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NUPACK: Analysis and design of nucleic acid systems

  1. Joseph N. Zadeh1,†,
  2. Conrad D. Steenberg1,†,
  3. Justin S. Bois1,†,
  4. Brian R. Wolfe1,†,
  5. Marshall B. Pierce1,
  6. Asif R. Khan1,
  7. Robert M. Dirks1,
  8. Niles A. Pierce1,2,*

Article first published online: 17 NOV 2010

DOI: 10.1002/jcc.21596

Issue

Journal of Computational Chemistry

Journal of Computational Chemistry

Volume 32, Issue 1, pages 170–173, 15 January 2011

Additional Information

How to Cite

Zadeh, J. N., Steenberg, C. D., Bois, J. S., Wolfe, B. R., Pierce, M. B., Khan, A. R., Dirks, R. M. and Pierce, N. A. (2011), NUPACK: Analysis and design of nucleic acid systems. J. Comput. Chem., 32: 170–173. doi: 10.1002/jcc.21596

Author Information

  1. 1

    Department of Bioengineering, California Institute of Technology, Pasadena, California, 91125

  2. 2

    Department of Applied and Computational Mathematics, California Institute of Technology, Pasadena, California, 91125

  1. †

    These authors contributed equally to this work.

*Department of Bioengineering, California Institute of Technology, Pasadena, California, 91125

  1. †

    These authors contributed equally to this work.

Publication History

  1. Issue published online: 17 NOV 2010
  2. Article first published online: 17 NOV 2010
  3. Manuscript Accepted: 10 MAY 2010
  4. Manuscript Received: 4 APR 2009

Funded by

  • National Science Foundation (The Molecular Programming Project). Grant Numbers: CCF-0832824, CHE-0533064, DMS-0506468
  • The National Institutes of Health. Grant Number: P50 HG004071
  • The Ralph M. Parsons Foundation
  • Beckman Institute at Caltech

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Keywords:

  • RNA;
  • DNA;
  • complexes;
  • concentrations;
  • sequence design

Abstract

The Nucleic Acid Package (NUPACK) is a growing software suite for the analysis and design of nucleic acid systems. The NUPACK web server (http://www.nupack.org) currently enables:

  • Analysis: thermodynamic analysis of dilute solutions of interacting nucleic acid strands.

  • Design: sequence design for complexes of nucleic acid strands intended to adopt a target secondary structure at equilibrium.

  • Utilities: evaluation, display, and annotation of equilibrium properties of a complex of nucleic acid strands.

NUPACK algorithms are formulated in terms of nucleic acid secondary structure. In most cases, pseudoknots are excluded from the structural ensemble. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010

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