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Sequence-Dependent Duplex Stabilization upon Formation of a Metal-Mediated Base Pair.

Philipp Scharf1,2, Biswarup Jash1,3, Jissy A Kuriappan4

  • 1Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, Corrensstrasse 28/30, 48149 Münster (Germany).

Chemistry (Weinheim an Der Bergstrasse, Germany)
|November 21, 2015
PubMed
Summary

An artificial nucleoside surrogate was integrated into DNA, forming metal-mediated base pairs. Its stability in DNA duplexes depends on sequence context, influenced by optimal fit and coordinative bonds.

Keywords:
DNAbioinorganic chemistryphenanthrolinequantum mechanics/molecular mechanicssilver

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Area of Science:

  • Synthetic organic chemistry
  • Biochemistry
  • Computational chemistry

Background:

  • Artificial nucleosides offer novel functionalities for DNA modification.
  • Metal-mediated base pairs are explored for unique DNA structures and applications.
  • Understanding sequence-dependent stability is crucial for DNA nanotechnology.

Purpose of the Study:

  • To investigate the stability of DNA duplexes containing an artificial nucleoside surrogate with a phenanthroline aglycone.
  • To explore the role of metal-mediated base pairs involving this surrogate.
  • To elucidate the sequence-dependent factors influencing duplex stability using computational methods.

Main Methods:

  • Synthesis and incorporation of an artificial nucleoside surrogate into DNA oligonucleotides.
  • Formation and characterization of DNA duplexes with Ag(I)-mediated base pairs.
  • Quantum mechanical/molecular mechanical (QM/MM) calculations to analyze sequence effects.

Main Results:

  • The artificial nucleoside surrogate functions as a bidentate ligand for metal-mediated base pairing.
  • DNA duplex stability incorporating Ag(I)-mediated base pairs is highly sequence-dependent.
  • QM/MM calculations revealed that optimal base pair fit and coordinative bond formation influence stability.

Conclusions:

  • Artificial nucleosides can be successfully integrated into DNA to form metal-mediated base pairs.
  • Sequence context significantly impacts the stability of these modified DNA duplexes.
  • Computational modeling provides valuable insights into the molecular basis of sequence-dependent stability in modified DNA.