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Published July 30, 2004 | public
Journal Article

An algorithm for computing nucleic acid base‐pairing probabilities including pseudoknots


Given a nucleic acid sequence, a recent algorithm allows the calculation of the partition function over secondary structure space including a class of physically relevant pseudoknots. Here, we present a method for computing base‐pairing probabilities starting from the output of this partition function algorithm. The approach relies on the calculation of recursion probabilities that are computed by backtracking through the partition function algorithm, applying a particular transformation at each step. This transformation is applicable to any partition function algorithm that follows the same basic dynamic programming paradigm. Base‐pairing probabilities are useful for analyzing the equilibrium ensemble properties of natural and engineered nucleic acids, as demonstrated for a human telomerase RNA and a synthetic DNA nanostructure.

Additional Information

© 2004 Wiley Periodicals, Inc. Version of Record online: 03 May 2004; Manuscript accepted: 19 March 2004; Manuscript received: 21 January 2004. Contract/grant sponsor: NSF graduate research fellowship (R.M.D.). Contract/grant sponsor: Defense Advanced Research Projects Agency (DARPA) and Air Force Research Laboratory under F30602-010200561 (N.A.P.). Contract/grant sponsor: Ralph M. Parsons Foundation (N.A.P.). Contract/grant sponsor: Charles Lee Powell Foundation (N.A.P.). We wish to thank C. Ueda for discussions on human telomerase RNA and E. Winfree for discussions on the DNA lattice.

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