Competitive binding exchange between alkali metal ions (K+, Rb+, and Cs+) and Na+ ions bound to the dimeric quadruplex [d(G4T4G4)]2: a 23Na and 1H NMR study

A comparative study of the competitive cation exchange between the alkali metal ions K⁺, Rb⁺, and Cs⁺ and the Na⁺ ions bound to the dimeric quadruplex [d(G₄T₄G₄)]₂ was performed in aqueous solution by a combined use of the ²³Na and ¹H NMR spectroscopy. The titration data confirm the different binding affinities of these ions for the G‐quadruplex and, in particular, major differences in the behavior of Cs⁺ as compared to the other ions were found. Accordingly, Cs⁺ competes with Na⁺ only for the binding sites at the quadruplex surface (primarily phosphate groups), while K⁺ and Rb⁺ are also able to replace sodium ions located inside the quadruplex. Furthermore, the ¹H NMR results relative to the CsCl titration evidence a close approach of Cs⁺ ions to the phosphate groups in the narrow groove of [d(G₄T₄G₄)]₂. Based on a three‐site exchange model, the ²³Na NMR relaxation data lead to an estimate of the relative binding affinity of Cs⁺ versus Na⁺ for the quadruplex surface of 0.5 at 298 K. Comparing this value to those reported in the literature for the surface of the G‐quadruplex formed by 5′‐guanosinemonophosphate and for the surface of double‐helical DNA suggests that topology factors may have an important influence on the cation affinity for the phosphate groups on DNA. Copyright © 2009 John Wiley & Sons, Ltd.     

Structure–Activity Relationship Study of a Potent α-Thrombin Binding Aptamer Incorporating Hexitol Nucleotides

The replacement of one or more nucleotide residues in the potent α-thrombin-binding aptamer NU172 with hexitol-based nucleotides has been devised to study the effect of these substitutions on the physicochemical and functional properties of the anticoagulant agent. The incorporation of single hexitol nucleotides at the T9 and G18 positions of NU172 substantially retained the physicochemical features of the parent oligonucleotide, as a result of the biomimetic properties of the hexitol backbone. Importantly, the NU172- T ^H9 mutant exhibited a higher binding affinity toward human α-thrombin than the native aptamer and an improved stability even after 24 h in 90 % human serum, with a significant increase in the estimated half-life. The anticoagulant activity of the modified oligonucleotide was also found to be slightly preferable to NU172. Overall, these results confirm the potential of hexitol nucleotides as biomimetic agents, while laying the foundations for the development of NU172-inspired α-thrombin-binding aptamers.     

Structural characterisation of trimethylsilyl-protected DNA bases

The structures of the silylated DNA bases, bis(trimethylsilyl)thymine (1), bis(trimethylsilyl)cytosine (2), bis(trimethylsilyl)adenine (3) and tris(trimethylsilyl)guanine (4), have been determined. 1 is O-silylated and displays no intermolecular interactions. 2 is silylated at both exocylic O, N positions and forms a chain structure through intermolecular NH…O and NH…N hydrogen bonds. 3 contains two SiMe₃ groups, on the exocylic NH and endocyclic N⁹ position, respectively; of two independent molecules in the asymmetric unit, one dimerises through complementary NH…N hydrogen bonds, while the other forms a strained intramolecular hydrogen bond through the same pair of donor and acceptor centres. 4 incorporates N, N, O–SiMe₃ moieties and forms chains via bifurcated CH…O/N hydrogen bonds, while the NH function remains unexploited. The effects of silylation on these pyrimidine and purine ring structures are also discussed in comparison with the native bases.

The structures of the silylated DNA bases, bis-(trimethylsilyl)thymine (1), bis-(trimethylsilyl)cytosine (2), bis-(trimethylsilyl)adenine (3) and tris-(trimethylsilyl)guanine (4), have been determined. While 1 displays no intermolecular interactions. 2 forms a chain structure through intermolecular NH…O and NH…N hydrogen bonds, 3 incorporates two independent molecules in the asymmetric unit, one dimerises through complementary NH…N hydrogen bonds while the other forms a strained intramolecular hydrogen bond through the same pair of donor and acceptor centres and 4 forms chains via bifurcated CH…O/N hydrogen bonds while the NH function remains unexploited.     

