Biomod/2011/IITM/AcidArtists/test

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Acid Artists

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The project aims at designing a molecular construct consisting of appendages in the form of single stranded DNA molecules which bind with target molecules to form an aggregate that can be filtered from the containing solution. The appendage strands have DNA sequences complementary to those present on the molecules of interest thus enabling binding between them. The construct is designed using caDNAno and single strands are added to it by extending staple strands at specific locations. The aggregate dimensions are sufficient to be filtered by a porosity of 0.2 μm. The binding between molecules is reversible in nature so as to facilitate reuse of molecules thereby enhancing cost effectiveness of the technique. The technique can be incorporated into DNA robotics wherein “nano-bots” can be withdrawn from their environment. The long-term objective of the proposed work is to develop similar DNA-origami constructs capable of high-affinity and high-selectivity bio-molecule targeting in vivo.
*Team name: Acid Artists
*Institution name and location:[http://www.iitm.ac.in/ Indian Institute of Technology, Madras (Chennai, India)]
*Faculty mentor: [http://www.biotech.iitm.ac.in/Manoj Prof. N. Manoj]
*Graduate Mentor: Nikhil Srinivasan
*The Team:
**Abhinav Gopal
**Amit Agrawal
**Dharav Solanki
**Govind Krishna Joshi
**Nisarg Shah
**Suraj Rathi
**Tanmay Pai
==29 Aug==
After our discussion with Prof. Manoj, we have made a few changes to the idea that we had finalized earlier on. The previous idea was to capture ions from their aqueous solutions. This was to be done by using DNA particles that have ligands incorporated into their structures which interact with the corresponding metal ions and bind to them. These particles would then be aggregated using central structure, again made out of DNA, and the binding of the two entities was to take place through ssDNA overhangs attached to both the entities that would be complementary (so as to fascilitate binding).
However, now, we have changed the project a little bit. Even though the context has changed, the core work of the project will not be affected much. This is because the structure to be made in this version of the project is the same.
Now, instead of working in an aqueous solution of a specific ion, we will be dealing with separation of proteins.

==Complex biochemical circuit engineered==

Summary
1) in the future a synthetic biochemical circuit could be introduced into a clinical blood sample, detect the levels of a variety of molecules in the sample, and integrate that information into a diagnosis of the pathology.
2)Now gates are made from pieces of either short, single-stranded DNA or partially double-stranded DNA in which single strands stick out like tails from the DNA's double helix. The single-stranded DNA molecules act as input and output signals that interact with the partially double-stranded ones.
3)The molecules are just floating around in solution, bumping into each other from time to time Occasionally, an incoming strand with the right DNA sequence will zip itself up to one strand while simultaneously unzipping another, releasing it into solution and allowing it to react with yet another strand
4)Circuits with their approach, but the largest - containing 74 different DNA molecules - can compute the square root of any number up to 15 (technically speaking, any four-bit binary number) and round down the answer to the nearest integer. The calculation takes about 10 hours, so it won't replace your laptop anytime soon. But the purpose of these circuits isn't to compete with electronics;
5) the molecular signals are never entirely on or off, as would be the case for ideal binary logic. But the new logic gates are able to handle this noise by suppressing and amplifying signals - for example, boosting a signal that's at 80 percent, or inhibiting one that's at 10 percent, resulting in signals that are either close to 100 percent present or nonexistent.

Comments:
[1]Seems like a good idea. Plus, circuitry means mathematical modelling. You guys might be interested in this for the future too. Nice work Amit.
Also, what is DNA Origami's contribution here? Is it to make the molecules that are part of the circuit?
[2] This looks great! I am glad we are already looking around and brainstorming ideas--I have been looking into methods similar to those described below as well as they seem very promising


==Mini-Time-Controlled-Reactor==

Summary
Can we make a structure which is like a mini-time-controlled-reactor?
Maybe we can make a nano scale structure which has 2 compartments containing reactants, which open on our signal. This can have many applications...
for e.g. [a random idea] if some drug needs to be such that only freshly made compounds are effective, we can load then in our machinery and make sure that they react when we want them to.....

==Ph based sensors==


In nanotech there are nano materials which can attract as well as repel bio molecules. Nano particles are charged particles and as bio molecules such as proteins have amphiprotic nature and so depending on the ph of the medium, it can either attract or repel the bio molecule. What if we can make some structure out of DNA(net charge negative as DNA is negatively charged) and has some drug as its payload. One of the applications of such a DNA nano material which we could think is a drug which can cure acidity. As Ph is low so there will be net positive charge on the bio molecules which in turn will get attracted towards our DNA nanomaterial and the drug will destroy the bio molecule.

