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DNA Nanotechnology - Science topic

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Nat Protoc 16, 86–130 (2021).
Table 2 of this article mentioned that DNA nano barrel structure is "Difficult to increase lumen diameter beyond ~3 nm". I do not really understand the reason for this phenomenon.
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Dear jiahoa
I recumend this document for you
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Hi
I'm trying to design a simple cube-shaped DNA origami with specific dimensions from just single stranded DNA oligos. 
Since there is no specific scaffold the origami is based on, cadnano is difficult to use...
I understand you can use Nupack... but I'm not sure how to create 3d objects using Nupack. 
Would there be a better program fit for this or what would be the ways doing so in nupack?
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Hi, I hope you already found an answer to this, but I think for cubes and other structures with specific dimensions ADENITA is a good option. Adenita SAMSON edition is a SAMSON (https://www.samson-connect.net/) plugin. you only need to add the app in the shop. You can use freeware option of SAMSON and it works quite nice.
De Llano, E.; Miao, H.; Ahmadi, Y.; Wilson, A.J.; Beeby, M.; Viola, I.; Barisic, I. Adenita: interactive 3D modelling and visualization of DNA nanostructures. Nucleic Acids Res. 2020, 48, 8269–8275, doi:10.1093/nar/gkaa593.
Best
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Hi all. I am trying to translocate and stretch a lambda-DNA (in 1xTBE buffer) through the 100x100 nm nanochannels, However, as soon as my DNA particles reach the funnel located between nano and microchannels, they are getting stuck and not entering the nanochannels. My nanochannels are fully functional and there is a current in them.
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Nanopores have emerged as versatile sensors for detection and analysis of single
molecules and particles over the past decade [1-7]. Similar to Coulter counters, nanopores
employ resistive pulse sensing in which ionic current through the pore changes during
translocation (passage) of a molecule through the pore [2]. Particularly, attention has
been focused on developing nanopores for rapid sequencing of DNA using α-hemolysin
and solid-state nanopores [1]. While close interactions between the nanopore and the
DNA molecule can yield structural information about the molecule, larger nanopores in
the 10-500 nm size range are better suited for analysis of physicochemical characteristics.
Saleh and Sohn [4] used rapid prototyping in PDMS (polydimethylsiloxane) to fabricate
200-400 nm nanopores for detection of λ-DNA, while Fan et al. [5] used silica nanotubes
for sensing λ-DNA. While larger nanopores are relatively easy to fabricate, the signal-to-
noise ratio is compromised due to the large size of the nanopore. To address this issue,
we are developing devices to perform multiple measurements on long DNA molecules,
which could significantly improve the signal-to-noise ratio by statistical averaging on the
same molecule [8, 9].
Knowledge of the factors that affect the frequency of translocation events is critical
for designing such nanopore devices and for understanding the mechanisms that govern
transport of these molecules through the nanopore. Study of DNA translocation through
α-hemolysin nanopores [10, 11] and solid-state nanopores [12] has yielded valuable
insights into the effect of voltage bias, DNA concentration, DNA length, etc. on the
translocation frequency, duration, and current blockage. However, relatively little is
known about translocation of long DNA molecules through larger nanopores that involve
a significantly different pore geometry, size, and electric fields. In this paper, we examine
the effects of voltage bias and DNA concentration on the translocation of λ-DNA through
PDMS nanopores.
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I am looking for an article that talks about the direct interaction of a nanoparticle and sars cov-2, but most of the articles talk about target proteins attached to gold nanoparticles, but I'm only looking for the interaction of sars cov2 with the nanoparticles. but I can't find that paper if exist.
(am trying to see the interaction in a solution of gold nanoparticles stabilized with povidone to see if they form clousters or how they interact in general)
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Dear Juan carlos Dominguez Solis
Nanoparticle-Based Strategies to Combat COVID-19
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Will the creation of mechanical nano-insects solve the problem of declining populations of bees and other pollinating insects?
