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Published October 2003 | Supplemental Material
Journal Article Open

A Partition Function Algorithm for Nucleic Acid Secondary Structure Including Pseudoknots


Nucleic acid secondary structure models usually exclude pseudoknots due to the difficulty of treating these nonnested structures efficiently in structure prediction and partition function algorithms. Here, the standard secondary structure energy model is extended to include the most physically relevant pseudoknots. We describe an O(N^5) dynamic programming algorithm, where N is the length of the strand, for computing the partition function and minimum energy structure over this class of secondary structures. Hence, it is possible to determine the probability of sampling the lowest energy structure, or any other structure of particular interest. This capability motivates the use of the partition function for the design of DNA or RNA molecules for bioengineering applications.

Additional Information

© 2003 Wiley Periodicals, Inc. Version of Record online: 13 AUG 2003. We wish to thank Dr. E. Winfree, our close collaborator in the ongoing effort to design and build functional nucleic acid systems, for many interesting discussions during the course of this work. NSF Defense Advanced Research Projects Agency (DARPA) Air Force Research Laboratory. Grant Number: F30602-010200561 Ralph M. Parsons Foundation.

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