==Water Purification==


Now a day’s water is purified using gold nano tubes ( core has Au(0), surface has Au(I) and coordinated with citrate to give an overall negative charge). If we can make some structure and use gold as a payload on DNA maybe we can purify water.

== Bio molecules and Nobel metal nano particle forms nano-bio conjugates==

Depending upon the size of the bio molecule aggregates are formed. And these aggregates give specific colour to the solution. As DNA has polymerization property so it might give colour to a solution.

==Enzyme catalysis==

DNA-protein interaction is well known. Can we use this property so as to increase the efficiency of an enzyme.

==Intra cellular imaging==

As DNA can easily enter inside a cell by transformation, we can use this property of DNA to tag a cell at early stage of development.
Single stranded DNA is anchored on a gold nano particle and the complementary strand is anchored on another gold nanoparticle. When the two DNA strands bind, the nano particles come close to each other and when they unbind they again move further apart. This can be of great use.

==Contraption using DNA nanotech==

We will achieve a specified goal using parts made up of DNA. For example in my last post I introduced a way of aggregating nanoparticles (Single stranded DNA is anchored on a gold nano particle and the complementary strand is anchored on another gold nanoparticle). When gold particles aggregate u get to see some colour in the solution and this change in colour can be used to do some other step using ( some light sensitive sensor). Like this after a series of steps we will finally achieve our goal.

==Nanotribometer==

Nanotribometer gives the measure of the friction force( stiction). We can make use of hydrogen bonding in DNA to measure this force or in other words a meter made up of DNA to calculate stiction.

==Dendrimers==

Dendrimers are branched tree shaped nanoparticles, which have an immense potential for use in clinical diagnostics and therapeutics. Researchers have also developed nanoparticles called tectodendrimers which are formed by attaching different types of dendrimers with each other through their branches. What if we can make tectodendrimers out of DNA?.

==Making Gates and switches out of DNA ==

We require either conformational change or configurational change or constitutional change in order to make a switch at molecular level. Because DNA can be easily converted from Bform( right handed) to Zform(left handed) by the presence of cobalt hexamine, Can we use this property off DNA to make a switch?
Azobenzene can also be used to make switches. As the incorporation of azobenzene unit into a crown ether gives azacrown molecule. E isomer of azacrown molecule does not have space to accommodate the alkali metal captions whereas Z isomer shows an affinity. Based on similar lines can we make a molecule using azobenzene and DNA, whose one form has different properties then the other form. ( Nikhil has also posted one idea on azobenzene). Gates : A rotaxane contains one or more bead-like components which can be threaded into a rod. A rotaxane has a rod, stoppers and beads. We can make rod, stoppers using DNA and proteins can be used as beads. Using the protein DNA interaction we can make gates. Please read more on rotaxene in order to get a feel of this idea.
Please let me know if I am not making myself clear at any point.

== Paper 1 ==
=== Title ===
=== Summary ===
==== To Do ====
* Review
* Expand
==== eMail ====
Paper one is a review of another paper on 3D nanostructures and self assembly by Douglas et al. The keyword here is 3D. The smiley faces that we have seen in DNA origami papers are 2D and have been made from techniques that have arisen from a different paradigm. Paradigm - a central concept that sprouts other supporting ideas. The paper outlines three different paradigms of DNA nanostructures and goes on to mention that Douglas et al.'s method produces intrinsically 3D structures. Exactly how this method produces INTRINSICALLY 3D structures is a subject dealt with in the main paper and not the review. Read on the second paper - the one on self assembly and DNA nanostructures by Douglas et. al.

== Paper 2 ==
== [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2688462/ Self-assembly of DNA into nanoscale three-dimensional shapes]==
Authors:
Shawn M. Douglas, Hendrik Dietz, Tim Liedl, Bjo¨rn Ho¨gberg, Franziska Graf , & William M. Shih
=== Summary ===
==== To Do ====
* Review
* Complete entire summary
* Provide Workable Information

==== eMail ====
the purpose is to get started and not make it perfect for archiving, so I start off with whatever I know.
If you can take an overview, four figures form the main crux of the article.
1) Explaining the intricate 3D structure - starting from a planar representation of Staples and scaffolds to merging them in an intrinsically 3D structure.
2) Is the TEM analysis of the arranged particles. Of central importance are imaging the particles and also the intensity versus position graph.
3) and 4) I expect someone else to explain. If however, i find no reply in due time, I'll update myself.
Well, The summary I post right now is makeshift, so a perfect one needs some time. Anyways, you gotta make a start somewhere, right?

