Melting Analysis of DNA Dumbbells with Repeating Dinucleotide Stem Sequences Reveals Evidence for Long Range Sequence Dependent Interactions in Short Duplex DNA.

Peter M. Vallone, Richard Owczarzy, Peter V. Riccelli, and Albert S. Benight
Department of Chemistry, University of Illinois, Chicago, IL 60607

Melting Analysis of DNA Dumbbells with Repeating Dinucleotide Stem Sequences Reveals Evidence for Long Range Sequence Dependent Interactions in Short Duplex DNA. Optical and DSC melting studies were performed on 12 DNA dumbbells in 85 mM Na+. The stems of the six DNA dumbbell molecules contained the central sequences (AA)n, (GG)n, (GC)n, (AT)n, (AC)n, (n=10). These six sequences were the minimal set required to represent the 10 possible dinucleotide sequences in DNA. Central sequences of all dumbbells were adjoined on both ends by the same 12 base pair sequences and T4 end-loops. Dumbbells with the (AG)n central sequences n = 5, 20, and 30 were also studied. Optical melting curves were analyzed in terms of the nearest-neighbor (n-n) model using a database comprised of optical melting results for 39 DNA dumbbells with the same end-loops and end sequences but different central sequences. In 85 mM Na+ the original database for 39 dumbbells indicated the n-n model could provide fits of the melting data with statistical accuracy. When the data for dumbbells with the (AG)10, (AT)10 or (GC)10 stem sequences were added to the database and analyzed, the n-n model was unable to accurately fit the data. This suggested the existence of sequence dependent interactions beyond n-n's in these repeating sequences. A correction factor required to account for these interactions in (AG)n sequences was evaluated.