Design, synthesis, conformational analysis and nucleic acid hybridisation properties of thymidyl pyrrolidine-amide oligonucleotide mimics (POM).
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.
Department of Chemistry, University of Manchester Institute of Science and Technology, Faraday Building, PO Box 88, Manchester, UK M60 1QD.
David T
DT
Hickman
T H Samuel
TH
Tan
Jordi
J
Morral
Paul M
PM
King
Matthew A
MA
Cooper
Jason
J
Micklefield
D020029:Base Pairing; D040761:Biomimetic Materials / Q000138:chemical synthesis / Q000737:chemistry*; D015195:Drug Design; D006863:Hydrogen-Ion Concentration; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D009691:Nucleic Acid Denaturation; D009693:Nucleic Acid Hybridization; D009841:Oligonucleotides / Q000138:chemical synthesis* / Q000737:chemistry*; D009994:Osmolar Concentration; D011759:Pyrrolidines / Q000737:chemistry*; D020349:Surface Plasmon Resonance; D013696:Temperature; D013936:Thymidine / Q000737:chemistry*
D009841:Oligonucleotides; D011759:Pyrrolidines; C032519:pyrrolidine; D013936:Thymidine