Adenosine Triphosphate Sensing by Electrocatalysis with DNAzyme

Electrocatalysis of redox enzymes shows wide application for biosensing. DNAzymes exhibiting specific catalytic activities have aroused great interest recently. However, there are few studies on the electrocatalysis between DNAzyme and electron mediator. In this paper, based on the electrocatalysis of methylene blue (MB) and horseradish peroxidase mimicking DNAzyme (HRP‐DNAzyme), an amplified electrochemical biosensor for the detection of adenosine triphosphate (ATP) was designed. In the present system, by means of the ATP‐aptamer interaction, two guanine‐rich DNA sequences, one of which was labeled with MB at the 5′ end, were assembled on the gold electrode. In the presence of K⁺ and hemin, the guanine‐rich DNA sequences transferred to HRP‐DNAzyme. The conformational change of the structure resulted in the approaching of MB and HRP‐DNAzyme which made the electrocatalytic process between MB and HRP‐DNAzyme possible. We used cyclic voltammetry and electrochemical impedance spectroscopy to study the electrocatalytic process. The system was therefore utilized for amplified detection of ATP without imposing any new constraints to the platform which showed satisfactory result.     

Direct and Single‐Molecule Visualization of the Solution‐State Structures of G‐Hairpin and G‐Triplex Intermediates

We present the direct and single‐molecule visualization of the in‐pathway intermediates of the G‐quadruplex folding that have been inaccessible by any experimental method employed to date. Using DNA origami as a novel tool for the structural control and high‐speed atomic force microscopy (HS‐AFM) for direct visualization, we captured images of the unprecedented solution‐state structures of a tetramolecular antiparallel and (3+1)‐type G‐quadruplex intermediates, such as G‐hairpin and G‐triplex, with nanometer precision. No such structural information was reported previously with any direct or indirect technique, solution or solid‐state, single‐molecule or bulk studies, and at any resolution. Based on our results, we proposed a folding mechanism of these G‐quadruplexes.     

Preparation of Benz[b]Indeno[1,2-e]Pyran-11(6H)-Ones and Benz[b]Indeno[1,2-e]Thiopyran-11(6H)-One from Dilithiated 2-Indanone and Lithiated Methyl Salicylates or Lithiated Methyl Thiosalicylate

Dilithiated 2-indanone was prepared with excess lithium diisopropylamide, and the resulting intermediate was condensed with several lithiated methyl salicylates or lithiated methyl thiosalicylate, which was followed by acid cyclization to benz[b]indeno[1,2-e]pyran-11(6H)-ones 3--9 or benz[b]indeno[1,2-e]thiopyran-11(6H)-one 10, which are rare fused-ring indeno-chromones and a new indeno-thiochromone, respectively.     

Reaction of hypochlorous acid with imidazole: formation of 2-chloro- and 2-oxoimidazoles

Reaction of hypochlorous acid (HOCl) with imidazole (Im) taken as a model for the 5-membered ring of guanine, leading to the products 2-chloro- and 2-oxo-imidazoles was investigated at the B3LYP/6-31+G* and B3LYP/AUG-cc-pVDZ levels of density functional theory. For all cases, single point energy calculations were performed at the MP2/AUG-cc-pVDZ level of theory using the geometries optimised at the B3LYP/AUG-cc-pVDZ level. Intrinsic reaction coordinate calculations were performed to ensure genuineness of all the calculated transition states. Effect of aqueous media was investigated by solvating all the species involved in the reactions using the polarizable continuum model. It is found that 2-chloroimidazole (2-ClIm) can be formed following three different reaction schemes while 2-oxoimidazole (2-oxoIm) can be formed following two different reaction schemes. The calculated barrier energies show that formation of 2-oxoIm would be less favored than that of 2-ClIm, which explains the experimental observations on relative yields of 8-chlorodeoxyguanosine and 8-oxodeoxyguanosine.