Biomod/2012/UCSD/tRiton Nano Architects/Brainstorm: Difference between revisions

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[[Image:brainstorm.jpg|200px|left|thumb]]
[[Image:brainstorm.jpg|200px|left]]
==DNA architecture log==
==DNA architecture log==
The tRiton Nano Architect spent a large effort in brainstorming project ideas from April 2012 to July 2012. Our effort help us learn the process of DNA nanotechnology as well as the current research stage of DNA nanotechnology. We analyzed various scientific papers cited from the resource section of past BIOMOD 2011 teams. With this knowledge, the project scope and project budget was taken into consideration when selecting our actual project/abstract.
The tRiton Nano Architect spent a large effort in brainstorming project ideas from April 2012 to July 2012. Our effort help us learn the process of DNA nanotechnology as well as the current research stage of DNA nanotechnology. We analyzed various scientific papers cited from the resource section of past BIOMOD 2011 teams. With this knowledge, the project scope and project budget was taken into consideration when selecting our actual project/abstract.
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'''DNA Structures:'''  
'''DNA Structures:'''  
{|border="1" cellpadding="5" cellspacing="0" align="center"
{|border="1" cellpadding="2" cellspacing="1" align="center"
|-
|-
! scope="col" style="background:#f9f9f9;" | Architecture
! scope="col" style="background:#f9f9f9;" | Architecture
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! scope="row" style="background:#f9f9f9;" |  
! scope="row" style="background:#f9f9f9;" |  
DNA walker
DNA walker
|Motion w/ cargo delivery along designated tracks
|Motion w/ cargo delivery along designated tracks.
|Creation of walker tracks, DNAzymes that move through the tracks
|Creation of walker tracks, DNAzymes that move through the tracks
|http://www.nature.com/nnano/journal/v5/n11/full/nnano.2010.190.html
|http://www.nature.com/nnano/journal/v5/n11/full/nnano.2010.190.html
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! scope="row" style="background:#f9f9f9;" |
! scope="row" style="background:#f9f9f9;" |
DNA topological structures
DNA topological structures
|DNA 3D Origami, Customizable 3D design. Stability/ tacking on other biological molecules
|DNA 3D Origami, Customizable 3D design. DNA statues.
|text for row 1, column 3
|DNA origami
|http://www.nature.com/nnano/journal/v5/n10/full/nnano.2010.193.html
|http://www.nature.com/nnano/journal/v5/n10/full/nnano.2010.193.html
|-
|-
! scope="row" style="background:#f9f9f9;" |
! scope="row" style="background:#f9f9f9;" |
DNA shapes – curved and twisted
DNA shapes – curved and twisted
|DNA 3D Origami, Customizable 3D design. DNA gears/DNA rings.
|DNA origami
|http://www.sciencemag.org/content/325/5941/725.abstract
|-
! scope="row" style="background:#f9f9f9;" |
Square Lattice
|DNA 3D Origami, Customizable 3D design.
|DNA 3D Origami, Customizable 3D design.
|text for row 1, column 3
|DNA origami
|text for row 1, column 3
|http://pubs.acs.org/doi/abs/10.1021/ja906381y
|-
|-
! scope="row" style="background:#f9f9f9;" |  
! scope="row" style="background:#f9f9f9;" |  
Liquid Crystal
Liquid Crystal
|text for row 2, column 3
|Biosensor material, DNA liquid crystal filtration.
|text for row 1, column 3
|Short oligos under various temperature and voltage.
|text for row 1, column 3
|http://www.pnas.org/content/early/2012/01/04/1117463109.abstract
http://www.nature.com/nmat/journal/v6/n12/full/nmat2010.html
|-
|-
! scope="row" style="background:#f9f9f9;" |
! scope="row" style="background:#f9f9f9;" |
DNA molecular robots [spider]
DNA molecular robots [spider]
|text for row 2, column 3
|Extension to the DNA walker
|text for row 1, column 3
|Functionalization of DNAzymes as legs and DNA arrays as tracks.
|text for row 1, column 3
|http://www.nature.com/nature/journal/v465/n7295/full/nature09012.html
|-
|-
! scope="row" style="background:#f9f9f9;" |
! scope="row" style="background:#f9f9f9;" |
DNA origami tubes
DNA origami tubes
|text for row 2, column 3
|Scaffold for drug carriers, biodetection.
|text for row 1, column 3
|DNA origami
|text for row 1, column 3
|Initial reading - http://pubs.acs.org/doi/abs/10.1021/nl101079u
http://pubs.rsc.org/en/content/articlelanding/2012/SC/C2SC20446K
|-
|-
! scope="row" style="background:#f9f9f9;" |
! scope="row" style="background:#f9f9f9;" |
Complex weaves
Complex weaves/ Programmable 2D DNA arrays
|text for row 2, column 3
|Scaffold for multifunctionalization using SAM (Self-assembled monolayers)/Biotin/other biolinkers to attach to functional groups/nanoparticles.
|text for row 1, column 3
|DNA origami
|text for row 1, column 3
|http://pubs.acs.org/doi/abs/10.1021/nl060994c
http://onlinelibrary.wiley.com/doi/10.1002/cphc.200600260/full
http://www.sciencedirect.com/science/article/pii/S0959440X1000062X
|}
|}


