Biomod/2011/Harvard/HarvarDNAnos:Data&Output

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Contents

Evan's Lab Notebook Image Repository

Box Container Design

2011-06-08

Evan's Denmark-like boxwithlid (single hinge)

2011-06-14

CanDo result of Evan's boxwithlid with a double hinge: Media:Boxwithliddoublehinge.avi

  • Looks much better than with single hinge
  • See my lab notebook entry from today for more information and source files

2011-06-17

Edited .json caDNAno file of boxwithlid_parlockmechanism and Excel file of staples for box using azobenzene sequence (F_n) lock:

NUPACK analysis of the "lock" F_n+; F_n+ with the minimal "box"; and F_n+ with the "box" and the "key" F_n+*:

2011-07-01

Scan of gel with 1000 bp ladder, M13mp18 scaffold, and folded origami Boxwithlid without lock staples

  • grey box indicates section of gel that was extracted for origami purification

2011-07-05

AFM images taken on 2011-07-01 by Ralf of folded origami Boxwithlid without lock staples (purified)

2011-07-11

Gel Scan of 2nd Boxwithlid Folding (see lane to the very right)

  • 72 hour folding only

2011-07-12

Gel Scan of All of 2nd Boxwithlid Folding

2011-07-18

Gel Scan of 3rd Boxwithlid Folding

2011-07-19

TEM of Bottom Band in 18 mM MgCl2 Folding of Box 3 - unknown structures

Nanoparticle Chain

2011-06-23

PAGE Gel of Handles+Ultramer Annealing Ladder

  • 100 V, 10% TBE, 45 minutes

2011-06-24

Second Attempt at PAGE Gel of Handles+Ultramer Annealing Ladder

  • 100 V, 10% TBE, 2 hours
  • still not enough separation, but clearly an upward trend indicating more and more handles attached to ultramer
  • unclear what the white horizontal blotch near the bottom is; perhaps quenching due to too high concentration of SYBR-Gold because a lot of excess staples

PAGE Gel of Ultramer + All Nine Handles

  • 100 V, 4 hours
  • enough separation for extraction of top band, but should not have used SYBR-Gold

2011-06-28

PAGE Gel of Ultramer + All Nine Handles

  • 100 V, 4 hours
  • SYBR-Gold that was used to stain gel is faulty

2011-06-29

Overlay of Photo of Post-extraction Gel On Top of Gel Scan of Ultramer + Nine Handles

2011-07-14

TEM Image of Possible Nanoparticle Chains - Unstained Grid

TEM Image of Possible Nanoparticle Chains - Stained Grid

TEM Image of Our Homemade 5 nm Gold Nanoparticles

Opening/Solubilization Schemes

Strand Displacement Locks (Method Inspired by Dave)

2011-07-27

Forming Strand Displacement Staple:Lock:Staple Conjugates

  • 10% TBE PAGE Gel, SYBR-Gold

2011-07-28

2nd Attempt at the 2011-07-27 Gel

2011-07-29

Dave's locks did not seem to work, nor did adding a select few of the equator staples

  • 1% agarose gel, 2.5 hours, 80 V

Photocleavable Spacers

2011-07-25

Photocleavage Test 1: Using two strands with internal photocleavable spacers, directly from manufacturer-shipped tubes

  • 10% TBE PAGE gel, 15 minute UV exposure for "cleaved" strands


Photocleavage Test 2: Using gel-purified uncleaved strands from Photocleavage Test 1

  • 10% TBE PAGE gel, 1 hour UV exposure for "cleaved" strands

Minimal Box Test of Azobenzene-like F_n+ Lock and F_n+* Key

2011-06-27

First PAGE Gel (Ladder, Minbox, Minbox + Lock, Minbox + Lock + Key, Ladder)

  • ladder spilled into adjacent lanes

Second PAGE Gel

2011-06-29

Third PAGE Gel (Ladder, Minbox, Minbox + Lock, Minbox + Lock + Key)

2011-06-30

Successful minimal box experiment PAGE gel!

  • shows locking and unlocking of box via strand displacement


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