Electrochemical and CD spectroscopy study of DNA and RNA hairpins
| Authors | |
|---|---|
| Year of publication | 2009 |
| Type | Article in Proceedings |
| Conference | International Symposium on Frontiers of Electrochemical Science and Technology - Book of Abstracts |
| MU Faculty or unit | |
| Citation | |
| Field | Electrochemistry |
| Keywords | hairpin; electrochemistry; CD spectroscopy |
| Description | Hairpins play an important role in many biological processes, including the triplet repeat expansion associated with neurodegenerative diseases, such as fragile X syndrome, Huntington s disease, Friedreich s ataxia or myoclonic epilepsy. They also form a part of several anomalous DNA or RNA arrangements as triplexes or quadruplexes. The shortest and most stable hairpin yet characterized is formed by the DNA heptamer d(GCGAAGC). This sequence is found in replication origins of phage X 174 and herpes simplex virus, in a promoter region of an Escherichia coli heat-shock gene, and in rRNA genes. We have studied the d(GCGAAGC) hairpin and its RNA analog by means of voltammetric methods, CD spectroscopy and electrophoresis. On mercury electrodes, both DNA and RNA hairpins provide voltammetric reduction signals of adenine and cytosine and oxidation signals of guanine. The dependences of cyclic voltammetry (CV), linear sweep voltammetry (LSV), and elimination voltammetry with linear scan (EVLS) signals on pH, accumulation time, scan rate, and loop sequences have been determined. CD spectroscopy in combination with gel electrophoresis showed a strong dependence of the hairpin arrangement and stability on the hairpin loop sequence. Replacement of the middle GAA triplet with the dinucleotide GA distinctly altered the hairpin structure and decreased its thermostability by more than 50oC. The RNA analog r(GCGAAGC) formed a hairpin at low temperatures only. At temperatures around 37oC the RNA hairpin transformed with a slow kinetics to a double-stranded A-form duplex. This was expected due to the rigidity of RNA, which is manifested in a preference for duplex over hairpin under many conditions. The study emphasizes the advantages of comparison of results obtained by in principle distinct methods. |
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