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|The idea was that this could be used in sensing. Once the target sequence of DNA (ie, a specific virus) was present, the DNAzyme would break, and the current across the chain would change.We would also attatch fluorophores and quenchers on opposite sides of the Y to enable us to verify whether the circuit was open or closed.
|The idea was that this could be used in sensing. Once the target sequence of DNA (ie, a specific virus) was present, the DNAzyme would break, and the current across the chain would change.We would also attatch fluorophores and quenchers on opposite sides of the Y to enable us to verify whether the circuit was open or closed.
|While it was a feasible concept, our mentor said this would be too hard to optimize in the given time due to the complexity of the interlocking rings and measuring the charges.
|While it was a feasible concept, our mentor said this would be too hard to optimize in the given time due to the complexity of the interlocking rings and measuring the charges.
|DNA attachment chemistry: http://journals.ohiolink.edu/ejc/article.cgi?issn=07437463&issue=v15i0019&article=6541_eirodfgu
|DNA attachment chemistry: http://pubs.acs.org/doi/abs/10.1021/la9905315
DNA rings: http://www.pnas.org/content/105/14/5289
DNA rings: http://www.pnas.org/content/105/14/5289
Conductivity: http://www.nature.com/nature/journal/v403/n6770/full/403635a0.html
Conductivity: http://www.nature.com/nature/journal/v403/n6770/full/403635a0.html
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|http://www.nature.com/nnano/journal/v5/n3/pdf/nnano.2010.5.pdf , http://pubs.rsc.org/en/content/articlepdf/2007/cp/b700410a
|http://www.nature.com/nnano/journal/v5/n3/pdf/nnano.2010.5.pdf , http://pubs.rsc.org/en/content/articlepdf/2007/cp/b700410a


|-
! scope="row" style="background:#f9f9f9;" |
DNA walker
|text for row 2, column 2
|text for row 2, column 3
|text for row 1, column 3
|
|-
|-
! scope="row" style="background:#f9f9f9;" |  
! scope="row" style="background:#f9f9f9;" |  
Swimming DNA dolphins
Swimming DNA dolphins
|The idea of creating tiny nanodolphins from DNA was intriguing so we considered potential practical applications for them, even though it was originally a mechanism of showing the agility of DNA folding software. Attaching magnetic metal nanoparticles to the noses and/or tails of the dolphins and allowing them to be moved by magnetic fields and thereby "swim" was contemplated.
|The idea of creating tiny nanodolphins from DNA was intriguing so we considered potential practical applications for them, even though it was originally a mechanism of showing the agility of DNA folding software. Attaching magnetic metal nanoparticles to the noses and/or tails of the dolphins and allowing them to be moved by magnetic fields and thereby "swim" was contemplated.
|...
|A modified dolphin could be able to used to demonstrate an artistic method of navigating DNA objects in fluids.  
|The practical applications of creating swiming nanodolphins didn't make the project worthwhile.
|The practical applications of creating swiming nanodolphins didn't make the project worthwhile.
| http://pubs.acs.org/doi/abs/10.1021/nn800215j
| http://pubs.acs.org/doi/abs/10.1021/nn800215j
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|-
|-
! scope="row" style="background:#f9f9f9;" |
DNA lock box
|text for row 2, column 2
|text for row 2, column 3
|text for row 1, column 3
|
|}
|}


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DNA architecture log

The tRiton Nano Architect spent a large effort in brainstorming project ideas from April 2012 to July 2012. Our effort help us learn the process of DNA nanotechnology as well as the current research stage of DNA nanotechnology. We analyzed various scientific papers cited from the resource section of past BIOMOD 2011 teams. With this knowledge, the project scope and project budget was taken into consideration when selecting our actual project/abstract.


