Oligonucleotides, stability conformation

In terms of physiological conditions, DNA exists almost totally in the double-helical conformation. Certain oligonucleotides also exhibit the ability to form triple-helixes with the DNA double strands. The stability of DNA secondary structures strongly depends on the environmental conditions, such as ionic strength, pH, temperature and solvents. Temperature is the most widely used environmental variable for the quantitative characterization of the helix-coil transitions. A commonly accepted characteristic of the thermal stability of DNA secondary structures is melting temperature, Tm. The binding of cationic species, such as multivalent... 

There are two reports describing the use of nucleosides with other sugar conformations. A method for preparing internally P-labelled l-DNA has been described using T4 polynucleotide kinase. Chimeric DNA composed of tandem a- and p-anomeric strands have been used in TFOs and shown to have enhanced thermal stability compared to all a- or p-anomeric oligonucleotides. ... 

The use of nonbiological nucleobases to enhance oligonucleotide duplex stability is widespread, and an exhaustive exploration of this field is beyond the scope of this review. At the same time, recent studies exist that go beyond this goal with the aim of understanding the function of base interactions in duplex stability and the impact of unusual nucleobases on both conformation and assembly. Herein, we focus on a few of these examples as representatives of the field and to highlight how modifications at nucleobase sites that are remote from the backbone can have profound architectural effects on... 

The 5 -phosphoramidite of the novel bicyclic nucleoside (14), restricted to an S-type conformation, has been synthesised in eight steps via double inversion of configuration at the C4 position of protected l-(3 -deoxy-p-D-psicofuranosyl)uracyl and introduction of an azide moiety. The secondary amino group at C4 permitted the subsequent incorporation of (14) into oligonucleotides via a 5 -3 directed variation of the standard phosphoramidite approach for synthesis of oligonucleotides. Thermal denaturation studies showed rather large decreases in duplex stabilities toward complementary DNA and RNA. ... 

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