Design, synthesis, conformational analysis and nucleic acid hybridisation properties of thymidyl pyrrolidine-amide oligonucleotide mimics (POM)

Org Biomol Chem. 2003 Oct 7;1(19):3277-92. doi: 10.1039/b306156f.

Abstract

Pyrrolidine-amide oligonucleotide mimics (POM) 1 were designed to be stereochemically and conformationally similar to natural nucleic acids, but with an oppositely charged, cationic backbone. Molecular modelling reveals that the lowest energy conformation of a thymidyl-POM monomer is similar to the conformation adopted by ribonucleosides. An efficient solution phase synthesis of the thymidyl POM oligomers has been developed, using both N-alkylation and acylation coupling strategies. 1H NMR spectroscopy confirmed that the highly water soluble thymidyl-dimer, T2-POM, preferentially adopts both a configuration about the pyrrolidine N-atom and an overall conformation in D2O that are very similar to a typical C3'-endo nucleotide in RNA. In addition the nucleic acid hybridisation properties of a thymidyl-pentamer, T5-POM, with an N-terminal phthalimide group were evaluated using both UV spectroscopy and surface plasmon resonance (SPR). It was found that T5-POM exhibits very high affinity for complementary ssDNA and RNA, similar to that of a T5-PNA oligomer. SPR experiments also showed that T5-POM binds with high sequence fidelity to ssDNA under near physiological conditions. In addition, it was found possible to attenuate the binding affinity of T5-POM to ssDNA and RNA by varying both the ionic strength and pH. However, the most striking feature exhibited by T5-POM is an unprecedented kinetic binding selectivity for ssRNA over DNA.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Pairing*
  • Biomimetic Materials / chemical synthesis
  • Biomimetic Materials / chemistry*
  • Drug Design*
  • Hydrogen-Ion Concentration
  • Magnetic Resonance Spectroscopy
  • Models, Molecular
  • Nucleic Acid Denaturation
  • Nucleic Acid Hybridization
  • Oligonucleotides / chemical synthesis*
  • Oligonucleotides / chemistry*
  • Osmolar Concentration
  • Pyrrolidines / chemistry*
  • Surface Plasmon Resonance
  • Temperature
  • Thymidine / chemistry*

Substances

  • Oligonucleotides
  • Pyrrolidines
  • pyrrolidine
  • Thymidine