Electrophoresis, Vol.23, No.7-8, 1013-1020, 2002
Circular dichroism signatures of features simultaneously present in structured guanine-rich oligonucleotides: A combined spectroscopic and electrophoretic approach
In order to identify possible signatures of the most typical structures adopted by guanine-rich oligonucleotides, we submitted them to the crossed fire of circular dichroism (CD) and electrophoresis. These signatures show up in the circular dichroism spectra even when simultaneously present within the same molecule. Guanine-rich oligonucleotides, when structured, manifest themselves by CID contributions around 260 or 295 nm. For instance, positive bands at 264 nm and 295 nm, respectively, signal the parallel and antiparallel guanine quartets, while a positive band around 261 nm may indicate the presence of a (parallel?) Hoogsteen duplex. A positive band at 264 nm may also reflect the presence of rigidly and unusually oriented GpT and TpG steps within loops. The signatures are additive with those of other structural features of the same molecule, such as hairpins or Watson-Crick duplexes, whose bands are observed at 280 nm.
Keywords:aptamer;bulges;floating tails;guanine quartets;Hoogsteen duplex;parallel and antiparallel tetraplex;Watson-Crick pairing