Stacking-unstacking dynamics of oligodeoxynucleotide trimers.
The structure and dynamics of DNA trimers are experimentally assessed using the fluorescent purine analogue 2-aminopurine (2AP), incorporating 2AP between purine and pyrimidine bases to form 5'dXp2APpY3' molecules. Circular dichroism and fluorescence quenching of the 2AP show that the bases are stacked; at the same time, fluorescence decay lifetimes are heterogeneous, indicative of conformational sampling. 2AP does not exhibit the long fluorescence decay time characteristic of the free nucleoside, suggesting that its motions in the trimers bring it into proximity of the neighboring bases, resulting in efficient charge transfer and average fluorescence lifetimes on the order of 1-2 ns.
Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, USA. jjean@wanda.wustl.edu
John M
JM
Jean
Kathleen B
KB
Hall
D015075:2-Aminopurine / Q000737:chemistry; D002942:Circular Dichroism; D005454:Fluorescence Polarization; D031541:Fluorescence Resonance Energy Transfer; D007700:Kinetics; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry*; D013696:Temperature; D013816:Thermodynamics
D009838:Oligodeoxyribonucleotides; D015075:2-Aminopurine