Circular dichroism of DNA

Azizi, A., Ranjbar, B., Moghadam, T.T., Bagheri, Z., Baglou, S.R., 2014. Surface plasmon resonance coupled circular dichroism of DNA—gold nanorods assembly. J. Phys. D Appl. Phys. 47 (31), 315-401. 

Paramasivan S, Rujan I, Bolton PH (2007) Circular dichroism of quadruplex DNAs Applications to structure, catione effects and ligand binding. Methods 43 324-331... 

The transition from B-DNA to Z-IMA was first observed in solution by the near inversion of the circular dichroism of... 

Fig. 1. Circular dichroism of genomic DNA in 0.01 M HEPES (pH 7.4). a Normal young DNA, b normal aged DNA, c moderately affected AD DNA, and d severely affected AD...

Burckhardt G, Zimmer C, Luck G (1976) Conformatitm and reactivity of DNA in the complex with protein IV. Circular dichroism of poly-l-histidine model ctunplexes with DNA polymers and specificity of the interactitm. Nucleic Acids Res 3 561-580... 

The unmodified and complementary oligonucleotides were also synthesized, in order to detect thermodynamic and spectroscopic differences between the double helices. Circular dichroism spectra revealed that the covalently bound anthracene does not stack in the centre of the DNA double helix. Mutagenic activity by intercalative binding of the anthracene residue is thus unlikely. Only in vitro and in vivo replication experiments with site-specifically modified... 

Small-angle X-ray scattering (SAXS), circular dichroism (CD), and UV spectroscopy at different temperatures were used to investigate the nature of calf-thymus DNA in aqueous solution, in the presence of [Me Sn] " (n = 1-3) species. The results demonstrate that the [MeSn(IV)] moiety does not influence the structure and conformation of the DNA double helix, and does not degrade DNA, as indicated by agarose gel electrophoresis. Inter alia, the radii of gyration, Rg, of the cross section of native calf-thymus DNA, determined by SAXS in aqueous solution in the presence of [Me Sn] " (n = 1-3) species are constant and independent of the nature and concentration of the [Me Sn] species. 

Peculiar DNA architecture was demonstrated in 25% aqueous ethanol when DNA was complexed with series of cationic detergents in the presence of poly(glutamic acid) [124]. Electron microscopy and x-ray scattering demonstrated that DNA can pack cetyltrimethylammonium bromide molecules into rodlike micelles, which form a hexagonal lattice. Interestingly, circular dichroism spectroscopy revealed that in these complexes DNA adopts left-handed conformation. 

The racemization of the phosphine (118) has been followed by optical rotation. The lack of a solvent effect indicates that there is little change in dipole moment in the formation of the planar transition state. Circular dichroism has been used to study the interactions of nucleotides with proteins and DNA with a histone. Faraday effects have been reviewed. Refraction studies on chloro-amino-phosphines, fluoro-amino-phosphines, and some chalcogenides are reported. 

Fig. 8 Interaction of palmatine with various B-DNAs as obtained from competition dialysis (a), spectrofluorimetric (b), circular dichroism (c) and thermal melting (d) studies. (Reprinted from [176] with permission from Elsevier)...

Measurement of the melting temperature (Tm) and the circular dichroism (CD) spectrum of AQ-DNA(l) shows that it is a duplex at room temperature... 

The first silver clusters made using DNA as template were reported by Dickson et al. in 2004 [32], The paper describes the time-dependent formation of silver clusters in a 12-base (5 -AGGTCGCCGCCC-3 ). The clusters have intense absorption in the region 400-550 nm (Fig. 2b) and emission at around 630 nm. The latter band could be decomposed as the emission bands of two distinct excitations at 540 and 580 nm, indicating the existence of two different emitters. As the clusters do not have inherent chirality, the induced circular dichroism associated with the silver cluster electronic transitions is evidence that the clusters are bound to DNA (Fig. 2c). 

Fig. 2 (a) Schematic of the formation of silver clusters using DNA oligonucleotide as scaffold. After complexation of DNA with silver cations, the mixture is reduced with NaBtL, and the fluorescent cluster is formed, (b) Absorption spectra of silver clusters acquired every 30 min using [5 -AGGTCGCCGCCC-3 ] = 10 uM. [Ag+] = 60 uM. and [BfLj-] = 60 pM. The foremost spectrum was acquired 9 min after adding the BH4, and it has at 426 nm. The inset spectrum shows the last spectmm in the series (692 min), with peaks at 424 and 520 nm. (c) Induced circular dichroism spectra. The cell path length was 5 cm. The spectra were collected 2 min (A, dashed-dotted line), 20 min (B, dotted line), 40 min (C,fine dashed line), 60 min (D, coarse dotted line), and 150 min (E, solid line) after adding the BH [32]... 

Ho et al. were able to verify the a-helical shape of the polymer by circular dichroism (CD) spectra. No structural elements were observed until the formation of the double helical DNA at which point they observed a right-handed a-helix in the polythiophene backbone. Their work demonstrates the power of fluorometric detection as they noted a seven order of magnitude increase in detection sensitivity (20 fM in 200 pi) simply through the use of fluorometric detection as opposed to UV-vis absorption. The polymer in solution has a high fluorescence yield with a maximum at 530 nm (Fig. 11a). Upon formation of the duplex the fluorescence is significantly quenched (Fig. lib), while with the addition of the complementary DNA and triplex formation, the fluorescence intensity is enhanced by a factor of 5 (Fig. 11c). The inherent sensitivity of the spectral shift even allowed distinction between DNA with only one and two mismatched bases (Fig. lOBd, e). 

Linear dichroism data with DNA oriented by an electric field [53, 54] or a linear flow [55, 56], under linearly polarised light, lead to determinations of the angle between the absorbing transition dipole moment of the chromophore in the molecule and the DNA helix axis conclusions concerning intercalation may thus be drawn from this technique. Finally, with chiral compounds, circular dichroism is also an attractive method to determine the enantioselectivity in the binding of the molecule [48, 57,58]. 

In the absence of conclusive data on the role of a positive supercoiling wave, static positive supercoiling elicited by nucleosome reconstitution on relaxed or slightly positively-supercoiled plasmids [51] or by ethidium bromide intercalation in the loop of mononucleosomes on DNA minicircles [52] did not succeed either in releasing dimers. Moreover, circular dichroism, histone chemical modi-flcation and H3-thiol accessibility failed to detect an even slight alteration in the structure of such torsionally-stressed nucleosomes [51]. The reason was later found to lie in the ability of nucleosome entry/exit DNAs to form a positive crossing [52]. 

Fig. 27. Circular dichroism spectra of calf thymus DNA at pH 7 (27 °C) in dilute concentrations of electrolytes72). The spectra displayed above are the average obtained in 0.01 M and 0.04 M concentrations of NaCl (-----------), KC1 (---------), LiCl (OOO), CsCl ( ) and NH4C1 ( ). The...

---