Hairpin duplex

Figure 17 Molecular structures of the electron acceptor methylviologen (MV2+) and of a DNA hairpin duplex (4GC) containing a 4,4 -stilbenedicarboxamide bridge (St).

F. Legendre, J. Kozelka, J.-C. Chottard, to be published (results with hairpin duplex). 

Parvoviridae is a family of small icosahedral, nonenveloped animal viruses that contain a linear ssDNA genome of approximately 5000 bases with short unique terminal palindromic sequences that fold back on themselves to form hairpin duplexes (van Regenmortel et al, 2000). They are further classified into two subfamilies, Parvcwirinae and Densovirinae, and various genera depending on host specificity, strand specificity of the genomic ssDNA, and on whether helper viruses are required for productive infection (dependoviruses). Members of the Parvoviridae... 

Figure 12 Schematic illustration of modes of inter- and intramolecular triple-helix formation (a) termolecular Y RY and R RY motifs (b) bimolecular from a hairpin duplex (RY) and a single strand (Y) (c) bimolecular from a hairpin loop (YY) and a single strand (R) and (d) single-strand intramolecular...

Analogues chelated to metal ions have been incorporated into oligonucleotides. The incorporation into an 11-mer DNA duplex of the bipyridine ligand (bpy), (78), such that two bpy units are complementary, yields a duplex that can be stabilised by copper ions. In the presence of copper, the duplex melts 10°C higher. In another report, phenanthroline-based (79) nucleosides have been incorporated into ODNs as hybridisation probes. Hairpin duplexes have been synthesised containing two phenanthroline nucleosides, one containing Ru" which exhibits a long-lived excited state, the other Os , which is non-emissive... 

NMR structure of a 2 -deoxy-2 -fluoro-D-arabinose (aF) nucleic acid duplex has been reported. The structure is a hybrid hairpin duplex containing a ribose-aF stem duplex and a four-residue DNA loop (177). The RNA strand adopted the classical A-form structure with endo sugar puckers, whilst the aF strand contained O -endo puckers and was intermediate between A- and B-form, similar to that found in DNA-RNA structures. 

The rich coordination chemistry of transition metal ions has been used not only to create metal-ligand complexes that play the role of alternative nucleo-base pairs within nucleic acid duplexes, but also to influence the secondary structure adopted by the nucleic acid, for example, hairpin, duplex, or triplex, and to create connectors for such nucleic acid structures. In this context, oligonucleotides that contain terminal ligands can lead to structures distinct from those accessible by using centrally-modified oligonucleotides, such as cyclic structures or hairpins (Fig. 3). 

Figure 6. P NMR spectra at 109.3 MHz of sonicated alternating purine—pyrimidine hairpin duplexes. Key a, poly(dAdT), 30°C b, poly(dAdbr U), 31°C c, poly(dAdU), 31°C d, poly(dldC). 39°C and e, poly(dGdC), 23°C all in 0.1 M NaCl, 0.05 mM EDTA, pH 6-7 except b in 5 mM tris-Cl, 0.1 mM EDTA (12).

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