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NMR imino proton exchange experiments on duplex DNA primarily monitor the opening of purine bases.

ABSTRACT: Molecular dynamics simulations were performed to investigate GC and AT base opening events in DNA. Calculated equilibrium constants between the base open (or flipped) and closed states were shown to be in good agreement with experimental data from NMR imino proton exchange experiments. Analysis of the computed results indicates that the equilbrium constants are dominated by the opening of the A and G bases in the AT and GC base pairs, respectively. Thus, the present results predict that NMR imino proton exchange experiments of base opening are primarily monitoring the opening of purine bases.

SUBMITTER: Priyakumar UD

PROVIDER: S-EPMC2542507 | biostudies-literature | 2006 Jan

REPOSITORIES: biostudies-literature

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NMR imino proton exchange experiments on duplex DNA primarily monitor the opening of purine bases.

Priyakumar U Deva UD Mackerell Alexander D AD

Journal of the American Chemical Society 20060101 3

Molecular dynamics simulations were performed to investigate GC and AT base opening events in DNA. Calculated equilibrium constants between the base open (or flipped) and closed states were shown to be in good agreement with experimental data from NMR imino proton exchange experiments. Analysis of the computed results indicates that the equilbrium constants are dominated by the opening of the A and G bases in the AT and GC base pairs, respectively. Thus, the present results predict that NMR imin ...[more]

PMID: 16417331

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Project description:BackgroundFor the conservation and management of migratory species that strongly decrease or increase due to anthropological impacts, a clear delineation of populations and quantification of possible mixing (migratory connectivity) is crucial. Usually, population exchange in migratory species is only studied in breeding or wintering sites, but we considered the whole annual cycle in order to determine important stages and sites for population mixing in an Arctic migrant.MethodsWe used 91 high resolution GPS tracks of Western Palearctic greater white-fronted geese (Anser A. albifrons) from the North Sea and Pannonic populations to extract details of where and when populations overlapped and exchange was possible. Overlap areas were calculated as dynamic Brownian bridges of stopover, nest and moulting sites.ResultsUtilisation areas of the two populations overlapped only somewhat during spring and autumn migration stopovers, but much during moult. During this stage, non-breeders and failed breeders of the North Sea population intermixed with geese from the Pannonic population in the Pyasina delta on Taimyr peninsula. The timing of use of overlap areas was highly consistent between populations, making exchange possible. Two of our tracked geese switched from the North Sea population flyway to the Pannonic flyway during moult on Taimyr peninsula or early during the subsequent autumn migration. Because we could follow one of them during the next year, where it stayed in the Pannonic flyway, we suggest that the exchange was long-term or permanent.ConclusionsWe have identified long-distance moult migration of failed or non-breeders as a key phenomenon creating overlap between two flyway populations of geese. This supports the notion of previously suggested population exchange and migratory connectivity, but outside of classically suggested wintering or breeding sites. Our results call for consideration of moult migration and population exchange in conservation and management of our greater white-fronted geese as well as other waterfowl populations.

Dataset Information

NMR imino proton exchange experiments on duplex DNA primarily monitor the opening of purine bases.

Publications

NMR imino proton exchange experiments on duplex DNA primarily monitor the opening of purine bases.

Similar Datasets

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