Origami - Science topic

1. How to use caDNAno to see the structure of design origami?

2. How to break the automatic pushpin?

3. The version I am using is caDNAno 2.4

We know that in space the compact size and light weight are key design features. The compact size can sometimes be constraint for high antenna performance. Deployable Origami antennas can be a good candidate to solve this problem. But is it robust enough to work in space environment.

I find myself doing research on self-assembly of single stranded tiles-based DNA nanotubes that use origami as a seed and I am observing -using FRET measurements via qPCR that not only that there are low nucleation seed concentrations in which no growth is appreciable -which suggests that there might be a critical concentration of seeds that allows to trigger effectively the phase transition- but also that above that concentration changes in the same order of magnitude in the number of seeds result in changes on the observed growth (in bulk) that go (seemingly -still haven't fitted parameters) beyond a linear trend.

Has this behaviour of these systems -or similar- been characterized before?

I was reading a paper that used escherichia coli origami DE3 strains to express a certain protein and the vector used was a pTrcHis-Topo with a trc promoter. I am wondering if they made use of the chromosomal copy of T7 RNA polymerase gene present in this strain or not because as far as I understand T7 rna polymerase needs a T7 promoter.

Hello, I am currently investigating the compressive behavior of an origami structure made from 3D printed PLA. I am confused on how to determine the yield strength from the graph. What method should I use? I have read ASTM D695 standard and I'm confused on how much offset should I apply to determine yield.

Attached below is the compressive curve obtained from experiment and what ASTM D695 says on determining yield strength.

Hello, I am trying to simulate compression test on origami structure using Abaqus Static General and see the elastic-perfectly plastic behavior of the structure. Data extraction of displacement and load is done at the Discrete Rigid Plate reference point. It is done at a time increment of 0.01 and 0.001. However, the load-displacement curve obtained is dependent on time increment since the slope of the elastic part changes significantly. That is due to the jump of data point from 0 to the first data point.

Do you have any suggestions to solve this issue and obtain the correct load-displacement curve of elastic-perfectly plastic behavior of the structure independent of data collection increment?

Pictures are attached below.

I have to choose an expression host with encoded rare codons for expressing pET vector insert. There are multiple choices of E.coli derived strains available from Novagen. The family of Origami strains carry the trxB and gor mutations for enhanced disulfide bond formation. I am wondering is there any method to analyse presence or required formation of disulfide bond in the final expressed protein. (Target protein is prokaryotic in origin)

I am currently working on a project related to bending origami actuator utilizing air pressure. I am confused on why pressure magnitude needs to be defined if I already define the tabular amplitude. What is the use of each (magnitude and amplitude)?

Attached below is the screenshot I taken regarding the magnitude and amplitude.

Thanks in advance.

I am developing a triangulation experiment design (mixed methods of quantitative, qualitative and behavioral methods) to test 5 origami structures and their effectiveness in reducing the real and perceived stress levels in participants. Self report information will be gathered through pre-trial and post-trial questionnaires. Then heart rate and EDA will be measured before and after the trial (this indicators are to contrast with the self reported methods, but as a support of the evidence of the effectiveness of Origami). I am not an expert in statistical analysis. I am aware that qualitative data has to be treated differently than quantitative data. Which methods are the most appropriate?

