We combined various experimental (scanning tunneling microscopy and Raman spectroscopy) and theoretical (density functional theory and molecular dynamics) approaches to study the relationships between the base-pairing patterns and the charge transfer properties in DNA 32-mer duplexes that may be relevant for identification and repair of defects in base pairing of the genetic DNA and for DNA use in nanotechnologies. Studied were two fully Watson-Crick (W-C)-paired duplexes, one mismatched (containing three non-W-C pairs), and three with base pairs chemically removed. The results show that the charge transport varies strongly between these duplexes. The conductivity of the mismatched duplex is considerably lower than that of the W-C-paired one despite the fact that their structural integrities and thermal stabilities are comparable. Structurally and thermally much less stable abasic duplexes have still lower conductivity but not markedly different from the mismatched duplex. All duplexes are likely to conduct by the hole mechanism, and water orbitals increase the charge transport probability.