amplification of a region of DNA which lies between two regions of known sequence.

Data analytical issues with high-density oligonucleotide arrays A model for gene expression analysis and data quality assessment.

Accurate Method for Fast Design of Diagnostic Oligonucleotide Probe Sets for DNA Microarrays Nazif Cihan Tas CMSC 838 Presentation.

DNA Computing: Mathematics with Molecules Russell Deaton Professor Comp. Sci. & Engr. The University of Arkansas Fayetteville, AR 72701

Introduction to DNA.

DNA Technology- Cloning, Libraries, and PCR 17 November, 2003 Text Chapter 20.

Analysis of Hot Spring Microbial Mat

Recombinant DNA Technology………..

Deliverables D9 Genetic diversity of protistan groups 1. Develop 18S rRNA gene based detection of selected protistan groups (testate amoebae) 2. Develop.

PCR Forensics. Today’s Lab There has been an outbreak of Salmonella poisoning in the Student Union cafeteria at Stanford University cafeteria. You have.

Biomolecular Computation in Virtual Test Tubes 7 th International Meeting on DNA Based Computers, p75-83, June 10-13, 2001 Max Garzon, Chris Oehmen Summarized.

Chapter 08 Author: Kelly Elkins © 2013 Elsevier, Inc. All rights reserved.

A PCR-based Protocol for In Vitro Selection of Non-Crosshybridizing Oligonucleotides R. Deaton, J. Chen, H. Bi, M. Garzon, H. Rubin and D. H. Wood.

1 DNA starts to Learn Poker David Harlan Wood Hong Bi Steven O.Kimbrough Dongjun Wu Junghuei Chen.

Overview of Microarray. 2/71 Gene Expression Gene expression Production of mRNA is very much a reflection of the activity level of gene In the past, looking.

A Software Tool for Generating Non-Crosshybridizing libraries of DNA Oligonucleotides Russell Deaton, junghuei Chen, hong Bi, and John A. Rose Summerized.

DNA Microarray Overview and Application. Table of Contents Section One : Introduction Section Two : Microarray Technique Section Three : Types of DNA.

From: Duggan et.al. Nature Genetics 21:10-14, 1999 Microarray-Based Assays (The Basics) Each feature or “spot” represents a specific expressed gene (mRNA).

Introduction to Oligonucleotide Microarray Technology

PCR Polymerase Chain Reaction PCR Polymerase Chain Reaction Marie Černá, Markéta Čimburová, Marianna Romžová.

DNASequenceGenerator: A Program for the construction of DNA sequences Udo Feldkamp, Sam Saghafi, Wolfgang Banzhaf, Hilmar Rauhe DNA7 pp Summarized.

PRINC E TON School of Engineering and Applied Science Characterizing Mathematical Models for Polymerase Chain Reaction Kinetics Ifunanya Nwogbaga, Henry.

Human telomerase specialization for repeat synthesis by unique handling of primer ‐ template duplex by Robert Alexander Wu, and Kathleen Collins EMBO J.

Research Techniques Made Simple: Polymerase Chain Reaction

Polymerase Chain Reaction

Topics to be covered Basics of PCR

EDVOKIT#300: Blue/White Cloning of a DNA Fragment

Author ：Shigeomi HARA Hiroshi DOUZONO Yoshio NOGUCHI

POA Simulation MEC Seminar 임희웅.

268nm UV spectrophotometry for the Theorem Proving strings

AMPLIFYING AND ANALYZING DNA.

On Template Method for DNA Sequence Design

PNA-mediated Whiplash PCR

© 2013 Elsevier, Inc. All rights reserved.

The Nature of Probability and Statistics

DNA Sequencing The DNA from the genome is chopped into bits- whole chromosomes are too large to deal with, so the DNA is broken into manageably-sized overlapping.

Rapid Detection of the Epidermal Growth Factor Receptor Mutation in Non-Small-Cell Lung Cancer for Analysis of Acquired Resistance Using Molecular Beacons

A DNA computing readout operation based on structure-specific cleavage

The characterisation of mtDNA deletions using long-read sequencing

Molecular Biology lecture -Putnoky

Fuzzy logic with biomolecules

DNA Library Design for Molecular Computation

Introduction to Bioinformatics II

Computational and experimental analysis of DNA shuffling

DNA-based Theorem Proving - Present Work

Gene expression profiling diagnosis through DNA molecular computation

Subhayu Basu et al. , DNA8, (2002) MEC Seminar Su Dong Kim

Biologically Inspired Synthetic Enzymes Made from DNA

Sequencing of t(2;7) Translocations Reveals a Consistent Breakpoint Linking CDK6 to the IGK Locus in Indolent B-Cell Neoplasia Edward P.K. Parker, Reiner.

DNA computing on surfaces

DNA Hybridization Catalysts and Catalyst Circuits

Molecular Computation by DNA Hairpin Formation

Volume 4, Issue 6, Pages (December 1999)

Self-Assembling DNA Graphs

DNA Transposition by the RAG1 and RAG2 Proteins

Matthew W Jones-Rhoades, David P Bartel Molecular Cell

Ye Bang-Ce, Chu Xiaohe, Fan Ye, Li Songyang, Yin Bincheng, Zuo Peng

Russell Deaton, junghuei Chen, hong Bi, and John A. Rose

A DNA Computing Readout Operation Structure-Specific Cleavage

Recursive construction and error correction of a simple combinatorial library. Recursive construction and error correction of a simple combinatorial library.

System-wide Analysis of the T Cell Response

Bioinformatics, Vol.17 Suppl.1 (ISMB 2001)

New Weight Encoding Method -FRET-

Research Techniques Made Simple: Polymerase Chain Reaction

Presentation transcript:

Summarized by In-Hee Lee Characterization of Non-Crosshybridizing DNA Oligonucleotides Manufactured In Vitro J. Chen, R. Deaton, M. Garzon, J. W. Kim, D. Wood, H. Bi, D. Carpenter, Y.-Z. Wang DNA10, pp. 132-141 2004. 6. 29. MEC Seminar Summarized by In-Hee Lee

Introduction In vitro protocol for generating non-crosshybridizing DNA oligonucleotides. Refer to DNA8 proceedings.

Introduction Advantages The oligonucleotides are selected in the conditions under which computations will be done. The potential for very large libraries. Prove the non-crosshybridizing characteristics of the library experimentally.

Cloning and Sequencing of Library Oligonucleotides Cycle # % Start 2(2) 20(20) 1 8(3) 22(8.3) 2 12(4) 33(11) 3 5(3) 23.8(14.3) 4 6(3) 28.6(14.3) Decrease in the # of stable crosshybridization(?)

Library Characterization with Gels Its intensity means the number of extended products. The intensity increase with cycle. More product is amplified over the cycle.

Library Characterization with Gels No self-hybridization in top and bottom strands.

Library Characterization with Spectroscopy Melting curve investigation Protocol product Random DNA samples of length 20. As a starting population of the protocol. 40 non-crosshybridizing oligonucleotides of length 20 [Deaton at al., 2003] Single-stranded oligonucleotide of length 20. 3 & 4 as a standard for non-crosshybridization. Watson-Crick pair of 2 sequences from 3. As a standard for hybridization.

Random seq. Top strands from cycle 4. NCH sequences Top and bottom strands from cycle 4. WC complements

Conclusion The experimental result indicate that the protocol was selecting for populations of non-crosshybridizing sequences.