DNA is represented in cylindrical form by the color of the staple strand.
XY plane to honeycomb lattice - this is something that needs to be done from the text of the article.
Issues with staple lengths…
To expand on the points: The first figure explains the making of a 3D (NOT 2D, see the paper 1 for a better (understanding) nanostructure. The first section shows the proposed structure with staple and scaffold strands in XY plane. Note particularly how one type of staple turns into a different type of staple strand. For example, in the first section itself, we can see that a blue strand turns into a white one when a semicircular arc is complete.

The next two sections show the structure in half rolled and fully rolled forms. There is not much to note here, except the pitch and turn (read the paper) and also an obvious question : if the planar structure is folded over itself, then surely the semicircular arcs were symbolic and NOT representing any physical manifestation. Otherwise, we'd have an issue with the consistency of the length of the staple strands!

FIGURE TWO
Starts off with projection and perspectives of all the expected particles.

What is not evident is the answer of the question : what do 5 different TEM pictures of the same type of particle do? Wouldn't one suffice? Answer is, ofcourse, in the article.

What are homogenous monodisperse fields? (These refer to a collection of 3D nanostructures in a gel like medium after the DNA has annealed!)

What is a monolith structure here?
Also, of note is the fact that we are now looking into DNA annealing and all other familiar details.
The type of medium required for TEM imaging has been described.
Two TEM images of a monolith particle, with an intensity profile have been shown. This is a way to analyze the fidelity of the structures with the proposed design. Obvious question, what physical parameter are we plotting when we plot "Intensity" versus the coordinates?
Other random points from my notes:
Experimental proofs? Intensity vs. expected grey intensity.
How does a correlation between peak to peak distance and diameter come about? --> questionTwo types of analysis been plotted --> Intensity and peak indices.
How was the second graph plotted? On the basis of what data? We are talking about h - the peak index versus the peak position
What instrument was required for measuring the intensity profile?
Then, what was it that made possible the exporting of the expected intensity profile?

== Paper 3 ==
Authors:
Hendrik Dietz, Shawn M. Douglas, William M. Shih
=== Summary ===
==== To Do List ====
* Insert Images
* Review
==== eMail ====

One line summary: “targeted insertions and deletions of base pairs cause the DNA bundles to develop twist of either handedness, or to curve”.
The whole lattice [honey-comb lattice, in which each double stand has 3 nearest neighbours] is divided into cell arrays to simplify the visualization of this bending and curving. Each bundle [the pipe like str.] is joined to its nearest 3 neighbours at intervals of 21bp. Thus a connection occurs at each 7bp interval. If we imagine a planes, perpendicular to the helix axis, at all such connections then we get small pieces of ‘double stranded 7bp pipes’. This is called a cell. So now we talk about the whole structure as an array of such cells.
We assume that the DNA is in B-form [B-DNA are right handed helices, B-DNA has major and minor grooves of similar depths, & the bases are nearly perpendicular to the helical axis, which runs through the centre of each base pair.]
Now all the arrays are joined to each other at the 7th base pair.
ð So if we delete 1 or 2bp, then there will be over-winding, resulting in a pull and a torque in the left hand thumb direction[fig C]
ð If we insert 2bp, there will be local underwinding, resulting in a push and a right hand thumb direction torque.[fig C second part]
== Paper 4 ==
== Paper 5 ==

== Paper 6 ==
Authors:Robert F. Service
=== Details ===
=== Summary ===
==== To Do ====
* Abhinav - Eliminate Copy Paste Paragraphs
* Paraphrase
* Abhinav - Format the text.

==== eMail ====

This paper gives us a decent idea about the different applications of dna nanotech which have been done. The paper in the beginning is about how seeman came to idea of dna nanotech. While drinking in a pub he thought about making dna lattices(crystals) in whose voids proteins can be trapped came into his mind for determing the structure of protein and even in different conformations.(he worked in the field of protein crystallography)
Over the next few years,Seeman’s lab turned out triangles, squares,and other shapes. Then came the 1991 cube,and by 1998 Seeman’s team had figured out how to assemble such parts into an extended two-dimensional array.