Hi,

I am trying to express an eukaryotic membrane protein (only ectodomain, 60kDa, pI 5.6) in BL21DE3. I have played around with IPTG con. and temperature of induction to get the protein in soluble form but was not successful. So decided to extract the protein from inclusion bodies and refold it. I know that other bacterial host like Rosetta, pLys or origami would have been a better choice. Even at 0.05mM whole protein was found in pellet only. With higher con. of IPTG protein aggregation was observed after lysis (cloudy/ flakes) (lysozyme + Dnase + sonication (amplitude 20, 10s on , 40s off total time 5min). At 0.05mM IPTG induction, the pellet after lysis has two layers. An upper yellow translucent layer (L1) and lower white layer (L2). As a control, I have transformed BL21DE3 with the other plasmid (xy) which express the protein as inclusion bodies. The pellet from these two expression vectors were different. The control (xy) gave complete translucent yellow pellet unlike my construct. I seperated the two layers (pellet of y protein) and found that my protein is found entirely in white bottom layer (L2). When I tried to solubilize the protein in buffer using pellet (L2) (8M Urea, Tris 25mM, pH 8) very little protein got solubilized. I came across an article which suggested to use alkaline pH for solubilization. Upon adjusting the pH to 13, I got lot of solubilized protein even at 2M Urea. As the pH was very alkaline (13) (Ni-NTA/Talon doesn't work above pH 9) the pH was lowered to 7.4 by adding HCl. Precipitation was not observed. But the problem is that when I tried to bind the protein (solubilized in 2M Urea) to Ni-NTA/Talon (used both) there was a little binding to the beads as most of the protein was retained in flow through. I repeated the experiment with 8M Urea as above, yet no difference in result. My protein has His tag at N and C terminal confirmed by western blot using anit-his anitbody. I checked the beads with other his tag protein (beads are working fine). I tried many additives like glycerol 10%, KCl 100mM, B-Mercatoethanol 10mM, DTT 5mM (I know Ni-NTA and Talon wont work at higher con. of DTT, usually it works fine at this con. as it did many times in my hand, also I replaced it with Mercaptoetahnol).

My questions are

1. Is the white part of the pellet is an aggregate? Does protein forms aggregate in inclusion bodies?. Is it mandatory to avoid it. If so how?

2. When the protein got solubilized, why it is not binding to the Ni-NTA/Talon beads as I can see that the elution pattern looks similar to the before binding (I have also avoided using EDTA and DTT).

3. How to avoid precipitation during dialysis. ( I tried to remove urea very slowly by continuous dialysis method which takes 5 days to remove urea).

Regards

My desired protein have 180 amino acid and 3 disulphide bond.

I tried to produce this protein in pet 22b and pet32 and with BL21 (DE3) ,Rosetta and origami as a host But I couldn't  get any protein with this systems.

The concentration of IPTG used in 0.2 ,0.4 and 1mm

The temperature 37 ,30 and 20 was examined

And OD in time of induction between 0.6 -0.9

Hi

While investigating if recovery of larger samples of a DNA origami annealing reaction is possible with my current gel electrophoresis set up I discovered that according to thermo fisher

The maximum quantity of DNA that can be clearly identified in a band is 100 ng.

In my project Im currently using 5ul (1.12ug) of P7249 scaffold (Where the total weight is 112ug in 500uL) in a single annealing 50uL reaction and then a ten fold excess of staples (~11ug) even if I only use 5uL of product per lane I'm already in excess of 100ng by roughly ten fold (~1.2ug per lane).

I feel like 100ng of DNA per well is low? That would be 0.5uL of my folding reaction. If I recovered this volume I would be left with a 0.1 nanomolar solution of origami assuming recovery from a DNA extraction column in a 50ul buffer. Does anyone have experience recovering larger sample volumes?

Hi,

Microcon filtration is a process of removing excess staples after the self-assembly of DNA origami. Molecular Weight Cut Off is a characteristic of the microcon filters - molecules smaller than the MWCO are filtered out of the filter. This is a very loose definition, because filtration is based on size exclusion so is driven more by the shape of the molecule than the weight.

My question is - should different MWCO filters be used for different origami shapes? The molecular weight of all origami nanostructures will be in the same range. If different MWCO filters should be used, could anyone provide advise for the 24hb of length ~60nm and length ~100nm? Or if I'm totally wrong in my thought process could someone guide me in the right direction?

I assembled a DNA origami, a 6HB, and I run a scaffold and assembled 6HB in a agarose gel. In a gel, the band of scaffold is higher than 6HB band. actually, the molecular weight of 6HB is more than scaffold, therefore the 6HB band should be higher than scaffold band. But it is not. 

Professor Prakash demonstrates a microscope build with orgigami craftmanship. Blue LED and roll-to-roll PCB is an amazing idea for cheap illuminatin. Single ball lens and a paper pinhole are the crown of "reduced to the max" complexity. XY translation stage is made of paper. In his talk http://tinyurl.com/foldscope he sketches lenses and a pinhole. Seems like it is based on diffraction optics like a pinhole camera like a camera obscura. In his arXiv paper a ball lens is listed in bill of materials. Further it is claimed, that his lens is aspheric.

Is the principle of a pinhole camera needed to achieve aspheric correction in a foldscope?