Local DNA base conformations and ligand intercalation in DNA constructs containing optical probes (Biophysical Journal)

Understanding local conformations of DNA at the level of individual nucleic acid bases and base-pairs is important for elucidating molecular processes that depend on DNA sequence. Here we apply linear absorption and circular dichroism (CD) measurements to the study of local DNA conformations, using the guanine base analogue 6-methyl isoxanthopterin (6-MI) as a structural probe. We show that the spectroscopic properties of this probe can provide detailed information about average local base and base-pair conformations as a function of the surrounding DNA sequence.