NMR spectroscopy and molecular dynamics simulations have been used to study the DNA complexes of the bisintercalating antitumour agent MLN 944 and two of its analogues, to shed light on the structure activity relationships amongst -(CH2)n-N(R)-(CH2)m-N(R)-(CH2)n-linked phenazine-1-carboxamide dimers (for MLN 944 R = H, n and m = 2). MLN 944 is known to be a template inhibitor of transcription, and to inhibit the binding of transcription factors to DNA. We were interested to know what influence the phenazine-9-methyl group, which imparts enhanced cytotoxic potency on MLN 944, has on the structure of the DNA complex, and in investigating the solution structure of the complex of the compound in which R = methyl, n = 2, and m = 3, C3N,N′-dimethyl MLN, since this linker also enhances biological activity in the MLN series. Accordingly, we have studied complexes of the 3 ligands, MLN 944, Des-methyl MLN, and C3N,N′-dimethyl MLN with the 3 self-complementary oligonucleotides d(ATGCAT)2, d(TATGCATA)2, and d(TACGCGTA)2 using a variety of 1D- and 2D-NMR methods and molecular dynamics simulations employing the AMBER 12 force field. The dynamics simulations were conducted in explicit solvent with neutralising Na+ ions for a duration of 10 ns using particle-mesh Ewald electrostatics. Simulations were performed with and without NOE-restraints, enabling an evaluation of the quality of the force field when used without experimental constraints. We find that all three compounds bind as dications, in which the chromophores are uncharged, to all three DNAs in the DNA major groove spanning the central 2 GC base pairs in a manner that maintains the dyad symmetry of the DNA. The carboxamide group lies in the plane of the chromophore, its NH making hydrogen bonding interactions with the phenazine N10 nitrogen, and the protonated linkers form hydrogen bonds with the O6 atom of guanine. We conclude that the 9-methyl group of MLN 944 little affects complex structure, but that it slows dissociation of the ligand. C3N,N′-dimethyl MLN has two chiral centres located at the linker nitrogens yielding RR, SS, and RS enantiomers, all three of which bind to DNA and are observed to be in fast exchange in the bound state. At equilibrium the linkers of these three bound forms effectively occupy a greater volume of space than found for MLN 944, a circumstance that better might antagonise DNA binding of transcription factors or RNA polymerase.