DNA Structures:

Architecture Uses Technique Source

DNA box with lid

1. Scaffold to encase nanosize cargo. 2. items for X-ray crystallography; Functionalize inside of box to trap pathogens (virus) then close DNA Origami http://www.nature.com/nature/journal/v459/n7243/full/nature07971.html

http://pubs.rsc.org/en/Content/ArticleLanding/2010/NR/b9nr00246d

DNA tetrahedron

1. Scaffold to encase nanosize cargo 2. items for X-ray crystallography DNA Origami http://pubs.rsc.org/en/Content/ArticleLanding/2004/CC/b402293a

http://pubs.rsc.org/en/Content/ArticleLanding/2010/NR/b9nr00246d

DNA octahedron

1. Scaffold to encase nanosize cargo 2.items for X-ray crystallography DNA Origami http://www.nature.com/nature/journal/v427/n6975/full/nature02307.html

http://pubs.rsc.org/en/Content/ArticleLanding/2010/NR/b9nr00246d

DNA bipyramid

1. Scaffold to encase nanosize cargo 2.items for X-ray crystallography DNA Origami http://pubs.acs.org/doi/abs/10.1021/ja071493b

http://pubs.rsc.org/en/Content/ArticleLanding/2010/NR/b9nr00246d

DNA walker

Motion w/ cargo delivery along designated tracks. Creation of walker tracks, DNAzymes that move through the tracks http://www.nature.com/nnano/journal/v5/n11/full/nnano.2010.190.html

DNA dolphins with flexible tails

Demonstration of unique DNA shapes; potentially a new propulsion system under high Reynolds number.

Motion in liquid, magnetic steering, surface coating for biological camoflage

DNA Origami http://pubs.acs.org/doi/abs/10.1021/nn800215j

Biochemical Aptamers

Biodetection of molecules or short oligos. SELEX process http://en.wikipedia.org/wiki/Aptamer, http://www.sciencedirect.com/science/article/pii/S0003269701951693

DNA computational circuits

Targeted Drug Delivery, error reduction upon recognition, close upon recognition of pathogen (through logic) Charging DNA with electricity between very thinly spaced electrodes DNA attachment chemistry: http://journals.ohiolink.edu/ejc/article.cgi?issn=07437463&issue=v15i0019&article=6541_eirodfgu

DNA rings: http://www.pnas.org/content/105/14/5289 Conductivity: http://www.nature.com/nature/journal/v403/n6770/full/403635a0.html

DNA topological structures

DNA 3D Origami, Customizable 3D design. DNA statues. DNA origami http://www.nature.com/nnano/journal/v5/n10/full/nnano.2010.193.html

DNA shapes – curved and twisted

DNA 3D Origami, Customizable 3D design. DNA gears/DNA rings. DNA origami http://www.sciencemag.org/content/325/5941/725.abstract

Square Lattice

DNA 3D Origami, Customizable 3D design. DNA origami http://pubs.acs.org/doi/abs/10.1021/ja906381y

Liquid Crystal

Biosensor material, DNA liquid crystal filtration. Short oligos under various temperature and voltage. http://www.pnas.org/content/early/2012/01/04/1117463109.abstract

http://www.nature.com/nmat/journal/v6/n12/full/nmat2010.html

DNA molecular robots [spider]

Extension to the DNA walker Functionalization of DNAzymes as legs and DNA arrays as tracks. http://www.nature.com/nature/journal/v465/n7295/full/nature09012.html

