Biomod/2011/Harvard/HarvarDNAnos:Data&Output

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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+*:

F nplus design identity.pngF nplus box locked configuration identity.png
What happens when key is added to box-lock complex.png

2011-07-01

07-01-2011 gel scan labeled extractboxed.jpg

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

Biomod1.bmp Biomod2.bmp Biomod3.bmp Biomod4.bmp

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

2011-07-11

2011-07-11 spheregel.jpg

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

  • 72 hour folding only

2011-07-12

2011-07-12 gel scan 2.jpg

Gel Scan of All of 2nd Boxwithlid Folding

2011-07-18

Boxes15-18 2--SYBR Gold--labeled.jpg

Gel Scan of 3rd Boxwithlid Folding

2011-07-19

File:Bottom-3.tif

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

Nanoparticle Chain

2011-06-23

GEL20.JPG

PAGE Gel of Handles+Ultramer Annealing Ladder

  • 100 V, 10% TBE, 45 minutes

2011-06-24

Chain ladder gel 3 3--SYBR Gold- edited.jpg

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

Chaingel4--SYBR Gold- edited.jpg

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

Completechain 1--SYBR Gold-.jpg

PAGE Gel of Ultramer + All Nine Handles

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

2011-06-29

Extraction overlay.jpg

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

2011-07-14

File:9x-1.tif TEM Image of Possible Nanoparticle Chains - Unstained Grid

File:9x-stained-1.tif TEM Image of Possible Nanoparticle Chains - Stained Grid

File:AuNP-size.tif TEM Image of Our Homemade 5 nm Gold Nanoparticles

Opening/Solubilization Schemes

Strand Displacement Locks (Method Inspired by Dave)

2011-07-27

Sdstaples lock conjugation 1-annotated.jpg

Forming Strand Displacement Staple:Lock:Staple Conjugates

  • 10% TBE PAGE Gel, SYBR-Gold

2011-07-28

2011-07-28 lockstaplegel.jpg

2nd Attempt at the 2011-07-27 Gel

2011-07-29

2011-07-29 spheregel.jpg

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-annotated.jpg

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


File:Photocleavage test 2 - 64cargo only.tif File:Photocleavage test 2 - PC Lock only.tif

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

Minbox 2--SYBR Gold-.jpg First PAGE Gel (Ladder, Minbox, Minbox + Lock, Minbox + Lock + Key, Ladder)

  • ladder spilled into adjacent lanes

Minbox2 2--SYBR Gold-.jpg Second PAGE Gel

2011-06-29

Gelscan1-box boxlock boxlockkey.jpg

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

2011-06-30

Labeled minboxnew copy.jpg Successful minimal box experiment PAGE gel!

  • shows locking and unlocking of box via strand displacement