Parallel and antiparallel A*A-T intramolecular triple helices.

Analytical resolution of parallel and antiparallel oligonucleotide triple helices formation and melting processes by means of Multivariate Curve Resolution

Specific loop modifications of the thrombin-binding aptamer trigger the formation of parallel structures.

Guanine-rich sequences show large structural variability, with folds ranging from duplex to triplex and quadruplex helices. Quadruplexes are polymorphic, and can show multiple stoichiometries, parallel and antiparallel strand alignments, and different topological arrangements. We analyze here the equilibrium between intramolecular antiparallel and intermolecular parallel G-quadruplexes in the t...

Spectroscopic studies of chimeric DNA-RNA and RNA 29-base intramolecular triple helices.

Fourier transform infrared (FTIR), UV absorption and exchangeable proton NMR spectroscopies have been used to study the formation and stability of two intramolecular pH-dependent triple helices composed by a chimeric 29mer DNA-RNA (DNA double strand and RNA third strand) or by the analogous 29mer RNA. In both cases decrease of pH induces formation of a triple helical structure containing either...

Comparison of antiparallel A.AT and T.AT triplets within an alternate strand DNA triple helix.

We have examined the formation of alternate strand triple-helices at the target sequence A11(TC)6.(GA)6T11 using the oligonucleotides T11(AG)6 and T11(TG)6, by DNase I footprinting. These third strands were designed so as to form parallel T.AT triplets together with antiparallel G.GC and A.AT or T.AT triplets. We find that, although both oligonucleotides yield clear footprints at similar concen...

Protein dissection of the antiparallel coiled coil from Escherichia coli seryl tRNA synthetase.

The alpha-helices of coiled-coil proteins are predominantly parallel, in contrast to the general preference for an antiparallel orientation of interacting alpha-helices found in globular proteins. One intriguing exception is the antiparallel, two-stranded coiled coil comprising the long helical arm of the bacterial seryl tRNA synthetases (SRS). A recombinant 82-residue peptide corresponding to ...