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

PDF Version Also Available for Download.

Description

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 ... continued below

Creation Information

Sherman, W.B. April 16, 2012.

Context

This article is part of the collection entitled: Office of Scientific & Technical Information Technical Reports and was provided by UNT Libraries Government Documents Department to Digital Library, a digital repository hosted by the UNT Libraries. More information about this article can be viewed below.

Who

People and organizations associated with either the creation of this article or its content.

Author

Sponsor

Publisher

Provided By

UNT Libraries Government Documents Department

Serving as both a federal and a state depository library, the UNT Libraries Government Documents Department maintains millions of items in a variety of formats. The department is a member of the FDLP Content Partnerships Program and an Affiliated Archive of the National Archives.

Contact Us

What

Descriptive information to help identify this article. Follow the links below to find similar items on the Digital Library.

Description

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.

Source

  • 9th Annual Conference Foundations of Nanoscience (FNANO12); Snowbird, UT; 20120416 through 20120419

Language

Item Type

Identifier

Unique identifying numbers for this article in the Digital Library or other systems.

  • Report No.: BNL--96912-2012-CP
  • Grant Number: DE-AC02-98CH10886
  • Office of Scientific & Technical Information Report Number: 1035543
  • Archival Resource Key: ark:/67531/metadc846416

Collections

This article is part of the following collection of related materials.

Office of Scientific & Technical Information Technical Reports

What responsibilities do I have when using this article?

When

Dates and time periods associated with this article.

Creation Date

  • April 16, 2012

Added to The UNT Digital Library

  • May 19, 2016, 3:16 p.m.

Description Last Updated

  • July 21, 2016, 6:20 p.m.

Usage Statistics

When was this article last used?

Yesterday: 0
Past 30 days: 0
Total Uses: 2

Interact With This Article

Here are some suggestions for what to do next.

Start Reading

PDF Version Also Available for Download.

Citations, Rights, Re-Use

Sherman, W.B. Holliday Triangle Hunter (HolT Hunter): Efficient Software for Identifying Low Strain DNA Triangular Configurations, article, April 16, 2012; United States. (digital.library.unt.edu/ark:/67531/metadc846416/: accessed September 21, 2017), University of North Texas Libraries, Digital Library, digital.library.unt.edu; crediting UNT Libraries Government Documents Department.