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Published November 6, 2002 | Supplemental Material
Journal Article Open

2-Aminopurine: A Probe of Structural Dynamics and Charge Transfer in DNA and DNA:RNA Hybrids


Spectroscopic techniques are employed to probe relationships between structural dynamics and charge transfer (CT) efficiency in DNA duplexes and DNA:RNA hybrids containing photoexcited 2-aminopurine (Ap*). To better understand the variety of interactions and reactions, including CT, between Ap* and DNA, the fluorescence behavior of Ap* is investigated in a full series of redox-inactive as well as redox-active assemblies. Thus, Ap* is developed as a dual reporter of structural dynamics and base−base CT reactions in nucleic acid duplexes. CD, NMR, and thermal denaturation profiles are consistent with the family of DNA duplexes adopting a distinct conformation versus the DNA:RNA hybrids. Fluorescence measurements establish that the d(A)−r(U) tract of the DNA:RNA hybrid exhibits enhanced structural flexibility relative to that of the d(A)−d(T) tract of the DNA duplexes. The yield of CT from either G or 7-deazaguanine (Z) to Ap* in the assemblies was determined by comparing Ap* emission in redox-active G- or Z-containing duplexes to otherwise identical duplexes in which the G or Z is replaced by inosine (I), the redox-inactive nucleoside analogue. Investigations of CT not only demonstrate efficient intrastrand base−base CT in the DNA:RNA hybrids but also reveal a distance dependence of CT yield that is more shallow through the d(A)−r(U) bridge of the A-form DNA:RNA hybrids than through the d(A)−d(T) bridge of the B-form DNA duplexes. The shallow distance dependence of intrastrand CT in DNA:RNA hybrids correlates with the increased conformational flexibility of bases within the hybrid duplexes. Measurements of interstrand base−base CT provide another means to distinguish between the A- and B-form helices. Significantly, in the A-form DNA:RNA hybrids, a similar distance dependence is obtained for inter- and intrastrand reactions, while, in B-DNA, a more shallow distance dependence is evident with interstrand CT reactions. These observations are consistent with evaluations of intra- and interstrand base overlap in A- versus B-form duplexes. Overall, these data underscore the sensitivity of CT chemistry to nucleic acid structure and structural dynamics.

Additional Information

© 2002 American Chemical Society. Received June 10, 2002. Publication Date (Web): October 12, 2002. We gratefully acknowledge the National Institutes of Health for financial support of this work (GM49216). We also thank the Natural Sciences and Engineering Research Council of Canada (NSERC) for a postdoctoral fellowship (M.A.O.). We appreciate the assistance of Prat Bhattacharya, Eric Stemp, and Julia Lyubovitsky with NMR experiments, nanosecond transient absorption, and picosecond fluorescence measurements, respectively.

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