Biomod/2013/IIT-Madras/Results: Difference between revisions
Atul Kaushik (talk | contribs) No edit summary |
Atul Kaushik (talk | contribs) No edit summary |
||
Line 16: | Line 16: | ||
The sequences for the strands L1 and I1 have been taken from the following paper<cite>Modi</cite>. The sequence of the bases was rationally designed using sequence symmetry minimization taking into account the constraint posed due to the fixed i-motif sequence using the ideas given in the following paper<cite>Seeman</cite>. | The sequences for the strands L1 and I1 have been taken from the following paper<cite>Modi</cite>. The sequence of the bases was rationally designed using sequence symmetry minimization taking into account the constraint posed due to the fixed i-motif sequence using the ideas given in the following paper<cite>Seeman</cite>. | ||
Programs were written in Python to design the sequences[https://www.dropbox.com/sh/csthka0zlkhfqb1/NZfcEL5u-Y Link]. The results of the program were then fed to NUPACK for secondary structure analysis (at Na<sup>+</sup> concentrations of 0.05 owing to the absence of Na<sup>+</sup> in the annealing mixture). | Programs were written in Python to design the sequences[https://www.dropbox.com/sh/csthka0zlkhfqb1/NZfcEL5u-Y Link]. The results of the program were then fed to NUPACK for secondary structure analysis (at Na<sup>+</sup> concentrations of 0.05 owing to the absence of Na<sup>+</sup> in the annealing mixture)[https://www.dropbox.com/sh/2x4115r5612wur7/wOxRshkv-j?m Link]. | ||
==Referneces== | ==Referneces== |
Revision as of 01:08, 27 October 2013
Structure of DNA Walker
PAGE Results
Sequence Design
The sequences for the strands L1 and I1 have been taken from the following paper[1]. The sequence of the bases was rationally designed using sequence symmetry minimization taking into account the constraint posed due to the fixed i-motif sequence using the ideas given in the following paper[2].
Programs were written in Python to design the sequencesLink. The results of the program were then fed to NUPACK for secondary structure analysis (at Na+ concentrations of 0.05 owing to the absence of Na+ in the annealing mixture)Link.
Referneces
-
Two DNA nanomachines map pH changes along intersecting endocytic pathways inside the same cell Souvik Modi, Clément Nizak, Sunaina Surana, Saheli Halder & Yamuna Krishnan, Nature Nanotechnology 8, 459–467 (2013) doi:10.1038
-
Seeman NC, Kallenbach NR. Design of immobile nucleic acid junctions. Biophys J. 1983;44(2):201–209. doi: 10.1016/S0006-3495(83)84292-1 [1]