Conformation and dynamics of nucleotides in bulges and symmetric internal loops in duplex DNA studied by EPR and fluorescence spectroscopies
- University of Iceland, Science Institute, Dunhaga 3, 107 Reykjavik (Iceland)
Highlights: Black-Right-Pointing-Pointer Bulges and loops were studied by both EPR and fluorescence spectroscopies using the probe C/C{sup f}. Black-Right-Pointing-Pointer One-base bulge was in a temperature-dependent equilibrium between looped-out and stacked states. Black-Right-Pointing-Pointer Bases in two- and three-base bulges were stacked at all temperatures, resulting in DNA bending. Black-Right-Pointing-Pointer Bases were stacked in symmetrical two- to five-base internal loops, according to EPR data. Black-Right-Pointing-Pointer Unexpectedly high fluorescence for the smaller loops indicated local structural perturbations. -- Abstract: The dynamics and conformation of base bulges and internal loops in duplex DNA were studied using the bifunctional spectroscopic probe C, which becomes fluorescent (C{sup f}) upon reduction of the nitroxide functional group, along with EPR and fluorescence spectroscopies. A one-base bulge was in a conformational equilibrium between looped-out and stacked states, the former favored at higher temperature and the latter at lower temperature. Stacking of bulge bases was favored in two- and three-base bulges, independent of temperature, resulting in DNA bending as evidenced by increased fluorescence of C{sup f}. EPR spectra of C-labeled three-, four- and five-base symmetrical interior DNA bulges at 20 Degree-Sign C showed low mobility, indicating that the spin-label was stacked within the loop. The spin-label mobility at 37 Degree-Sign C increased as the loops became larger. A considerable variation in fluorescence between different loops was observed, as well as a temperature-dependence within constructs. Fluorescence unexpectedly increased as the size of the loop decreased at 2 Degree-Sign C. Fluorescence of the smallest loops, where a single T{center_dot}T mismatch was located between the stem region and the probe, was even larger than for the single strand, indicating a considerable local structural deformation of these loops from regular B-DNA. These results show the value of combining EPR and fluorescence spectroscopy to study non-helical regions of nucleic acids.
- OSTI ID:
- 22207808
- Journal Information:
- Biochemical and Biophysical Research Communications, Vol. 420, Issue 3; Other Information: Copyright (c) 2012 Elsevier Science B.V., Amsterdam, The Netherlands, All rights reserved.; Country of input: International Atomic Energy Agency (IAEA); ISSN 0006-291X
- Country of Publication:
- United States
- Language:
- English
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