Please reply
I invite you to the discussion
Thank you very much
Best wishes
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...Nanotechnology has tremendous applications in the food, pesticide, fertilizer, chemical, and agriculture industries. Nanostructures or nanoformulations are fabricated by manipulating, at atomic or molecular level, reactants in definite ratios for improving the physical, chemical, and conduction properties as well as strengthening the functioning materials applicable in agriculture, medicine, and environmental monitoring. ... The nanoparticles, APC molded into functional nano-biopesticides via green technology, could selectively target insects for plant and environmental safety. ... Lade, B. D., & Gogle, D. P. (2019). Nano-biopesticides: Synthesis and Applications in Plant Safety. In Nanobiotechnology Applications in Plant Protection (pp. 169-189). Springer, Cham.
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I am interested in potentially using commercially available customized HPC molecular dynamics simulations. However, I cannot find pricing information on the websites of the vendors. Could someone who has had experience with such services please let me know what kind of price range I might expect for a customized molecular dynamics service? To give context, here are some of the vendors that I am considering:
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Hi Logan,
Since you already have interested suppliers, why not contact their customer service for quotations? Different companies have different technical support services and final delivery quality, so it’s difficult to compare, depending on whether you care more about data quality or cost.
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Hi all,
Am working on a DNA based biosensor, DNA are thiolated. i reduce thiolated ssDNA by TCEP and dip cast it on a gold nanoparticle coated electrode.
I have tried with 500nM , 1uM, 2uM, 3uM, 4uM and 5uM concentrations, but am not getting a constant value by DPV.
i use methylene blue as indicator, should i have to refrigerate the methylene blue after use.
i need to fix the probe concentration.
Can some one share their insights on this, that would be great help.
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Dear Hammond,
The oligo am using is Thiol C6-Modified, The electrodes are so small that, it can be dipped in 96 Well plates. Am adding 150ul of Oligo's of different concentrations to the well (the volume is made such that the working electrode has to be completely submerged) and dipped the electrode for 180 mins at 30o C. Washed with buffer to remove any unbound oligo's and treated with 6-Mercapto-1-hexanol (MCH) for an hour at 30o C, further washed with buffer to remove any unbound MCH and electrochemical studies are carried out.
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i get no transfection when i load my gene to protein nanoparticle what shall be done
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What protocol are you using? If you're having issues with the binding of the proteins to the nanoparticles it means your nanoparticles are problematic. Try using a nanoparticle reagent with cationic elements to ensure that you get through the cell membrane (see https://altogen.com/product/nanoparticle-in-vivo-transfection-reagent/). That should help improve your results, and once again, be sure to follow protocols.
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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 raster/honeycomb/pixelated approach. Apparently I need to upload a .ply file to be read by the DAEDALUS algorithms but im having a hard time finding the correct software.
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MeshLab? 
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Is there any special modification needed to be done for nanoparticles.... anyone acquainted with the methodology
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If the particles are stable in an aqueous buffer you can follow the procedure described by Hermanson (Bioconjugate Techniques 2nd ed) in Chapter 24. 
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Hi 
I know that mica is better and I have protocols for this, which I will use, when I get my mica in a couple of weeks...
Could a strategy of using divalent ions be used to anchor DNA to either glass or silicon?
Unfortunately I have a presentation before then and my end of year review is coming up. I dont get easy access to the afm, its hard to get an hour or so, but I can get a lot of time over the next week so Id really like to take advantage.
Are there any viable protocols available for glass or silicon or is this a fools errand and I should just wait?
Thanks
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Divalent cations have been used to deposit DNA origami on silicon oxide, but the concentration required is above 100 mM Mg2+ and the surface coverage is low. (See Kershner et al, Nature Nanotechnology, 2009, 4, 557-561 and Albrechts et al. "Adsorption studies of DNA origami on silicon dioxide." In: 21st Micromechanics and Micro Systems Europe Workshop, MME 2010).
