Simon Butler

18 Questions 15 Answers 0 Followers

Questions related from Simon Butler

Are they any methods of purifying sub 100 base pair ssDNA sequences directly from gel electrophoresis?

Im working with DNA origami and I curious if it is possible to recover the staple strands from an agarose seperation of DNA structures and their components

06 September 2019 5,340 3 View

Gel electrophoresis of a sample - and then recovery from agarose - followed by further electrophoresis - causes change in bind color? Green to red?

Hi all My DNA origami sample goes into a redsafe stained gel. I seperate the sample into species/bands containing the scaffold strand, the staples and the DNA origami. All bands appear...

04 March 2019 3,977 3 View

Can Magnessium Chloride be used to adhere DNA origami to TEM slides?

Hi Can magnessium chloride be used to adhere DNA origamis to TEM slides in the same way it does mica? Im very excited to get new images but im very unfamiliar with the process. Some papers dont...

19 January 2019 8,621 0 View

When using PEG to precipitate DNA origami from fabrication solution is the pellet visible?

Hi Id like to try creating some quite high concentration DNA origami solutions. Using PEG precipitation seems like a really good method but Im unsure if I should look for a pellet after the...

29 October 2018 7,161 1 View

What yield could be expected of ~10nm gold nanoparticles formed by citrate reduction of gold hydrochlorate?

Hi Ive bought gold nanoparticles in the past but feel a higher concentration would be interesting to work with than is currently feasible for me to buy commercially. If I purchased a gram of...

04 June 2018 6,696 8 View

Cleaning gold nanoparticles by centrifuge. Seems to end up as an aggregated mess?

Hi Im functionalising gold nanoparticles with thiolated oligos. Part of all (Or all that Im aware) protocols require spinning the final solution down at 13,300 rpm for 20 minute cycles to...

22 November 2017 5,794 3 View

Gel electrophoresis of naked gold nanoparticles, DNA oligo functionalised gold nanoparticles and the DNA oligo used to functionalise the gold?

I thought itd be nice to run a gel contrasting gold nanoparticles, dna functionalised gold nanoparticles and the dna used to functionalise the gold nanoparticles. This would effectively provide 2...

16 October 2017 6,903 6 View

Im getting very faint agarose gel electrophoresis bands when running DNA origami structures?

Im trying to identify good protocols. I get very faint bands. I anneal at a 10:1 ratio of staples:scaffold. I run a 1% gel at 70 volts in 1x TBE buffer using a 10000x sybrsafe green stain. I use...

20 September 2017 6,394 1 View

Can I use a PCR purification column to remove TCEP from a sample of reduced, thiolated, ssDNA sequences?

Can a PCR purification column be used in this manner? Thanks

19 September 2017 7,962 3 View

Could litmus paper be used to adjust a small ~1ml solution from ~7 to ph 3 then back up to ~7?

I want to functionalise thiolated oligonucleotides with gold nanoparticles. To this I need to adjust the ph of the solution to 3, add Na+, mix, then bring the solution back to 7. I cant be sure...

07 September 2017 5,726 3 View

Difference when seperating linear and non linear particles by size exclusion?

Hi If i wanted to seperate a DNA origami of 7249 base pairs size, conformed into a rigid hollow, wire frame sphere, would I need a device with a different molecular weight cut off than a standard...

30 August 2017 9,286 3 View

Can I use agarose gel electrophoresis to purify and desalt nucleotides (In TCEP) with attached reduced thiol groups?

Hi I need to desalt a DNA sample before lyophilising it. Papers mention using a C18 column (I looked at columns and pipette tips) but when I examine the manuals available for these products they...

04 August 2017 9,280 3 View

What is a realistic lifespan for DNA origami once recovered/purified/seperated from buffer solution for imaging purposes, for example, under AFM?

Hi I have a good paper which suggests DNA origami will break down and should be imaged as soon as possible once fixed on a substrate. Would anyone have any specific advice about DNA origami life...

07 June 2017 5,237 1 View

Maximum amount of DNA (In micro or nano grams) that can be successfully identified and recovered in a agarose gel electrophoresis?

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...

25 May 2017 9,402 3 View

Matlab script to define N Z Mu and Epsilon from HFSS scatter parameters from a C resonator in the optical wavelength spectrum?

Hi I am having trouble accurately finding the refractive index of a structure I simulate in HFSS. I have been using chapter 3 of optical metamaterials (Wenshan Cai Vladimir Shalaev) to aid me in...

03 April 2017 4,852 2 View

Advice regarding SEM of DNA origami seeded with amine bound nanogold?

Hi I'm not having any success (Nothing visible on SEM) binding amine bound 1.4nm nanogold to DNA origami structures. I'm currently using a 100Kd protein concentration column, where origami and...

14 March 2017 1,885 3 View

Does anyone have experience using the online DAEDALUS DNA origami sequence finder? What kind of software is easy to use to create simple .ply designs?

I'm just trying to create nonlinear DNA origami constructs. I've been using caDNAno but its unsuitable for the creation of truly curved shapes as opposed to pseudo shapes created through a...

04 January 2017 1,274 2 View

Setting a tolerance in mathcad where a variable will automatically change +1 if a certain tolerance is breached between 2 calculated values?

Hi all. So I'm trying to use mathcad to calculate the refractive index (n) of a simulated metamaterial. The equation for the real part of n relies on a branching integer m. Where changing m (m...

08 December 2016 6,498 2 View