Thermal stability oligomer duplex

Since Nielsen et al introduced peptide nucleic acids (PNA), this area has received vast attention, and continues to do so. More recently, the main area of interest has been in novel analogues, and many new ones have been reported. The solid phase synthesis of DNA-3 -PNA chimeras have been described, in which the DNA is attached to the amino terminal of the PNA via the 3 -phosphate or thiophosphate. All chimeras were shown to have superior thermal stability towards either DNA or RNA than a DNA oligomer, and the phosphodiester linkage was more stable than the phosphorothioate. Hybridisation studies with PNA and PNA-DNA chimeras demonstrate that there is a sequence effect for the junction between PNA and DNA on duplex stability. A decamer pyrimidine bis-PNA oligomer, separated by a linker, when targeted to complementary dsDNA formed three distinct structures. One structure contained two bis-PNA units, and the other two were believed to be structural isomers. 

PNA occurs as both E- and Z-rotamers in un-complexed forms, but in duplexes it is uniformly oriented in the Z-form. Schutz et u/. have prepared olefinic PNA (OPA) in which the amide bond is replaced by the isostructural C-C double bond in both E- and Z-configurations (19, 20). Incorporation of either isomer into OPA resulted in a decrease in thermal stability against DNA with similar affinity. Homopolymers of OPA also did not form triplexes. OPA also binds preferentially in the parallel mode. A PNA oligomer to which has been attached diethylenetriamine (DETA) via a urea bond was shown to cleave an RNA target at micromolar concentrations under physiological conditions. ... 

The thermal stability of the duplex, and therefore the possibilities of observation under optimal conditions for NMR spectroscopy (ambient temperature, low or medium ionic strength, 1 10 mM oligomer concentration) depends upon several factors, e.g. 

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