A more reliable way that I use to deposit DNA origami on silicon (with native oxide in my case) is through APTES functionalization. The APTES monolayer is covalently bound to the oxide and the terminal amine is protonated in DNA origami buffer conditions. This provides the positive charge for the electrostatic interaction with the negatively charged DNA origami backbone. I have used 2D origami as well as DNA "nanotubes" with APTES on silicon with good results. However, you may find that it is the spherical nature of your nanostructures that is making it difficult to image. There are well established protocols for SiO2 APTES functionalization (only a few resources: Sarveswaran et al. Proc. of SPIE-Int. Soc. Opt. Eng, 2010, 7637, No. 7637M; Kim et al. Soft Matter, 2011, 7, 4636-4643; Pillers et al. Journal of Visualized Experiments, 2015, 101, e52972).
Are you imaging in liquid or in air? If you are imaging in liquid, "anchoring" the DNA origami with the methods described above is not feasible because, as you said, the DNA origami is mobile. If in air, are you using tapping/non contact mode? This is essential to ensure that the fragile DNA origami is not ruined by the AFM imaging (contact mode imaging will tear the nanostructures).
Feel free to directly message me if you have any other questions.
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We are doing with protein nanotechnology by assembling molecular protein into protein nanoparticles in aqueous solution (PBS or other buffer). A difficulty in our lab is lacking equipped facilities effective to investigate the process of assembly process. Recently, we are lucky to get some instrumental budget. Can anyone suggest a list of instruments that may be helpful for this purpose?
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You have to check first if the assembly has occurred or not. Some of nanoparticles might be not conjugated to the protein. I suggest making the assembly according to one of the reproducible protocols in the literature. Thereafter, use electrophoresis to separate the assemblies, take some samples and do TEM or SEM ( based on the particle size you expect). You might try Cryo-TEM if your particles are small, which I think can help you a lot.   
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Using siRNA, modified siRNA and PLK1-conjugated siRNA. which is better for siRNA therapy? 
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Both should work provided your conjugation strategy (reaction condition!) does not impede the activity of siRNA; as well as it releases the siRNA well under desired target site.
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Hi everyone, I got a C-rich linear strand DNA and want it to form i-motif upon low pH. The question is how can I prove the formation of the i-motif in solution. Has anyone done that? Maybe CD or electrophoresis?
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Circular dichroic (CD) spectroscopy
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I have a DNA origami structure which i need to validate its proper folding. I am having a tough time visualizing the structures using TEM. I suspect the reason being bad sample prep.
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Hi, 
Yes, if you use a sample from a glycerol gradient directly for TEM, I suspect the glycerol can  affect your TEM samples. When I have used glycerol gradient centrifugation I have removed the glycerol by dialysis or spin filtration before TEM imaging.  Glycerol gradient centrifugation may not be the most simple way to remove staples from an origami sample, for simple TEM studies agarose gel extraction should be enough. 
Have you tried TEM on the sample without removing the staples? This is should be no problems. 
As for the incubation times in the TEM sample prepartaion, we normally only leave our samples on the grid for 20 seconds and only stain in uranyl formate for 20s. 
It may be helpful if you share the protocol you are using now so we can comment on it. 
Erik 
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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?
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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
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Dear Researchers,
I have a doubt regarding the molarity convention used for MD simulation of DNA. I neutralized the charge of DNA molecule with Na+ ions in a water box.
I want to simulate the system at a given molarity of Na+ ions.
Now, if I want to calculate the molarity of Na+, should I count these ions used in the process of neutralization or I should add more Na+ ions to get the desired molarity.
Any suggestion or idea would be highly appreciated.
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Method 2: requires only the number of water molecules in the box.
N_ions = 0.0187 x ionConc(M) x no. of Water molecules
This discussion related to this is available in VMD forum n the link is provided here.
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I am working with 50 nM gold magnetic nanoparticle.I have conjugated Thiolated ss DNA with nanoaparticle using pH assisted method .Now, I want to see difference between only nanoparticle and conjugated dna nanoaparticle using gel electrophoresis.On agarose gel, I am not able to see any band neither of nanoparticle nor conjugated dna nanoparticle.What would be the reason and how to confirm that dna is conjugated with nanoparticle.
