Nucleic acids, resonance energy

Algar WR, Krull UJ (2008) Quantum dots as donors in fluorescence resonance energy transfer for the bioanalysis of nucleic acids, proteins, and other biological molecules. Anal Bioanal Chem 391 1609-1618... 

Clegg, R. M. (1992). Fluorescence resonance energy transfer and nucleic acids. Methods. Enzymol. 211, 353-358. 

Klostermeier, D. and D. P. Millar. Time-resolved fluorescence resonance energy transfer A versatile tool for the analysis of nucleic acids. Biopolymers 61, 159-179 (2002). 

Walter, N. G. (2003). Probing RNA structural dynamics and function by fluorescence resonance energy transfer (FRET). Curr. Protoc. Nucleic Acid Chem. Chapter 11, Unit 11 10. 

Ozaki, H., and Mclaughlin, L. W. (1992). The estimation of distances between specific backbone-labeled sites in DNA using fluorescence resonance energy transfer. Nucleic Acids Res. 20, 5205—5214. 

ASAXS provides valuable spatial information about ions associated to nucleic acids. Because ion resonance is X-ray energy specific, a particular ionic species can be targeted in ASAXS experiments (even in conditions where there are multiple ionic species in the bulk solution). In this section, we provide several examples of how ASAXS experiments can be used to study counterion atmospheres around DNA and RNA. 

A third type of information available from NMR comes from the nuclear Overhauser enhancement or NOE. This is a direct through-space interaction of two nuclei. Irradiation of one nucleus with a weak radio frequency signal at its resonant frequency will equalize the populations in its two energy levels. This perturbation of population levels disturbs the populations of nearby nuclei so as to enhance the intensity of absorbance at the resonant frequency of the nearby nuclei. This effect depends only on the distance between the two nuclei, even if they are far apart in the bonding network, and varies in intensity as the inverse sixth power of the distance. Generally the NOE can only be detected between protons (XH nuclei) that are separated by 5 A or less in distance. These measured distances are used to determine accurate three-dimensional structures of proteins and nucleic acids. 

What is remarkable is that all of these early measurements of the UV resonance Raman spectra of nucleic acid components involved computational and theoretical support to their experimental findings. For example, Spiro used CINDO calculations to determine the nature of the excited electronic states of the nucleotides [157], In the early and mid 1970 s, many researchers were also attempting to understand resonance Raman spectroscopy, the types of information it could provide, and a unifying theoretical framework to the intensities [147, 159-172], UV resonance Raman spectra provided some of the first experimental evidence to test the various theoretical models. Peticolas attempted to fit the observed experimental excitation profiles of AMP [156], UMP [151, 154] and CMP [152, 153] to the sum-over-states model for the resonance Raman cross-sections. From these simulations, they were able to obtain preliminary excited-state structural dynamics of the nucleobase chromophores of the nucleotides for UMP [151, 153, 158] and CMP [153], For AMP, the experimental excitation profiles were simulated with an A-term expression, but the excited-state structural changes were not obtained. Rather, the goal of that work was to identify the electronic transitions within the lowest-energy absorption band of adenine [156],... 

While the capture on DNA chips of fluorophore-labelled targets, and the extension of arrayed primers with fluorophore-labelled nucleotides has been widely used for some time, it is only more recently that assay formats have developed that utilize immobilized nucleic acids already modified with fluorophores. Fundamental analyses of surface monolayer structures and chemistries can be readily performed by immobilizing such modified oligonucleotides into SAM structures [105,106], but it is those interactions that can be monitored using fluorescence quenching or fluorescence resonance energy transfer (FRET) that have gained the most attention. 

Marras SA, Kramer FR, Tyagi S. Efficiencies of fluorescence resonance energy transfer and contact-mediated quenching in oligonucleotide probes. Nucleic Acids Res. 2002 30 el22. 

Cardullo RA, Agrawal S, Flores C, Zamecnik PC, Wolf DE. Detection of nucleic acid hybridization by non-radiative fluorescence resonance energy transfer. Proc. Natl. Acad. Sci. U.S.A. 36. 1988 85 8790-8794. 

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