DNA Origami Based Magnetic Nanopropellers

I worked on designing and characterizing DNA origami based magnetic nano-propellers. I also worked on size optimization of mono-dispersed magnetic iron oxide (Fe3O4) nanoparticles.

Project had 4 phases

1. Lab Training and Orientation

Literature survey and conceptualizing previous research
- DNA origami CAD structure conceptualized by a colleague
- Atomic Force Microscopy training
- Conceptualizing co-precipitation method to optimize size of iron oxide nanoparticles
Nano-characterization training
- Dynamic light scattering (DLS)
- Scanning electron microscopy (SEM)
- X-Ray Diffraction (powder)
- Nanostructures handling
- DNA origami biochemistry lab training
Experimental planning
- Mixing and thermocycling of DNA origami scaffold and staples
- Preparing DNA buffer and storage protocols for origami components
- Characterization scheduling for Fe3O4 nanoparticles (DLS, SEM, XPS, XRD, Raman) and DNA origami (AFM, gel electrophoresis)

Training and Orientation

Fe3O4 Nanoparticles

2. Size Optimization of Fe3O4 Nanoparticles

Experiment setup and planning
SEM, DLS characterization and statistics
Conference paper and poster presentation titled - 'Two-tier Size Optimization of Monodispersed Magnetic Iron Oxide Nanoparticles' at ICEE 2016, IIT Bombay.

Conference Paper submitted to International Conference of Emerging Electronics 2016 at IIT Bombay

3. Characterization of DNA origami cylindrical nanostructures

Sample preparation of thermocycled DNA 6-helix bundles over mica under AFM using scan-assist mode
Observing monomers, dimers and trimers (A, B and C cylinders) and counting per unit area
Troubleshooting the protocol at each stage of synthesis (12 attempts before observing nanostructures)
Optimizing scaffold strand (M13mp18 phage DNA) storage conditions
Reducing time between synthesis and AFM observation of nanostructures
Optimizing buffer to reduce salt concentration
Optimizing mica surface for clear observation
Mixing and matching staple strands for A, B and C and observing their cross-linking frequency
Attempting one-pot synthesis for DNA origami

DNA Origami

4. Gel electrophoresis, streptavidin-biotin interaction studies and bioconjugation of iron oxide nanoparticles with DNA origami nanostructures

Poster on 'Towards DNA Origami Based Magnetic Nanopropellers' in Chemical Engineering Symposium at IISc Bangalore
Observed DNA origami migration via gel electrophoresis
Observed streptavidin-biotin connectivity of DNA nanostructures under AFM
Observed bioconjugation of Fe3O4 nanoparticles (30 nm diameter) with DNA nanostructures
Thesis submission and defense

Bioconjugation

Abstract

Using DNA nanotechnology, we design complex nanostructures that are embarking in the field of application. We mimic a silicon dioxide-based magnetic nano propeller (SiO2-NP) system fabricated via a top-down synthesis, to generate a DNA-origami based bio-compatible propeller system fabricated via a bottom-up process.

We do this in two steps—

(1) modifying the SiO2-NP with magnetic iron oxide (Fe3O4) nanoparticles (IONPs),

(2) building the nano propeller using DNA origami six-helix bundles (6HBs).

In this report, we demonstrate a method for folding long, single-stranded circular genomic DNA obtained from M13mp18 bacteriophage, known as the scaffold strand. For this, we use complementary sequences of DNA oligonucleotides, known as the staple strands, that cross-link to the scaffold strand at predetermined locations.

Through CAD programming, this folding creates about 400 nm long cylindrical 6HBs externally modified with amine (NH2) functional groups that covalently couple to carboxy-modified IONPs across its backbone. We control the length of these cylinders through an axial, sticky-ended cohesion in multiples (monomer, dimer or trimer) of 400 nm.

We check the bio-conjugation of DNA origami with IONPs using fluorescence and characterize the cylinders using atomic force microscopy (AFM).

Abstract

Poster

Thesis

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