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Title: Holliday Triangle Hunter (HolT Hunter): Efficient Software for Identifying Low Strain DNA Triangular Configurations

Abstract

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.more » Structures with low strain (that is, good fit between the rods and the helices) on all three edges are recorded as promising for assembly.« less

Authors:
Publication Date:
Research Org.:
Brookhaven National Laboratory (BNL) Center for Functional Nanomaterials
Sponsoring Org.:
USDOE SC OFFICE OF SCIENCE (SC)
OSTI Identifier:
1035543
Report Number(s):
BNL-96912-2012-CP
R&D Project: NC-001; KC020401H; TRN: US201205%%140
DOE Contract Number:  
DE-AC02-98CH10886
Resource Type:
Conference
Resource Relation:
Conference: 9th Annual Conference Foundations of Nanoscience (FNANO12); Snowbird, UT; 20120416 through 20120419
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 77 NANOSCIENCE AND NANOTECHNOLOGY; COMPUTER CODES; DNA; NANOSTRUCTURES; SHAPE; STRAINS; TRIANGULAR CONFIGURATION; Holliday; strain; triangle; HoIT; functional nanomaterials

Citation Formats

Sherman, W B. Holliday Triangle Hunter (HolT Hunter): Efficient Software for Identifying Low Strain DNA Triangular Configurations. United States: N. p., 2012. Web.
Sherman, W B. Holliday Triangle Hunter (HolT Hunter): Efficient Software for Identifying Low Strain DNA Triangular Configurations. United States.
Sherman, W B. Mon . "Holliday Triangle Hunter (HolT Hunter): Efficient Software for Identifying Low Strain DNA Triangular Configurations". United States. https://www.osti.gov/servlets/purl/1035543.
@article{osti_1035543,
title = {Holliday Triangle Hunter (HolT Hunter): Efficient Software for Identifying Low Strain DNA Triangular Configurations},
author = {Sherman, W B},
abstractNote = {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.},
doi = {},
journal = {},
number = ,
volume = ,
place = {United States},
year = {2012},
month = {4}
}

Conference:
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