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Hydrogen Bond Mediated Association of Dinucleotide Analogs

Abstract Several dinucleotide analogs, in which two of the nucleobases adenine, thymine and uracil are connected by a hexadecamethylene linker have been synthesized and studied for their base-base interaction in a chloroform solution. Using 1H NMR spectroscopic techniques intramolecular base pair formation through hydrogen bonding is observed at ambient temperatures but found to strongly depend on the identity of paired bases. Thus, whereas cyclization through intramolecular base-base interactions predominate for adenine–(CH2)16–thymine and adenine–(CH2)16–uracil, no intramolecular adenine-adenine pairing was observed. Upon addition of acetic acid to adenine–(CH2)16–thymine, strong adenine-acetic acid interactions result in the disruption of preformed intramolecular adenine-thymine base pairs.