DNA origami tubes

Scaffold for drug carriers, biodetection. DNA origami Initial reading - http://pubs.acs.org/doi/abs/10.1021/nl101079u

http://pubs.rsc.org/en/content/articlelanding/2012/SC/C2SC20446K

Complex weaves/ Programmable 2D DNA arrays

Scaffold for multifunctionalization using SAM (Self-assembled monolayers)/Biotin/other biolinkers to attach to functional groups/nanoparticles. DNA origami http://pubs.acs.org/doi/abs/10.1021/nl060994c

http://onlinelibrary.wiley.com/doi/10.1002/cphc.200600260/full http://www.sciencedirect.com/science/article/pii/S0959440X1000062X

Project Ideas

Below is a selection from the multitude of ideas we considered before settling on our final project:

Idea Concept Uses Reason Rejected Sources

DNA sensing circuit with DNAzymes

This idea utilizes DNAs conductivity. Many structural versions of this design were contemplated but the most popular structure was interlocking rings of DNA in a Y shape, which would be connected to two electrodes at one end and one at the other. On one of the Ys would contain aDNAzyme, so cleavage of that strand of DNA would occur when a trigger of a specific DNA sequence was added. The idea was that this could be used in sensing. Once the target sequence of DNA (ie, a specific virus) was present, the DNAzyme would break, and the current across the chain would change.We would also attatch fluorophores and quenchers on opposite sides of the Y to enable us to verify whether the circuit was open or closed. While it was a feasible concept, our mentor said this would be too hard to optimize in the given time due to the complexity of the interlocking rings and measuring the charges. DNA attachment chemistry: http://pubs.acs.org/doi/abs/10.1021/la9905315

DNA rings: http://www.pnas.org/content/105/14/5289 Conductivity: http://www.nature.com/nature/journal/v403/n6770/full/403635a0.html

DNA Robotic Arm with Light-activated Joints and Tweezers as Hands

This idea was inspired by DNA walkers. We wanted to see if we can create the arms of a molecular robot, knowing that others have already designed the legs. Our robotic idea utilized DNA tweezers as hands and photoreceptive molecules that would change chemical conformation in order to bend the "shoulders", "elbows", and "wrists" of the DNA arms. We planned to test our project by attaching it to a platform and controlling it with light to pick up nanoparticles placed on certain locations. This would have been a useful contribution to nanorobotics. Based on our current skills, the idea was unfeasible. http://www.ncbi.nlm.nih.gov/pubmed/18850700

DNA Art

creating 2D masterpieces out of colored/fluorescent nanomaterials on a DNA weave. This could incorporate quantum dots or other materials that have differing colors at different sizes such as silver and gold. This aesthetic use of nanomaterials to create a new artform could have had nano barcoding or labeling applications. This was one of our more considered ideas if sensing hadn't taken a higher priority. http://dx.doi.org/10.1016/j.sbi.2010.03.009,

Nanophage

Function is to engulf target and prevent release, potential approach in pathology. Verification of target engulfed by luminescence. This could be useful in pathology and/or sensing. This idea was judged by an advisor to be time consuming to optimize and too large of a project to expect results within the timeframe. http://www.nature.com/nnano/journal/v5/n3/pdf/nnano.2010.5.pdf , http://pubs.rsc.org/en/content/articlepdf/2007/cp/b700410a

Swimming DNA dolphins

The idea of creating tiny nanodolphins from DNA was intriguing so we considered potential practical applications for them, even though it was originally a mechanism of showing the agility of DNA folding software. Attaching magnetic metal nanoparticles to the noses and/or tails of the dolphins and allowing them to be moved by magnetic fields and thereby "swim" was contemplated. A modified dolphin could be able to used to demonstrate an artistic method of navigating DNA objects in fluids. The practical applications of creating swiming nanodolphins didn't make the project worthwhile. http://pubs.acs.org/doi/abs/10.1021/nn800215j

Nanodiamond tipped DNA Tweezers or Scissors

This idea mixed the nanorobotics concept with nanodiamonds, which are a relatively inexpensive material with interesting properties. It was brought up out of curiosity over what unique properties diamonds possess at the nanoscale. Robotics, or nanoscale assembly. Other ideas were more compelling. pg 94+ http://www.mse.ncsu.edu/CompMatSci/pdf/full4.pdf


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