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.
Hickman
David T
DT
Department of Chemistry, University of Manchester Institute of Science and Technology, Faraday Building, PO Box 88, Manchester, UK M60 1QD.
Tan
T H Samuel
TH
Morral
Jordi
J
King
Paul M
PM
Cooper
Matthew A
MA
Micklefield
Jason
J
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