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Manuel Loos1, Lion Thurecht2, Jiaojiao Wu1

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DNA mimic foldamers, structurally similar to B-DNA, exhibit comparable flexibility. Their stability is influenced by side chain charge and environmental conditions, revealing complex interactions beyond simple electrostatics.

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Area of Science:

  • Biomimetic chemistry
  • Structural biology
  • Computational chemistry

Background:

  • DNA mimic foldamers are oligoamides designed to replicate B-DNA structure and charge.
  • These foldamers can bind DNA-binding proteins more effectively than DNA itself.
  • Previous studies characterized their static structure via X-ray crystallography.

Purpose of the Study:

  • To investigate the structural dynamics of DNA mimic foldamers.
  • To compare foldamer flexibility with that of B-DNA.
  • To understand the role of charged side chains and environmental factors on foldamer stability.

Main Methods:

  • Molecular dynamics simulations using optimized AMBER force field parameters.
  • Systematic variation of side chain position, charge state, and salt concentration.
  • Experimental validation using 1H NMR, UV-vis absorption, and circular dichroism spectroscopies.
  • Development of an assay to measure helix stability via diastereomeric conformer interconversion.

Main Results:

  • Foldamer helices display global flexibility (twisting, bending) comparable to B-DNA, involving unique kinking motions.
  • Foldamers exhibit stability across wide temperature, pH, and salt ranges in aqueous solutions.
  • Structural changes occur upon modification of environmental conditions.
  • Unexpected destabilization was observed upon removal of some charged side chains, indicating complex roles.

Conclusions:

  • DNA mimic foldamers possess dynamic properties similar to B-DNA.
  • Foldamer stability is robust but sensitive to environmental changes and side chain composition.
  • The role of charged side chains in foldamer structure and stability is more intricate than previously assumed, extending beyond simple electrostatic repulsion.