Thermodynamic insights of base flipping in TNA duplex: Force fields, salt concentrations, and free-energy simulation methods

Zhaoxi Sun, John Z.H. Zhang

Research output: Contribution to journalArticlepeer-review


Threofuranosyl nucleic acid (TNA) is an analogue of DNA with a shift in the internucleotide linkages from the wild-type 5’-to-3’ direction to 3’-to-2.’ This alteration leads to higher chemical stability, less reactive groups, and lower conformational flexibility. Experimental observations indicate that these characteristic changes are attributable to a minimal perturbation of the interaction network, but the thermodynamic stability of the duplex remains unaltered in the TNA mutation. We applied the equilibrium and nonequilibrium free-energy simulations employing three popular assisted model building with energy refinement (AMBER) force fields for nucleotides to investigate this mutation-dependent behavior in the base flipping from T (DNA) residue to the T-to-TFT mutation (TNA) computationally. The force fields were performed similarly, as described in the base-paired state. However, after exploring the high-energy regions with free-energy simulations, we observed that these three force fields behaved differently. Previous reports conclude that the net-neutral and excess-salt simulations provided similar results. Nonetheless, our free-energy simulation indicated that the presence of excess salt affected the thermodynamic stability. The free-energy barrier along the base-flipping pathway was generally elevated upon the addition of excess salts, but the relative height of the free-energy barriers in DNA and TNA duplexes did not change significantly. This phenomenon emphasizes the importance of adding sufficient salts in the simulation scheme to reproduce the experimental condition.

Original languageEnglish (US)
Pages (from-to)1026-1039
Number of pages14
JournalCCS Chemistry
Issue number2
StatePublished - Feb 2021


  • AMBER force fields
  • Base flipping
  • Free-energy simulation
  • Salt concentration
  • TNA

ASJC Scopus subject areas

  • General Chemistry


Dive into the research topics of 'Thermodynamic insights of base flipping in TNA duplex: Force fields, salt concentrations, and free-energy simulation methods'. Together they form a unique fingerprint.

Cite this