Parallel stranded DNA with AT base pairing

The concentration and temperature dependences of the UV and CD spectra of the oligonucleotide 3′-d(ApTpApTpApTpApTpApTp)-O(CH 2) 6O-5′-d(pApTpApTpApTpApTpApT) (eicosamer) in aqueous solution at pH 7 in the presence of 0.5 M NACl were studied. At less than 10 −6 M, the eicosamer was shown to form in solution a hairpin with parallel orientation of chains (parallel hairpin). From thermal denaturation profiles [ A 260( T)] the thermodynamic parameters, ΔH°, ΔS° and T m for parallel hairpin formation were calculated to be −90±8 kJ/mol. −300±20 J · mol −1 · K −1 and 40.5°C, respectively. The CD spectra of the parallel double helix differed from those of B-form DNA and had characteristic features: decreasing magnitude of the positive maximum at 265 nm and a negative peak at 285 nm.