Biomod/2011/Harvard/HarvarDNAnos:Data&Output

To Add

 * .rtf mismatches file, python scripts, etc.
 * new DLS data from Nick
 * SphereCadSimple (Nick's excel file)
 * disulfide gel
 * sphere gel

2011-06-13
Nick's Hemisphere [[Media:Perkons_Hemisphere.json]]

2011-06-15
Sherrie's sphere: [[Media:Sphere.json]]
 * Note: Black staples match those of Han et al. while red ones do not (for thus far unknown reasons)

Scaffold Permutation Analysis Python script used to determine if our produced staples match those provided by the literature: [[Media:Sphere debug.zip]]

2011-06-17
NUPACK analysis of the sphere's lock and key strands, respectively, for a strand displacement opening mechanism.

2011-06-20
An excel file containing all the staples for the sphere: [[Media:Sphere_staples.xlsx]]

2011-06-24
Sherrie's sphere: [[Media:Sphere match.json]]
 * All of the staples now match those of Han et al.!!!

2011-06-29
First Folding of the Sphere (unsuccessful due to too-low buffer concentration)

Gel:



AFM of unpurified spheres:



AFM of purified spheres:



2011-06-30
TEM of purified spheres. Do we see spheres or just water droplets?





2011-07-06
The Second Folding of the Sphere

There are some mismatches here w.r.t Han's original staples, due to using a different sequence of the m13 clone.

 Gel 



 AFM

Unpurified closed spheres:





Unpurified open spheres:





 TEM

Unpurified closed spheres:



Unpurified open spheres:



2011-07-11
Gel:

2011-06-08
Evan's Denmark-like boxwithlid (single hinge)
 * CanDo fluctuations video: [[Media:Boxwithlidcando.avi]]
 * caDNAno JSON file: [[Media:Boxwithlid.json]]
 * Via Tom's idea
 * Will need more than one hinge I think, but not sure how to do that in cadnano without making inner loop

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:


 * [[Media:Boxwithlid parlockmechanism-edited.json]]


 * [[Media:New Staple Sequences for boxwithlidwithlockmechanism.xlsb]]

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)
 * looks like a box with a lid, but the "lid" could just be an scanning artifact

2011-07-11


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

Disulfide Linkage & Subsequent Cutting by DTT

 * The above image shows Disulfide linkage and subsequent cutting by DTT at pH 7 & 8. The first non-ladder lane (reading left to right) contains disulfide linkage (un-cut) at pH 7, the second lane contains cut disulfide bonds at pH 7, the third lane contains un-cut bonds at pH 8, and the fourth lane contains cut disulfide bonds at pH 8.  The large bands in all four lanes contain unconjugated thiols (or cut disulfide bonds).  In lanes 1 and 3 we can see faint bands, which we believe represent conjugated disulfides.  Our future goal is to beef up the percentage of conjugated disulfides prior to cutting by DTT by finding an optimal pH or solvent mixture.

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

2011-06-27


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

2011-06-21
Nick's excel file correlating caDNAno bp number with theta/phi position and whether the bp points into our out of the sphere: [[Media:CoordinatesSpreadsheet2.xlsx]]

2011-07-06
SphereCADBasic, Version 1

2011-06-06

 * Sherrie's Aarhus box: CanDo gives bad input file error

2011-06-07
Evan's middle-opening hexagonal box:


 * Screenshot of CanDo fluctuations video:


 * caDNAno JSON file: [[Media:Boxwithmiddleopening.json]]

2011-06-10
Evan's caDNAno implementation of Han et al's 9-layer concentric ring (using curved DNA):
 * all DNA strands (scaffold and staple) are in reverse orientation, making it impossible to match my staple strands with those reported by Han et al in their supplementary information.

2011-06-22
Here is DLS data for 5 nm gold nanoparticles ordered from a company (?) that are about 2 months old. As you can see, there is quite a bit of aggregation:



Here is DLS data for 5 nm gold nanoparticles that we made in-house. Much better:



Here is DLS data for 15 nm gold nanoparticles that we made in-house. They were a little warm when we took this data, so it may be a little inaccurate:



2011-06-23

 * Below you will find some data outputs from the DLS machine, which overall shows that the more gold particles from a stock solution of 15nm particles introduced to a given volume of AuCl, the smaller the gold aggregates that form (more particles = wider distribution of the aqueous gold). This is a third method of making gold nanoparticles, when you want sizes >15 nm.


 * Hydrodynamic Radius of Particles after Addition of 500 uL of 15nm Au Particle Stock Solution


 * Hydrodynamic Radius of Particles after Addition of 200 uL of 15nm Au Particle Stock Solution


 * Hydrodynamic Radius of Particles after Addition of 50 uL of 15nm Au Particle Stock Solution


 * Hydrodynamic Radius of Particles after Addition of 20 uL of 15nm Au Particle Stock Solution


 * Hydrodynamic Radius of Particles after Addition of 5 uL of 15nm Au Particle Stock Solution

2011-07-05

 * [[Media:PrePhosphene Original.pdf]]
 * [[Media:PrePhosphene 4DaysLater.pdf]]
 * [[Media:PostPhosphene PostMixing.pdf]]
 * [[Media:PostSaltAddition.pdf]]
 * The above files are links to the DLS measurements of my samples from various times. The first measurement shows a uniform distribution of particles upon initial synthesis (with a hydrodynamic radius of about 12 nm).  The second document, "PrePhosphene_4DaysLater" shows that there was a degree of aggregation of AuNP after sitting at 4 degrees C for four days without the addition of phosphene.  The third measurement shows that the addition of phosphene stabilized the particles and prevented aggregation.  The final measurement file, "PostSaltAddition" shows minimal aggregation of AuNP, but this is probably a result of using the centrifuge (which is required in the procedure).

 