Revision as of 06:18, 26 October 2017

ssDNA for producing in-vivo tetrahedral structure strand2

Design Notes

This sequence is a modification of the parts BBa K2054001,BBa K2054002, BBa K2054003 ,BBa K2054004 , BBa K2054005 from the iGEM Hong University Team 2016 team. This year our team is produced a Pre-tetrahedron structure which folds upon binding to the Huntington's disease biomarker Hsa-miR-34b ^[1]. The Parts BBa K2202000,BBa K2202001,BBa K2202002,BBa K2202003,BBa K2202004 work together to form the nanostrucuture. The sequence was generated using a DNA nanotechnology software called Tiamat ^[2]

Shown below is the schematic of how the Pre-tetra nanostructure folds only upon binding to the target to produce a G-quadruplex and hence we expect the signal to noise ratio to improve from last year's nanostructure.

Fig 1: Schematic of the functioning of the nanostructure.

Gel Images

The gel bands of the individual oligonucleotides allow for the estimation and verification of the sizes of the oligonucleotides by comparison with the DNA ladder. The formation of the 3-dimensional structure from the 2-dimensional DNA nanostructure in the presence of the specific target can also be clearly observed from the above gel image as a prominent shift from the gel band in lane 9 to the gel band in lane 10 can be distinctly seen.

Fig 2: PAGE gel (8%, 70V) showing bands of individual oligonucleotides (O1-O6) of DNA nanostructure, along with target, 2-dimensional nanostructure without presence of target (pre-tetra) and 3-dimensional nanostructure after detection of target (tetra).

Source

This Part was generated using a DNA nanotechnology software called Tiamat. This is a computationally designed sequence.

References

1. Gaughwin, P.M., Ciesla, M., Lahiri, N., Tabrizi, S.J., Brundin, P. and Björkqvist, M., 2011. Hsa-miR-34b is a plasma-stable microRNA that is elevated in pre-manifest Huntington's disease. Human molecular genetics, 20(11), pp.2225-2237.

2. Williams, S., Lund, K., Lin, C., Wonka, P., Lindsay, S. and Yan, H., 2008, June. Tiamat: a three-dimensional editing tool for complex DNA structures. In International Workshop on DNA-Based Computers (pp. 90-101). Springer, Berlin, Heidelberg.

3. Nakayama, S. and Sintim, H.O., 2009. Colorimetric split G-quadruplex probes for nucleic acid sensing: improving reconstituted DNAzyme’s catalytic efficiency via probe remodeling. Journal of the American Chemical Society, 131(29), pp.10320-10333.

4. Elbaz, J., Yin, P. and Voigt, C.A., 2016. Genetic encoding of DNA nanostructures and their self-assembly in living bacteria. Nature communications, 7.