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Nucleic Acids Research, 1990, Vol. 18, No. 21 6353-6359
© 1990

CHEMISTRY

Circular dichroism studies of an oligodeoxyribonucleotide containing a hairpin loop made of a hexaethylene glycol chain: conformation and stability

M. Durand, K. Chevrie, M. Chassignol, N.T. Thuong and J.C. Maurizot*

Centre de Biophysique Moléculaire, 1A Avenue de la Recherche Scientifique 45071 Orleans Cedex 2, France

*To whom correspondence should be addressed

Received July 30, 1990. Revised September 20, 1990. Accepted September 20, 1990.

An ollgodeoxyribonucteotide. d(GCTCACAAT-X-ATTGT-GAGC), where X represents a hexaethylene glycol chain, was studied using circular dichroism spectroscopy. Its conformation and conformatlonal stability were compared to those of compounds where X was replaced by four thymines and to the duplex of same sequence without loop. The compound with the hexaethylene glycol chain can form a hairpin looped structure as well as a bulged duplex structure. In both cases the duplex region of the oligodeoxyribonucleotide exhibits the same conformation. In similar conditions the oligodeoxyribonucleotide with a four thymines loop forms exclusively a hairpin structure. Comparison between the thermodynamic parameters ({delta}H,{delta}S,{delta}G) associated with the formation of the structure of the three compounds are presented. In the case of the compound with the hexaethylene glycol chain it is shown that the large increase in its melting temperature (by about 35°C in our experimental conditions) when compared to the non looped structure is mainly due to the fact that its melting process is intramolecular (monomolecular) whereas the other one is bimolecular.


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