Paul Rothemund and colleagues developed a technique called DNA origami with viral genome and staple strands. In 2009, Seeman mapped out the structure of crystal lattice of a series of triangles with a resolution of 4 angstroms which was still smaller for protein structure.


william Shih (hms) reported that he had for the first time used DNA nanotech tools to map the structure of a previously unsolved protein, using nuclear magnetic resonance (NMR) spectroscopy. The technique works by identifying the magnetic signature of atoms in proteins relative to their neighbors. By knowing each atom’s neighbors, researchers can piece together the structure of an overall protein.


In 1997 some researchers spiked a protein-containing NMR solution with a compound that spontaneously forms liquid crystals, materials that flow but have a regular molecular orientation like a crystal in which the protein was trapped and the the NMR results showed to spot clues such as the angle between two atoms bonded in a protein. A big drawbackto the technique and later variations of it isthat many cell-membrane proteins can stay in solution only with the help of detergents, which often tear apart the liquid crystals. Shih and colleagues replaced liquid crystals with origami-based DNA nanotubes that weren’t affected by detergents.


DNA nanotech’s growth isn’t limited to mapping proteins. At Kyoto University in Japan, chemical biologist Hiroshi Sugiyama has turned to DNA nanotechnology to help him watch protein catalysts carry out reactions in real time. Biophysicists are also looking to DNA constructions to help them investigate molecules one at a time. Dietz reported that he and his colleagues are using DNA origami to improve a now-standard set of biophysics tools to see what happens to proteins and DNA as they are pulled apart. the standard way is to use laser, beads and linkers. But linkers are floppy so So Dietz and his colleagues replaced the usual fl oppy linkers with stiff rods made fromDNA origami containing as many as 18 helical tubes each to see changes in protein activity under tension.


Shawn Douglas, lab of George Church at HMS, is working on a DNA origami nanorobot designed to seek out and destroy cancer cells. Douglas’s “robot” looks more like a hollow cylinder some 60 nanometers long and 25 nanometers across. He built it from DNA origami and stapled it closed using DNA strands called aptamers, which in this case were designed to bind specifi cally to molecules specific to cancer cells.the cylinders are loaded with fl uorescent immune-system proteins that bind to cancer cells and induce apoptosis and added them to cancer cells in an in vitro assay. The loaded cylinders bound to their targets, released their cargo, and killed up to 40% of the cells.
== Paper 7 ==
=== Title ===
=== Summary ===
==== To Do ====
==== eMail ====

Paper 7 is an article on DNA robots. In the initial part it tells how this field emerged. They have already given up on making DNA computers for computational work because DNA computers are slow, error-prone, and difficult to scale up to perform millions of operations. But these DNA computers can process information inside organisms where conventional computer chips can’t go. DNA robot works on a very simple principle. The robots’ legs are DNA strands that bind to specific complementary DNAs on a predesigned surface. a specific DNA snippet,known as a “fuel” strand was added. Each fuel strand acts like a computer command telling the walker what to do next. The first fuel strand binds the site on the track holding the back “leg” of a two-legged walker, causing it to unbind from its DNA partner on the surface, and then bind to another DNA sequence past the front leg. Another snippet is then added to move the second leg forward, and so on.


==22 July 2011== 1) Deciding on a thesis/problem statement 2) Summaries of the 5.5 articles out of 7 that were posted by Nikhil 3) Having a plan in mind about what exactly are we supposed to do when we get back to college - <2 weeks remain! -- requires clarity about the job 4) caDNAno operations and CanDo. How many of us have made ourselves familiar with using the software? 5) Sponsorship details 6) On Ground details - What exactly do we need to do in the Lab and clarity on permissions/privileges 7) Game Plan on using the size of our team for our own advantage. For example, dividing the team into 3 groups, each researching a specific topic, or performing a different task. THIS IS ESSENTIAL, but will be out of our reach if we do not have any clarity on what we are supposed to do. 8) Getting in touch with our Masters and PhD students and making them our advisers. THIS IS IMPORTANT. We want to minimize mistakes, so we need continuous guidance 9) Getting in touch with people from campus to do our RSA animate video. If deemed unfeasible, need to find other ways to present the video. (Assuming obviously that Raps, Music Videos etc. do not convey the same energy that the people start off with, and become more of a liability than asset!)

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