Duplex-Stabilization Properties of Oligodeoxynucleotides Containing N 2 -Substituted Guanine Derivatives by Ramon Eritja* a ) 1 ), Antonio R. Díaz a ), and Ester Saison-Behmoaras b ) a ) European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, D-69117 Heidelberg b ) Museum National d Histoire Naturelle, 43 rue Cuvier, F-75231 Paris Cedex 05 Dedicated to Prof. Dr. Frank Seela on the occasion of his 60th birthday Oligodeoxynucleotides 3 ± 13 carrying different guanine derivatives with substituents at the N 2 position have been prepared from a common precursor. Duplexes containing these modified bases are more stable than unmodified duplexes. The highest stability is found in guanine derivatives carrying at N 2 an ethyl and propyl group substituted with a group that is protonated under physiological conditions, which is compatible with a possible interaction of the protonatable group with the phosphates. 1. Introduction. ± The ability of oligonucleotides to form double-stranded structures with their complementary RNA and DNA sequences has been widely used for the isolation of cloned DNA sequences, the detection of specific genes, and the identification of specific mRNA sequences [1]. More recently, this ability is being used to inhibit gene expression (antisense and antigene strategy) [2] and to analyze the expression patterns of a large number of genes using oligonucleotide microarrays [3]. All these approaches rely on nucleic-acid hybridization, and they are expected to benefit from oligonucleotide analogs with better hybridization properties. A large number of nucleic-acid derivatives with enhanced binding properties have been developed [4]. Peptide nucleic acids (PNA) [5], hexitol nucleic acids (HNA) [6], 2'- fluoro-N3'-P5' phosphoramidates [7], and locked nucleic acids (LNA) [8] are examples of backbone-modified derivatives with enhanced binding properties. However, simple substitutions in the sugar moiety such as 2'-O-alkyl-RNA derivatives [9] and substitutions in the nucleobases also lead to substantial increases in duplex stability. N 2 -Substituted derivatives of guanine ( Fig. 1) are among these base-modified analogs with interesting binding properties [10 ± 15]. First, the interest in the preparation of oligonucleotides carrying N 2 -substituted derivatives of guanine was generated by the reaction of some carcinogenic compounds with guanine to yield adducts bound to the NH 2 C(2) group of guanine. These modified oligonucleotides were important intermediates in the carcinogenesis of polycyclic aromatic hydro- carbons (PAH) [16]. Later, the attachment of an imidazole moiety to the exocyclic amino group of guanine was described [11]. Oligonucleotide-imidazole conjugates were prepared to promote RNA hydrolysis [12]. Later, it was found that imidazolyl Helvetica Chimica Acta ± Vol. 83 (2000) 1417 1 ) Present address. C.I.D.-C.S.I.C. , Jordi Girona 18 ± 26, E-08034 Barcelona, Spain (phone:  34 93 4 00 61 45, fax:  34 93 2 04 59 04; e-mail: recgma@cid.csic.es).