Improved synthesis of natural isomeric naphthoxanthenones

[Display omitted] •A pair of natural isomeric naphthoxanthenones were prepared with efficiency and in the mmol scale.•Cyclocondensation and Buchwald hydroxylation were implemented as key steps.•The compounds show DNA-intercalation ability. 5-methoxy-1H-naphtho[2,1,8-mna]xanthen-1-one (1) and 5-methoxy-3H-naphtho[2,1,8-mna]xanthen-3-one (musafluorone 2), a pair of positional isomers isolated from Wachendorfia thyrsiflora and Musa acuminata, were synthesized in six steps in an overall yield of 53% and 59% starting from the corresponding methoxyphenalenones and employing an acid mediated cyclocondensation strategy. Preliminary assays demonstrated the intercalation ability of compounds 1 and 2 into DNA.