I've been searching for articles, but I was not able to find anything similar. Even though there are a lot of papers regarding enzyme immobilization in magnetic nanoparticles (mNPs), some using modified nucleotides and some just linking gDNA to mNPs through non-covalent interactions I couldn't find any protocols using " wild type" DNA and mNPs.
I am completely open to suggestions, even if you never done it yourself or have just speculations about how one might do it. The task is simple in principle: I just have to link any nucleotide inside it (neither the 5' or 3' end) to the mNP coating without messing up too much with the structure.
Any ideas?
Dear Tiago,
It will be quite hard to achieve this because you will have to avoid electrostatic interactions with the other parts of the DNA brands. As a consequence, this should modify the DNA structure.
Good luck !!
Jérôme Fresnais
Hi Tiago,
From your question, I guess that you want to link unmodified DNA with a nanoparticle in a way that ensures that your structure is not disturbed.
I'm not sure if this is feasible. You could extend one of the strands of your origami and have a freely floating sticky end in solution. You could then take magnetic nanoparticles with the complement of the sticky end attached to it. This could be done by using thiolated DNA and gold nanoparticles. The sticky ends on the nanoparticle and the origami should hybridize, connecting both.
This issue is complicated by the size of the origami and the nano-particles; whether they are too big to be effectively connected by dsDNA. I'm aware that sticky ended cohesion can be used to link gold nanoparticles together. Another issue is that this interaction is not permamanent.
On a related note, you could extend one of the strands in the origami and place a thiolated base at the end of the same.
Regards,
Atul
You could use attach a biotin to the 3' end of your DNA and bind it to MNPs that are coated with streptavidin. This would give you a stronger DNA-MNP complex due to the tightness of biotin-streptavidin linkage. This would have minimal effect on origami structure. One problem is that if you want 1:1 MNP:DNA complexes, this can be difficult to achieve.
Thank you all for your answers!
Jerome,
I'm aware of the problem regarding electrostatic interactions, and it is indeed a big deal, but I think that it might work . There is an interesting recent paper in which they couple DNA aptamers ( a bit smaller than DNA cages and quite different, indeed) to streptavidin beads and the function is well preserved and stuff.
Blu-ray based optomagnetic aptasensor for detection of small molecules (Jaeyoung Yang et al, 2015)
http://www.sciencedirect.com/science/article/pii/S0956566315303882
Atul, I'm not sure if that's feasible either, that's why I asked for opinions! And thanks for the opinion. We were trying to avoid sticky/hanging DNA strands, we are aiming to build an rather solid DNA cage. Theoretically, we wouldn't even have free 3' ends. Anyway, I'll take a look at the possibility of using thiolated DNA.
And Brian, this seems to be the most feasible way of doing that, with readily avaible chemicals and not so expensive. However, I'd rather do this without using proteins, just using conjugation chemistry techniques. I don't think the stoichiometry matters that much, so I won't tackle that right now. Anyway, thank you!