Holliday Triangle Hunter (HolT Hunter): Efficient Software for Identifying Low Strain DNA Triangular Configurations
Synthetic DNA nanostructures are typically held together primarily by Holliday junctions. One of the most basic types of structures possible to assemble with only DNA and Holliday junctions is the triangle. To date, however, only equilateral triangles have been assembled in this manner - primarily because it is difficult to figure out what configurations of Holliday triangles have low strain. Early attempts at identifying such configurations relied upon calculations that followed the strained helical paths of DNA. Those methods, however, were computationally expensive, and failed to find many of the possible solutions. I have developed a new approach to identifying Holliday triangles that is computationally faster, and finds well over 95% of the possible solutions. The new approach is based on splitting the problem into two parts. The first part involves figuring out all the different ways that three featureless rods of the appropriate length and diameter can weave over and under one another to form a triangle. The second part of the computation entails seeing whether double helical DNA backbones can fit into the shape dictated by the rods in such a manner that the strands can cross over from one domain to the other at the appropriate spots. Structures with low strain (that is, good fit between the rods and the helices) on all three edges are recorded as promising for assembly.
- Research Organization:
- Brookhaven National Lab. (BNL), Upton, NY (United States). Center for Functional Nanomaterials (CFN)
- Sponsoring Organization:
- USDOE SC OFFICE OF SCIENCE (SC)
- DOE Contract Number:
- DE-AC02-98CH10886
- OSTI ID:
- 1035543
- Report Number(s):
- BNL-96912-2012-CP; R&D Project: NC-001; KC020401H; TRN: US201205%%140
- Resource Relation:
- Conference: 9th Annual Conference Foundations of Nanoscience (FNANO12); Snowbird, UT; 20120416 through 20120419
- Country of Publication:
- United States
- Language:
- English
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