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Nucleic acids containing double-headed nucleotides with additional nucleobases attached to the 5′(S)-position of thymidine through a methylene linker are studied. The additional bases are oriented towards base-base interactions in the minor groove of the DNA-double helix. Two new examples with adenine or cytosine as the additional bases as well as an analogue with a 4N-methylpiperazine in the same position are introduced, and in a combined study with the original double-headed nucleotide containing two thymines, interactions between the additional nucleobases across the minor groove are detected. Finally, a duplex with two thymines in the minor groove is cross-linked using UV irradiation.

Double-headed nucleotides in DNA-zipper structures; base–base interactions and UV-induced cross-coupling in the minor groove