| Abstract
| - A new design for DNA bases and base pairs is described in which the pyrimidine bases arewidened by naphtho-homologation. Two naphtho-homologated deoxyribosides, dyyT (1) and dyyC (2), weresynthesized and could be incorporated into oligonucleotides as suitably protected phosphoramiditederivatives. The deoxyribosides were found to be fluorescent, with emission maxima at 446 and 433 nm,respectively. Studies with single substitutions of 1 and 2 in the natural DNA context revealed exceptionallystrong base stacking propensity for both. Sequences containing multiple substitutions of 1 and 2 pairedopposite adenine and guanine were subsequently mixed and studied by several analytical methods. Datafrom UV mixing experiments, FRET measurements, fluorescence quenching experiments, and hybridizationson beads suggest that complementary “doublewide DNA” (yyDNA) strands may self-assemble into helicalcomplexes with 1:1 stoichiometry. Data from thermal denaturation plots and CD spectra were less conclusive.Control experiments in one sequence context gave evidence that yyDNA helices, if formed, are preferentiallyantiparallel and are sequence selective. Hypothesized base pairing schemes are analogous to Watson−Crick pairing, but with glycosidic C1‘−C1‘ distances widened by over 45%, to ca. 15.2 Å. The possibleself-assembly of the double-wide DNA helix establishes a new limit for the size of information-encoding,DNA-like molecules, and the fluorescence of yyDNA bases suggests uses as reporters in monomeric andoligomeric forms.
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