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Nucleic Acids Research, 2001, Vol. 29, No. 12 2522-2534
© 2001 Oxford University Press

The effect of amino groups on the stability of DNA duplexes and triplexes based on purines derived from inosine

Elena Cubero, Ramon Güimil-García1, F. Javier Luque2, Ramon Eritja1 and Modesto Orozco*

Departament de Bioquímica i Biologia Molecular, Facultat de Química, Universitat de Barcelona, Martí i Franques 1, Barcelona 08028, Spain, 1Instituto de Biología Molecular de Barcelona, C.S.I.C., Jordi Girona 18-26, Barcelona 08034, Spain and 2Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Avgda Diagonal s/n, Barcelona 08028, Spain

The effect of amino groups attached at positions 2 and 8 of the hypoxanthine moiety in the structure, reactivity and stability of DNA duplexes and triplexes is studied by means of quantum mechanical calculations, as well as extended molecular dynamics (MD) and thermodynamic integration (MD/TI) simulations. Theoretical estimates of the change in stability related to 2'-deoxyguanosine (G) -> 2'-deoxyinosine (I) -> 8-amino-2'-deoxyinosine (8AI) mutations have been experimentally verified, after synthesis of the corresponding compounds. An amino group placed at position 2 stabilizes the duplex, as expected, and surprisingly also the triplex. The presence of an amino group at position 8 of the hypoxanthine moiety stabilizes the triplex but, surprisingly, destabilizes the duplex. The subtle electronic redistribution occurring upon the introduction of an amino group on the purine seems to be responsible for this surprising behavior. Interesting ‘universal base’ properties are found for 8AI.

* To whom correspondence should be addressed. Tel: +34 93 402 1719; Fax: +34 93 402 1219; Email: modesto@luz.bq.ub.es Correspondence may also be addressed to Ramon Eritja. Tel: +34 93 400 6145; Fax: +34 93 204 5904; Email: recgma{at}cid.csic.es


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