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Title: HolT Hunter: Software for Identifying and Characterizing Low-Strain DNA Holliday Triangles

Abstract

Synthetic DNA nanostructures are most commonly held together via Holliday junctions. These junctions allow for a wide variety of different angles between the double helices they connect. Nevertheless, only constructs with a very limited selection of angles have been built, to date, because of the computational complexity of identifying structures that fit together with low strain at odd angles. I have developed an algorithm that finds over 95% of the possible solutions by breaking the problem down into two portions. First, there is a problem of how smooth rods can form triangles by lying across one another. This problem is easily handled by numerical computation. Second, there is the question of how distorted DNA double helices would need to be to fit onto the rod structure. This strain is calculated directly. The algorithm has been implemented in a Mathematica 8 notebook called Holliday Triangle Hunter. A large database of solutions has been identified. Additional interface software is available to facilitate drawing and viewing models.

Authors:
Publication Date:
Research Org.:
Brookhaven National Lab. (BNL), Upton, NY (United States)
Sponsoring Org.:
USDOE SC OFFICE OF SCIENCE (SC)
OSTI Identifier:
1044780
Report Number(s):
BNL-96398-2012-JA
Journal ID: ISSN 0192-8651; R&D Project: NC-001; TRN: US201214%%828
DOE Contract Number:  
DE-AC02-98CH10886
Resource Type:
Journal Article
Journal Name:
Journal of Computational Chemistry
Additional Journal Information:
Journal Volume: 33; Journal Issue: 15; Journal ID: ISSN 0192-8651
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 77 NANOSCIENCE AND NANOTECHNOLOGY; ALGORITHMS; DNA; NANOSTRUCTURES; STRAINS

Citation Formats

B, Sherman W. HolT Hunter: Software for Identifying and Characterizing Low-Strain DNA Holliday Triangles. United States: N. p., 2012. Web. doi:10.1002/jcc.22975.
B, Sherman W. HolT Hunter: Software for Identifying and Characterizing Low-Strain DNA Holliday Triangles. United States. doi:10.1002/jcc.22975.
B, Sherman W. Tue . "HolT Hunter: Software for Identifying and Characterizing Low-Strain DNA Holliday Triangles". United States. doi:10.1002/jcc.22975.
@article{osti_1044780,
title = {HolT Hunter: Software for Identifying and Characterizing Low-Strain DNA Holliday Triangles},
author = {B, Sherman W},
abstractNote = {Synthetic DNA nanostructures are most commonly held together via Holliday junctions. These junctions allow for a wide variety of different angles between the double helices they connect. Nevertheless, only constructs with a very limited selection of angles have been built, to date, because of the computational complexity of identifying structures that fit together with low strain at odd angles. I have developed an algorithm that finds over 95% of the possible solutions by breaking the problem down into two portions. First, there is a problem of how smooth rods can form triangles by lying across one another. This problem is easily handled by numerical computation. Second, there is the question of how distorted DNA double helices would need to be to fit onto the rod structure. This strain is calculated directly. The algorithm has been implemented in a Mathematica 8 notebook called Holliday Triangle Hunter. A large database of solutions has been identified. Additional interface software is available to facilitate drawing and viewing models.},
doi = {10.1002/jcc.22975},
journal = {Journal of Computational Chemistry},
issn = {0192-8651},
number = 15,
volume = 33,
place = {United States},
year = {2012},
month = {6}
}