Deoxyadenosine sugar puckering pathway simulated by the stochastic difference equation algorithm

Karunesh Arora, Tamar Schlick

Research output: Contribution to journalArticle

Abstract

The conformational transition pathway of sugar puckering between the C2′-endo and C3′-endo conformations of deoxyadenosine (dA) is reported using the stochastic difference equation (SDE) algorithm, which approximates long-time pathways. The south pucker is favored over the north by 0.34±0.2 kcal/mol, and the free energy barrier is about 2.2±0.2 kcal/mol above the global minimum. The transition occurs through the east barrier, with significant decrease in puckering amplitude near the barrier. These results are consistent with prior studies on sugars in nucleic acids and indicate that the SDE has potential for large nucleic acid and nucleic acid/protein systems.

Original languageEnglish (US)
Pages (from-to)1-8
Number of pages8
JournalChemical Physics Letters
Volume378
Issue number1-2
DOIs
StatePublished - Aug 29 2003

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difference equations
Difference equations
nucleic acids
sugars
Sugars
Nucleic Acids
Energy barriers
Free energy
Conformations
free energy
proteins
acids
2'-deoxyadenosine
Proteins

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry
  • Spectroscopy
  • Atomic and Molecular Physics, and Optics

Cite this

Deoxyadenosine sugar puckering pathway simulated by the stochastic difference equation algorithm. / Arora, Karunesh; Schlick, Tamar.

In: Chemical Physics Letters, Vol. 378, No. 1-2, 29.08.2003, p. 1-8.

Research output: Contribution to journalArticle

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