Design, synthesis, conformational analysis and nucleic acid hybridisation properties of thymidyl pyrrolidine-amide oligonucleotide mimics (POM)Electronic supplementary information (ESI) available: experimental details (16 Figures, 3 Tables). See http://www.rsc.org/suppdata/ob/b3/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.

Biophysical and Cellular‐Uptake Properties of Mixed‐Sequence Pyrrolidine–Amide Oligonucleotide Mimics

“…Indeed X‐ray crystallographic evidence, along with molecular modelling and NMR spectroscopy data suggest that when protonated, the pyrrolidine ring of POM oligomers can favour an N 1′‐ endo (pseudo‐ C 3′‐ endo ) conformation similar to that adopted by ribose in RNA 21. 22 The C 3′‐ endo conformation is known to favour the formation of RNA A‐type duplexes;29 this can also explain why the rate of annealing of POM to RNA is increased to a greater extent than is the rate of association/dissociation with DNA upon the lowering of pH. Additionally, in the free amine form inversion of configuration of the pyrrolidine nitrogen is possible and the resulting equilibrium between configurations can also lead to a reduction in the rate of association/dissociation at higher pH.…”

“…This is consistent with the previous observations with POM homopolymers, which also hybridise more slowly than do native nucleic acids. [20][21][22][23][24][25] The first mixed-sequence POM oligomer Lys-POM-TCA-CAACTT-NH 2 (1) was synthesised with an N-terminal lysine residue to enable comparison with the isosequential PNA, which requires the Lys residue to improve its solubility. [26] It is possible that attachment of Lys to a POM or PNA oligomer will have an effect on the DNA and RNA hybridisation properties.…”

“…[19] Short homo-oligomers of the previously reported pyrrolidine-amide oligonucleotide mimics (POM) have shown promising binding affinity for DNA and RNA (Scheme 1). [20][21][22][23][24][25] In addition, a Boc-Z solid-phase synthesis protocol was developed, which led to the first mixed-sequence POM (Lys-TCACAACTT-NH 2 , 1). [26] Preliminary UV thermal denaturation studies revealed that mixed-sequence POM 1 is capable of hybridising with sequence specificity to both complementary parallel and antiparallel RNA and DNA.…”

Solid-Phase Synthesis of Positively Charged Deoxynucleic Guanidine (DNG) Tethering a Hoechst 33258 Analogue: Triplex and Duplex Stabilization by Simultaneous Minor Groove Binding

“…One approach is the incorporation of neutral internucleoside linkages that eliminate mutual repulsions between the negatively charged phosphodiester backbones. − Another approach is to replace the entire phosphodiester backbone, such as in the cases of peptide nucleic acid (PNA), phosphonic ester nucleic acids (PHONA), and nucleic acid analogue peptide (NAAP) . Recent studies have shown that the introduction of positively charged groups at multiple sites in the backbone, , sugar, or base can produce stable duplexes and triplexes . Our approach is to replace the phosphodiester linkages with positively charged achiral guanidinium groups.…”