1 / 16

A DNA Computing Readout Operation based on Structure-Specific Cleavage

A DNA Computing Readout Operation based on Structure-Specific Cleavage. Liman Wang, Jeff G. Hall, Manchum Lu, Qinghua Liu, Lloyd M.Smith. Nat. Biotechnol. 19, 1053-1059(2001). 2001. 12. 14 Park, Ji-Yoon. Abstract. Abstract. Previous work

lulu
Download Presentation

A DNA Computing Readout Operation based on Structure-Specific Cleavage

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. A DNA Computing Readout Operation based on Structure-Specific Cleavage Liman Wang, Jeff G. Hall, Manchum Lu, Qinghua Liu, Lloyd M.Smith Nat. Biotechnol. 19, 1053-1059(2001) 2001. 12. 14 Park, Ji-Yoon

  2. Abstract Abstract Previous work » the solution of a SAT problem using surface-based DNA computing : Nature 403, 175 - 179 (2000) Problem “READOUT” step - identify the DNA molecules present at the end of the computational process - based on PCR » false-positive signal » non-uniform amplification from mixtures of DNA targets Alternative READOUT approach » Structure-specific cleavage-based readout » higher uniformity of detection of the DNA computing products compared to that obtained with PCR amplification » simple, accurate, compatible with multiple-word DNA computing

  3. Surface-based DNA SAT Calculation Introduction How?

  4. Introduction Structure-specific Cleavage = Design of Two Oligonucleotide • Two sequence-specific oligonucleotides • Upstream oligonucleotide • Probe oligonucleotide • »analyte-specific region: forms a duplex with the target • » non-complementary 5’-arm • Hybridized region of the probe sequence • » have a melting temperature near the temperature of the • reaction • » rapid turnover of the probe oligonucleotides • » amplifying the signal ~ 1000 probe oligonucleotides / target

  5. Result- (I) Invasive Cleavage Reaction ( B ) ( A )

  6. Result- (II) Invasive Cleavage Readout Strategy

  7. Result- (III) DNA oligonucleotides in the READOUT

  8. Result- (IV):A DNA oligonucleotides in the READOUT

  9. Result- (IV):B DNA oligonucleotides in the READOUT

  10. Result- (IV):C DNA oligonucleotides in the READOUT

  11. R Two Principal differences Substantially less signal variability »invasive cleavage- based: » PCR- based: Much less false-positive signals

  12. Readout for Multiple-Word DNA Computing To adapt this approach to multiple-word DNA computing » upstream oligonucleotides seq : 13 nts(total)

  13. Result- (V) Histogram of Average Background-to-Signal Ratio during the Surface-based DNA Computation

  14. Word Complements/Upstream Oligonucleotides

  15. Structure-specific cleavage- based Requires substantially less time & effort » Collection of the DNA strands from the surface »Invasive cleavage reaction » Fluorescence detection » Take < 2 hr PCR-based READOUT Additional time & effort »Collection of DNA strands from the surface » PCR reaction »Strand separation of the ds product » Hybridization to addressed arrays » Fluorescence detection » Take < 4-5 hr False-positive signals - carryover contamination Variability in signal amplitude - varying efficiencies of PCR amplification for different targets Result & Discussion Comparison with PCR-based READOUT • Si gnal amplification process rather • than target amplification

  16. Experimental Protocol Experiment Oligonucleotide synthesis DNA Surface Attachment Chemistry DNA Computation Surface Hybridization Collection of DNA strands from surface Invasive cleavage reactions

More Related