Difference between revisions of "Biomod/2013/BU/design"

From OpenWetWare
Jump to: navigation, search
Line 5: Line 5:
<br />
<br />
<br />
<br />
In their publication, <i>Encapsulation of Gold Nanoparticles in a DNA Origami Cage</i>, Zhao Zhao, Erica Jacovetty, Yan Liu, and Hao Yan demonstrate how to create a rectangular box with a cavity using the bottom-up self-assembly properties of DNA origami. In this particular study, this structure is used to encapsulate gold nanoparticles. This structure allows the surface of the nanoparticles to be tagged with a a controlled number of unique molecules and to control the orientation and intermolecular distance between the nanoparticles. It is stated that a significant advantage in using DNA origami is the spatial resolution of binding sites, on the order of ~6nm, that can be achieved. This structure exhibits a relatively high folding yield and was also found to be fairly robust, withstanding moderate mechanical strain from large nanoparticles placed in the cavity.
Beyond this particular structure, DNA origami has a number of inherent advantages over other types of nanoparticles used for similar applications. Currently there exists no equivalent technology capable of making a seemingly infinite number of arbitrary shapes like one can with DNA nanotechnology. Additionally, the surfaces of these structures can be functionalized simply by extending oligonucleotides and capping the oligonucleotides with a complimentary sequence bound to a functional polymer.

Revision as of 10:58, 12 October 2013

Boston University

BIOMOD 2013 Design Competition


<style> body { background: #fff; margin: 0; padding: 0; font-family: 'Open Sans', sans-serif; }

  1. globalWrapper { background: #ffffff; }
  2. content { background: none; border-style: none; margin: 0; padding: 0; }
  3. column-one, #contentSub, .firstHeading, #footer { display: none; }

  1. BU-header { padding: 15px; width: 100%; background: #000000; height: 20px; }
  2. BU-title { background: #DF0101; padding: 1.8em 0 1.8em 11.5em; line-height: 1.1em; }
  3. BU-content { min-width: 768px; width: 1000px; margin: 3.5em auto; }
  4. BU-body { margin-left: 11em; }
  5. BU-menu { float: left; padding-top: 0; padding-left: 5px; height: 100%; }

.BU-h1, .BU-h4 { color: white; border-bottom: none; padding: 0; margin-top: 14px; margin-bottom: 14px; }

  1. BU-header a { color: white; font-size: 19px; }

h1 { font-size: 44px; font-weight: 500; border-bottom: none; } h3 { font-size: 27px; font-weight: 300; border-bottom: none; } h4 { font-size: 23px; font-weight: 300; border-bottom: none; } ul.side-nav { display: block; list-style: none outside none; margin: 0; padding: 0; font-size: 14px; line-height: 1.6;} ul.side-nav li.divider { border-top: 1px solid #2383A1; height: 0; padding: 0; } </style> <link href='http://fonts.googleapis.com/css?family=Open+Sans' rel='stylesheet' type='text/css'> </html>

Design Goals


With an increasing number of unanswered questions in neuroscience, one prominent barrier has been a difficulty in transporting drugs across the blood-brain-barrier. Creating a vehicle capable of delivering drugs to the brain, concentrating the biodistribution within the brain, would be an extremely valuable tool towards advancing treatment for neurological diseases. Additionally, it still is very difficult to study neuronal activity in the brains of monkeys and humans. When working with mice and rats, there exists a wide variety of recording equipment that can be inserted in the brain with ease. If these particles can be delivered to the brain with ease, they can also be packaged with entities that can record or stimulate neurons.


The aim of our project is to develop a general strategy to functionalize DNA structures with bioactive cues, namely peptides.

We will demonstrate the utility of this approach with two applications. First, we will attempt to get structures into cells in an organized and controlled fashion, and second, get structures to pass through the blood-brain-barrier and enter the brain through the bloodstream.

We will begin with the rectangular box with the cavity, described by Zhao et al. in Encapsulation of Gold Nanoparticles in a DNA Origami Cage.


Oligonucleotides are extended from the two ends of the box perpendicular to the plane of the cavity.

Extended ends.png

Once the crude folded structure has been purified to remove stables and misfolded structures, a synthesized carrier polymer can be attached to a complimentary capping sequence that will bind to the extended ends to create functional sites at each extended helix.


Peptides will then be attached to the carrier polymers and the functionalization process will then be complete.

Project Goals

1. Modify the original literature box with extended ends.

2. Cap the extended ends with a fluorophore to verify functionalization capabilty.

3. Make the polymer for functionalization and verify binding.

3. Scale up products.

4. Test in cells and mice and compare to control.