An FTIR spectroscopic study of calf-thymus DNA complexation with Al(III) and Ga(III) cations.
ABSTRACT The interaction of calf-thymus DNA with trivalent Al and Ga cations, in aqueous solution at pH = 6-7 with cation/DNA(P) (P = phosphate) molar ratios (r) 1/80, 1/40, 1/20, 1/10, 1/4 and 1/2 was characterized by Fourier Transform infrared (FTIR) difference spectroscopy. Spectroscopic results show the formation of several types of cation-DNA complexes. At low metal ion concentration (r = 1/80, 1/40), both cations bind mainly to the backbone PO2 group and the guanine N-7 site of the G-C base pairs (chelation). Evidence for cation chelate formation comes from major shifting and intensity increase of the phosphate antisymmetric stretch at 1222 cm-1 and the mainly guanine band at 1717 cm-1. The perturbations of A-T base pairs occur at high cation concentration with major helix destabilization. Evidence for cation binding to A-T bases comes from major spectral changes of the bands at 1663 and 1609 cm-1 related mainly to the thymine and adenine in-plane vibrations. A major reduction of the B-DNA structure occurs in favor of A-DNA upon trivalent cation coordination.
SourceAvailable from: Alfredo Gonzalez-Perez
Article: Reversible DNA Compaction.[Show abstract] [Hide abstract]
ABSTRACT: In this review we summarize and discuss the different methods we can use to achieve reversible DNA compaction in vitro. Reversible DNA compaction is a natural process that occurs in living cells and viruses. As a result these process long sequences of DNA can be concentrated in a small volume (compacted) to be decompacted only when the information carried by the DNA is needed. In the current work we review the main artificial compacting agents looking at their suitability for decompaction. The different approaches used for decompaction are strongly influenced by the nature of the compacting agent that determines the mechanism of compaction. We focus our discussion on two main artificial compacting agents: multivalent cations and cationic surfactants that are the best known compacting agents. The reversibility of the process can be achieved by adding chemicals like divalent cations, alcohols, anionic surfactants, cyclodextrins or by changing the chemical nature of the compacting agents via pH modifications, light induced conformation changes or by redox-reactions. We stress the relevance of electrostatic interactions and self-assembly as a main approach in order to tune up the DNA conformation in order to create an on-off switch allowing a transition between coil and compact states. The recent advances to control DNA conformation in vitro, by means of molecular self-assembly, result in a better understanding of the fundamental aspects involved in the DNA behavior in vivo and serve of invaluable inspiration for the development of potential biomedical applications.Current topics in medicinal chemistry 01/2014; DOI:10.2174/1568026614666140118221948 · 3.45 Impact Factor
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ABSTRACT: Metal-mediated base pairs by the interaction between metal ions and artificial bases in oligonucleotides have been developed for their potential applications in nanotechnology. We recently found that a natural T:T mismatched base pair bound with Hg2+ ion to form a novel T–Hg–T base pair. Here, we examined the thermodynamic properties of the binding between Hg2+ and each of the single and double T:T mismatched base pair duplex DNAs by isothermal titration calorimetry. Hg2+ specifically bound with the T:T mismatched base pair at 1:1 molar ratio with 106M−1 binding constant, which was significantly larger than those for nonspecific metal ion–DNA interactions. In the Hg2+–double T:T mismatched base pair interaction, the affinity for the second Hg2+ binding was significantly larger than that for the first Hg2+ binding. The positively cooperative binding may be favorable to align multiple Hg2+ in duplex DNA for the application of the metal-mediated base pairs in nanotechnology.Thermochimica Acta 03/2012; DOI:10.1016/j.tca.2011.03.018 · 2.11 Impact Factor