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Several possibilities.  Without additional details given specifics are hard to sort out but:
  • inability to detect Au/Au/DNA NPs on agarose gel might be related to the overall size/agglomeration state of the AU NPs?  If there are too big and the % Agarose to high (e.g. 0.75-1.5%) they may not even enter the gel.  This of course assumes that the overall net charge of the NPs/NP conjugate are indeed charged (net negative).   If no net charge they will not migrate in an applied electric field, if positively charged you will need to reverse the electrode polarity.
  • Detection of NP/DNA conjugate - since you mention that these are magnetic, separate any unconjugated "free" DNA with supermagnets, wash the Au particles very well. then do a standard "stain" for DNA (e.g. ethidium bromide/UV is quick and easy) use other fluorescent dyes to quantitate amount.  To increase sensitivity, generate the complimentary oligo and try a qPCR quantification.
Hope this helps...
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Hi, I am working on DNA Nanotechnology. I have prepared the DNA solution with 200nM concentration for 200uL which consists of (178uL of DI, 20uL of 1XTAE buffer and 8 uL of DNA strands.) Now i wanna add some uL of 40uM drug to the DNA mixture. So does my DNA concentration changes in this case? If so, How to calculate the final concentration of Drug-DNA complex? Thanks in advance !!
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Hello,
You absolutely right. Your final DNA and drug concentrations will change in this case. You will need increase concentration of DNA and drug on the factor of dilution. For exp. if you will dilute to 1:1, you will need take of 2 fold large of concentration of both (DNA and drug).
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I am looking for a efficient and easy protocol for attaching thiolated dna to citrate stabilize gold nanoparticle. 
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DNA aptamers can bind their targets specifically. Eg. the ATP aptamer binds ATP. What are the thermodynamic parameters (deltaG, deltaH, deltaS) for this process? And what are the respective thermodynamic parameters for interaction of a non-target (e.g. GTP) with the ATP aptamer? Any example values?
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Dear Kan,
RNA and DNA aptamers against lysozyme have been taken to town on their biophysics. The paper I unsuccessfully tried to attach (Potty et al., DOI: 10.1016/j.ijbiomac.2010.12.007) has a fairly clear discussion on the contribution of each thermodynamic parameter.
Best wishes,
Vitor
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I have some doubts.hope u guys can clear. I am attaching thioated dna with gold nanoparticle. I know my thiolated dna concentration in molars but I don`t know  how to calculate gold nanoparticle concentration in molars. my 2nd question is if i mix 2 different oligo then how to caculate gold oligo coverage.Also, i am going to use a dna sequence partial complementary to my dna linker attached to nanoparticle then how to calculate that coverage part.
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I hope this paper can help you
W. Haiss et al., Determination of Size and Concentration of Gold Nanoparticles from UV-VIS Spectra,
Anal. Chem. 2007, 79, 4215-4221
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I am looking at a protocol of binding AuNPs with thiolated DNA. It says AUNPs that were lyophilized with thiol-functionalized DNA (AuNP/DNA 1: 160 for high coverage, 1: 80 for low coverage). How can I calculate this ratio?
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well, if you know the DNA conc. and also AuNP conc. then you just need to divide DNA conc. over AuNP. You will get how many DNAs are on the gold nano particles. Let me give you an example: if your thiol-DNA conc is 2 micro M and Gold conc. is 13 nM then 2000 nM/13 nM= 153 DNA per gold nano particles. For your case, it looks you have 160 DNA per nano particles at high coverage, and 80 DNA per gold nano particles at low coverage.
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I am working with using gold nanoparticles to find sequence specific proteins. I attached the thiolated sequence specific oligo (sequence specific to one DNA binding protein) to gold nanoparticle for control. I transfect the nanoparticle inside the cell but I am getting lot of noise. I am getting many non specific protein attached to my nanoparticle only. I did the MS. It has 135 proteins including albumin of serum media. I heard of innovacoat of innova biosciences in which there coating material will not react to any protein inside the cell and proteins will bind to my oligo. Is there anything like that or any protocol of coating nanoaprticle? I am confused. Help please.
