Abstract
Triplex stability is studied in crowding conditions using small cosolutes (ethanol, acetonitrile and dimethylsulfoxide) by ultraviolet (UV), circular dichroism (CD) and nuclear magnetic resonance (NMR) spectroscopies. The results indicate that the triplex is formed preferentially when the triplex forming oligonucleotide (TFO) is RNA. In addition, DNA triplexes (D:D·D) are clearly less stable in cosolute solutions while the stability of the RNA triplexes (R:D·D) is only slightly decreased. The kinetic of triplex formation with RNA-TFO is slower than with DNA-TFO and the thermal stability of the triplex is increased with the salt concentration in EtOH-water solutions. Accordingly, RNA could be considered a potential molecule to form a stable triplex for regulatory purposes in molecular crowding conditions.
Highlights
The structural polymorphism of nucleic acids is due to the inherent conformational flexibility
Changes in the conformation of nucleic acids can be detected by circular dichroism (CD), so that the comparison of experimentally measured spectra with those corresponding to known structures may suggest a particular conformation
In EtOH, we observed an increase in the intense negative band upon addition of the RNA triplex forming oligonucleotide (TFO) to the hairpin indicating the formation of the triplex
Summary
The structural polymorphism of nucleic acids is due to the inherent conformational flexibility. We studied the effect of small cosolutes (EtOH, acetonitrile (ACN) and DMSO) that “mimic” molecular crowding or dehydrating agents on the formation and stability of short triplex structures. These structures are formed by short polypurine-polypyrimidine hairpins and DNA or RNA polypyrimidine triplex forming strands (Table 1). As in the case of hairpins 1 and 2, addition of 20% DMSO and 20% EtOH in RNA triplexes produces a small destabilization in relation to the values observed in the absence of cosolutes.
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