Biomod/2013/IIT-Madras/Project

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'''Module 1'''
'''Module 1'''
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[[Image:PH 5 - Module 1.png]]
'''Module 2'''
'''Module 2'''
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[[Image:PH 5 -Module 2.png]]
'''Complete Picture :: DNA "Hopping"'''
'''Complete Picture :: DNA "Hopping"'''
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Translation of Input (I1) from Module 1 to Module 2
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[[Image:PH 5.png]]
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Translation of Input (I1) from Module 1 to Module 2 triggered by pH (change in cellular environment)

Revision as of 18:32, 23 October 2013

Contents

Background

DNA walkers are nanomachines which exhibit linear motion along a DNA strand. It was initially constructed with the aim of mimicking the intracellular motion of molecular motors such as kinesin so that these can in turn serve as mechanical parts for future Nano-bots. It mainly consists of two strands - a moving strand and a stationary strand along which the moving strand "walks". The major components of the DNA walker system are:

  1. Walker (the moving strand)
  2. Track (the stationary strand)
  3. Attachment strands/Set strands : These hybridize to single stranded segments thereby linking them.
  4. Detachment strands/Unset strands : Displace the set strands as these greater affinity.

There have been several modifications to this construct over the past decade like the use of Nicking enzyme to power the unidirectional motion of DNA fragment, autonomously.

In this project, we demonstrate the displacement of DNA in response to stimuli such as pH change.

History of DNA Walkers

DNA Walkers in the Past have primarily used other synthetic DNA oligonucleotides in order to exhibit motion over a track, or have used restriction enzymes to perform the task.

These systems have been extremely effective in controlling motion along a track, but faces the major drawback of not being able to translate in endogenous cell environment ie without the addition of "Extra" synthetic biomolecules.


Idea!

In an attempt to correct this drawback, we embarked upon designing DNA machines that respond to changes in cell environment by "hopping" along the track.

We intend to control the DNA Walker using

  1. pH
  2. A short DNA Strand (serves as a proxy for caging DNA with photo-activatable groups)



Resting State of DNA "Hopper"

  1. Module I: pH Switch

This Switch exploits the formation of intra-molecular i-motif at lower pH.

pH = 8.3

The mismatches required in the input strand (I1) is calculated based on the Gibbs free energy of i-motif formation and input (I1) -stator (L1) hybridization energy.


  1. Module II: short complementary DNA (Proxy for caging DNA with photo-activatable compounds)

This ssDNA Strand can be caged at dA and dC residues by NDBF (photo-activatable groups). Due to the un-availability of photo-activatable caged DNA, we have caged DNA strands using a short stretch of complementary DNA.

Image:PH 8.3 - Module 2.png

Final Structure of DNA Walking Platform

These modules are linked to form the DNA Walking Platform.

Image:PH 8.3.png


DNA "Hopper" in motion

At Low pH (pH<5.5), L1 folds into an intra-molecular i-motif due to the formation of CHC+ (hemi-protonated Cytosine base pairs). This folding doesn't release the Input (I1) into the solution, but assists toehold mediated strand-displacement to module 2.

Module 1

Image:PH 5 - Module 1.png


Module 2

Image:PH 5 -Module 2.png

Complete Picture :: DNA "Hopping"

Image:PH 5.png

Translation of Input (I1) from Module 1 to Module 2 triggered by pH (change in cellular environment)

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