Circular dichroism nucleic acids

C. Helene, T. Montenay-Garestier, and J. L. Dimicoli, Interactions of tyrosine and tyramine with nucleic acids and their components. Fluorescence, nuclear magnetic resonance, and circular dichroism studies, Biochim. Biophys. Acta 254, 349-365 (1971). 

Optical Spectroscopy General principles and overview, 246, 13 absorption and circular dichroism spectroscopy of nucleic acid duplexes and triplexes, 246, 19 circular dichroism, 246, 34 bioinorganic spectroscopy, 246, 71 magnetic circular dichroism, 246, 110 low-temperature spectroscopy, 246, 131 rapid-scanning ultraviolet/visible spectroscopy applied in stopped-flow studies, 246, 168 transient absorption spectroscopy in the study of processes and dynamics in biology, 246, 201 hole burning spectroscopy and physics of proteins, 246, 226 ultraviolet/visible spectroelectrochemistry of redox proteins, 246, 701 diode array detection in liquid chromatography, 246, 749. 

Several direct methods are available to analyze the tertiary structure of ODNs like nuclear magnetic resonance (NMR) and X-ray crystallographic (XRC) techniques, which needs a sophisticated setup and infrastructure. An alternative but indirect method to study the structure and conformations of nucleic acids is circular dichroism spectroscopy (CD spectroscopy) (25, 26), where circular dichroism refers to the differential absorption of left and right circularly polarized light (27). 

Baase WA, Johnson WC Jr (1979) Circular dichroism and DNA secondary structure. Nucleic Acids Res 2 797-814... 

Induced Circular Dichroism in Nucleic Acid-Dye Systems... 

Circular Dichroism Spectral Properties of Nucleic Acids... 

Feasibility of the Induced Circular Dichroism Technique for Nucleic Acid Research... 

The significance of light absorption in biochemical studies lies in the great sensitivity of electronic energy levels of molecules to their immediate environment and to the fact that spectrophotometers are precise and sensitive. The related measurements of circular dichroism and fluorescence also have widespread utility for study of proteins, nucleic acids, coenzymes, and many other biochemical substances that contain intensely absorbing groups or chromophores.58... 

Vibrational circular dichroism involves IR absorption bands. The technique has been applied to sugars,110 oligosaccharides,111 proteins,112 and nucleic acids.113 The related vibrational Raman optical activity has also been applied to polyribonucleotides.114... 

Evdokimov, Y.M., Pyatigorskaya, T.L., Polyvtsev, O.F., Akimenko, N.M., Kadykov, V.A., Tsvanki, D.Y. and Marshavsky, Y.M. (1976) A comparative x-ray diffraction and circular dichroism study ofDNA compact particles formed in water-salt solutions, containing polyethylene glycol). Nucleic Acids Res., 3, 2353-2366. 

Bioactive macromolecules like peptides, proteins, and nucleic acids have been successfully embedded in planar LbL films. An important question is the retention of the bioactivity of the film-embedded biomolecules. The structural properties and stability of the LbL films formed from synthesized polypeptides of various amino acid sequences were recently reported [50]. The authors showed that control over the amino acid sequence enables control over non-covalent interpolypeptide interaction in the film, which determines the film properties. Haynie and coworkers showed by circular dichroism spectroscopy that the extent of adsorption of poly(L-glutamic acid) (PGA) and poly(L-lysine) (PLL) in the LbL films scales with the extent of secondary structure of the polypeptides in solution [51]. Boulmedais demonstrated that the secondary structure of the film composed of these polypeptides is the same as the peptide structure in the complex formed in solution [52], as found by Fourier transform IR spectroscopy (FUR). 

Protein-DNA Complexes. Circular dichroism has been used to characterize protein secondary structure in many kinds of nucleic acid-binding proteins, their mutants, and derivatives. Similarly, CD has been employed to characterize the structural changes which occur in the nucleic acids as well, but these are beyond the scope of the present work. Our discussion here will center on a few examples of the use of CD for characterizing structural changes which occur in DNA-binding proteins. 

Circular dichroism(CD) is the differential absorption of left- and right-handed circularly polarized light, due to molecules that have optical handedness or optical activity (this happens for most molecules of biological interest—for example, the a helix, [1 sheet, and random coil regions of proteins and the double helix of nucleic acids have recognizable CD spectral signatures). 

Combined SAXS/Circular dichroism beamline. Biological macromolecules, such as proteins, carbohydrates and nucleic acids, are composed of many optically active or chiral units that exhibit large Circular Dichroism (CD) signals. CD spectroscopy has therefore been used extensively in the study of proteins, where asymmetric carbon atoms in their amino acid backbone give rise to a CD spectrum. The shape of the spectrum depends on the protein s secondary structure content and allows the proportions of helix, beta structure, turns and random to be determined. 

Aside from the intrinsic circular dichroism originating from the molecular structure, a so-called induced optical activity may result when a molecule is situated in an asymmetric environment. Magnetic circular dichroism, for instance, maybe produced by applying an external magnetic field to an absorbing sample. Adsorption of pigment molecules on nucleic acids or protein molecules may also induce circular dichroism. 

Fixation of ais- and trons-DDP, but not [Pt(dien)Cl]Cl, disrupts DNA basestacking. Spectroscopic studies such as UV hyperchromism and circular dichroism reflect the immediate environment of the base and are sensitive probes of conformational changes involving, at most, several nucleic acid bases. Between... 

Yang Jen Tsi and SamejimaTatsuya (1971) Optical Rotatory Dispersion and Circular Dichroism of Nucleic Acids. Ed. University Press, California, San Francisco. 

Typical CD spectra for proteins and nucleic acids are shown in Figures 2.20 and 2.21. It is important to remember that only chiral samples can give rise to circular dichroism or other optical activity phenomena. Because circular dichroism is made up of a difference between absorbances, a CD spectrum may be positive or negative depending on wavelength, and the shape of the spectrum is generally characteristic of the conformation of the molecules involved. 

Circular dichroism measurements can give information about secondary structure in proteins and nucleic acids. 

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