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Thank you sir for your pointers.That would definitely lead me to right direction. I will read and try to modify and do experiment as per your suggestions.Will get back to you for sure. :)
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I am working with using gold nanoparticles to find sequence specific proteins.For control,  I attached the thiolated sequence specific oligo (sequence specific to one dna binding protein) to gold nanoparticle. I transfect the nanoparticle inside the cell but I am getting lot of noise. I am getting many non specific protein attached to my nanoparticle only. I did the MS . It has 135 proteins including albumin of serum media. I heard of innovacoat of innova biosciences in which there coating material will not react to any protein inside the cell and proteins will bind to my oligo.Is there any thing like that or any protocol of coating nanoaprticle. I am confused. Help please.
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PEG can help reduce protein adsorption. There is commercial lipoic acid-PEG-maleimide molecule you can purchase to still be able to use thiolated DNA on top of the PEG coating. However, I would always expect a protein corona around DNA coated particles, irrespective of the specific DNA sequence. There is a lot of work on protein corona out there, just search for it.
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I am looking to do further analysis work on DNA origami-which are in essence pseudo-knots. Currently, the software I am familiar with are unable to incorporate these. Any input would be beneficial.
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You can go for MFold version 3.6 available at http://mfold.rna.albany.edu/?q=mfold/download-mfold
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Is there any method which do not requires DNA modification (adding thiol etc) for attaching DNA with gold nanoparticle. I am searching a protocol for DNA attachment but as far as I know it requires DNA to be modified (I can  modify gold surface)
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As far as you have for example poly-A end of your DNA, you can follow some protocols. Otherwise you can modify AuNPs with some short thiolated DNA, partially complmentary to your DNA and then bind your DNA.
Attaching DNA to AuNP without any treatment is not so effective. You will only achieve non stable DNA@AuNPs because of the nonspecific interactions. DNA without thiol binds to gold via backbone or N+ from the bases, but these bonds are realy weak.
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I understand this may be an unusual and maybe not even a feasible approach. In comparison to a cluster of small quantum dots, around 5nm is bound by a conic dna structure, versus a larger quantum dot of the same size comparatively to a cluster of quantum dots. I am interested in using DNA origami to cluster small quantum dots to increase the emission intensity.
I have attached a publication regarding DNA origami used to attach quantum dots.
Also I am aware that larger quantum dots will have emission spectrums of increased wavelengths.
Thank you!
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While clustering of small nanoparticles should in theory increase the emission intensity, at least in the sense that the local concentration of emitters will be higher, it may not be quite this simple.  For one thing, are you planning on using core or core-shell Quantum Dots? I ask as clustering of particles may result in quenching of particles if they are too close due to electron transfer between adjacent particles, especially if you are using core particles.  At the very least the interparticle separation may prove important.
Another consideration, depending on what environment the particles will be in, is that a small cluster of particles that have the same 'footprint' on a 2D substrate will have a lower volume and a greater surface area.  While the lower volume may not be critical, the higher surface area means they will be more easily quenched by surface effects.  
Lastly, if you are simply interested in having high intensity green emission, it might be better to use one of the recent approaches to particle synthesis that employ either 'giant shells' of CdS on a CdSe core, or alloying of CdSe/CdS/ZnS.
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Glycine is the shortest amino acid.
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its a very slow process, but the pH must maintain at 8 to 9 and keep the sample for a while.
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I am currently working to design a DNA origami to bind to an antibody that could bind to a specific integrin. I was wondering if there is anyone who is familiar with it that I could discuss with.
To be more specific, I have looked at various papers that discuss how antibody binding may inhibit integrin mechanotransduction but I want to know if binding a larger complex to the antibody binding the integrin may facilitate or inhibit movement to a greater degree.
As far for significant I believe this may serve medical values such as in endothelial diseases where the integrin mechanotransduction actually resaches the nucleus which causes difference in translation. Please refer to paper:
DNA Origami: Synthesis and Self-Assembly (for DNA origami) and Regulation of Integrin Activation for integrin targeting.
This is mostly a student project and I am very appreciative if anyone could possibly help. Thank you.
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Hello
I have worked on DNA origami platform. I have fabricate DNA logic gates as well as nano materials to DNA origami. I have experience to characterise this assembly by Atomic force microscope and alternative methods. If you need help in this regard, let me know.
