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. 

Hydrophobic interactions exerted by substituents at position 5 of cytosine or uracil enhance stability of DNA/RNA-hybrids (70,71) [163]. Derivatives with longer alkyl chains reduce duplex stability [169], with aminoalkyl residues being an exemption [170]. Above all, ethinyl substitution at position C5 of pyrimidine bases results in significantly increased binding affinity, as shown with binding of modified poly(rU) and poly(rA) [164]. Also, substitution with propinyl showed the same effect (73,74), which was attributed to ji-ji-interactions of the alkinyl substituent with the nucleobase in the 5 -neighbourhood. Oligomers of this type form duplexes with RNA, which can activate RNase-H. Since there is only a minor influence on nuclease resistance, such modifications are preferentially applied in combination... 

PNA oligomers are synthetic DNA mimics possessing an amide backbone which are able to base pair with DNA and RNA in an anti-parallel fashion (Fig. 7) [25]. The most interesting difference between DNA and PNA is the neutral backbone possessed by PNA at physiological pH. Consequently this leads to an increased stability of the duplexes they form with DNA and PNA oligomers can therefore be shorter than corresponding ONDs when used... 

The above described model sequences have been studied both as oligomers [7,8,11-13,19] and as polymers [9,11,20]. An increase in the size of the helix is known to reinforce its stability, as revealed by their melting curves [18] and attested by X-ray diffraction measurements in solution [21]. Therefore, in this chapter we focus on the polymeric duplexes poly(dGdC).poly(dGdC) [= 1000 base-pairs], poly(dAdT).poly(dAdT) [= 200-400 base-pairs] and poly(dA).poly(dT) [= 2000 base-pairs] studied by us. First we discuss the absorption spectra, which reflect the properties of Franck-Condon states, in connection with theoretical studies. Then we turn to fluorescence properties fluorescence intensity decays (hereafter called simply fluorescence decays ), fluorescence anisotropy decays and time-resolved fluorescence spectra. We... 

The luminescence of the hybridized [Ru(phen)2(dppz)]2+ derivative may be used to characterize the molecular assembly (77). Dilution experiments show that intercalation is intramolecular at concentrations <5 mM duplex addition of unmodified duplex to the covalently bound duplex results in <5% change in the luminescence. The results of experiments performed on duplexes containing mismatches in various positions along the duplex are also consistent with intramolecular intercalation. In this series, luminescence is higher for mismatches near the ruthenated end of the oligomer, where the ruthenium complex can intercalate intramolecularly and stabilize the mismatched site. 

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