Amit
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A quick literature search showed that only single-walled carbon nanotubes have fluorescent properties, and Strano's group works with the SWNT's with an attached repeating (AT) oligonucleotide chain to detect nitric oxide. Are there any other nanotubes that would be a suitable substitute to achieve fluorescence or possibly induce color change in the presence of other nano-materials?
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Surface passivation of MWCNT in conjugation with organic molecules result fluorescence. Similarly DWNT by interaction with single stranded DNA shows fluorescence. One can use different potential molecules for similar surface passivation to invoke fluorescence and can tune the intensity of the fluorescence or even can change the emission energy. In contrast carbon dots, onions or graphene simply on oxidation result peripheral hydroxylation and/or carboxylation in carbon dots or carbon onions to fluoresce in aqueous solution. Similarly oxidation of graphene to graphene oxide which can be readily done through its chemically oxidative synthetic procedure in aqueous medium as precursor of graphene shows fluorescence. I stress aqueous medium because in biological investigation that is the best medium
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We can make lots of modification on 3' or 5' of the DNA oligonucleoties. Say, I add a modification group to 3' of oligonucleotide (such as thiol, amino, biotin, phosphate, or a fluorophore) . Does this modification inhibit/promote the degradation of DNA by exonuclease ExoI that degrades single-stranded DNA in a 3'→5' direction? In another case, If I attached the DNA to nanoparticles at 3', does nanoparticles protect DNA from degradation by exonuclease?
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In many cases, this will inhibit exonuclease activity. For example, ExoI is blocked by 3' phosphoryl or acetyl groups (http://www.jbc.org/content/239/8/2628.long).
For ExoI, I would assume that this holds true for most other modifications.
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Suppose we have nanoparticles of ZnO, Ag, Au and Ferrites - how will the interaction between aforesaid biomolecules be governed?
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The surface coverage will depend on the radius of the NPs as well as its charge. The surface charge density will depend on the ionic strength and the pH of the solution. But basically all protein will adsorb to gold, the time of residence is just not the same. If your protein has a cystein group , you can expect a stronger affinity via covalent bond ( thiol bonding). DNA is the most charged polymer in nature so you can expect strong electrostatic interaction with the DNA lying down onto the NPs surface
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I am specifically interested in knowing which programs are used for sequence design and how to avoid cross-hybridizations, etc.
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Hi, i use NUPARM/NUCGEN and "nanoengineer" to device small DNA designs like tetra, icoshedron cages, as well bundles of DNA tubes. i can let you know the details if this what u r looking for
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I didn't understand how only 10 pair were chosen in the 1997 PNAS paper (A unified view of polymer, dumbbell) by Santalucia. I don't know on what basis these 10 sets have been chosen. The parameter for . AA/TT, AT/TA, TA/AT, CA/GT, GT/CA, CT/GA, GA/CT, CG/GC, GC/CG, GG/CC have been given in the paper but what will be the parameter for AG/TC, AC/TG, TG/AC, TC/AG, TT/AA, CC/GG which are not given in the paper.
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HI Himanshu,
You should have called me over phone or dropped a mail. this is my bread and butter. :)
Good that i saw it in RG, some more points to mr RGScore :)
Ok, coming to your question.
DNA is made of four bases A,T,G and C. and A pairs with T and G pairs with C. a sequence of DNA which forms a duplex will have one base pair stacked over the other. The paper talks about wat is known as "dinucleotide steps.". Its nothing but the combination of base pair stacked. a total of 16 possible combination can occur. Take "AA/TT" as a example. It refers to stacking of Adenine bases in strand_I and Thymine base in strand_II. Ur question is why is that they have not calculate the energy for TT/AA. "TT/AA " has thymine in strand_I and Adenine in strand_II. if u pass a pseudo-symmetry axis in the center of the step. u can go btw AA/TT and TT/AA.
I suggest u take coordinates of these two steps . superpose n observe that 5' to 3' direction is maintained even after 180 degree rotation.
Thus, Instead of 16 steps there is only 10 possible unique combination of steps.
Hope this helps.