A Chimeric DNA/RNA Antiparallel Quadruplex with Improved Stability

Nucleic acid quadruplexes are proposed to play a role in the regulation of gene expression, are often present in aptamers selected for specific binding functions and have potential applications in medicine and biotechnology. Therefore, understanding their structure and thermodynamic properties and designing highly stable quadruplexes is desirable for a variety of applications. Here, we evaluate DNA→RNA substitutions in the context of a monomolecular, antiparallel quadruplex, the thrombin-binding aptamer (TBA, GGTTGGTGTGGTTGG) in the presence of either K⁺ or Sr²⁺. TBA predominantly folds into a chair-type configuration containing two G-tetrads, with G residues in both syn and anti conformation. All chimeras with DNA→RNA substitutions (G→g) at G residues requiring the syn conformation demonstrated strong destabilization. In contrast, G→g substitutions at Gs with anti conformation increased stability without affecting the monomolecular chair-type topology. None of the DNA→RNA substitutions in loop positions affected the quadruplex topology; however, these substitutions varied widely in their stabilizing or destabilizing effects in an unpredictable manner. This analysis allowed us to design a chimeric DNA/RNA TBA construct that demonstrated substantially improved stability relative to the all-DNA construct. These results have implications for a variety of quadruplex-based applications including for the design of dynamic nanomachines.     

Oxidation of guanines in the iron-responsive element RNA: similar structures from chemical modification and recent NMR studies

Background: The translation or stability of the mRNAs from ferritin, m-aconitase, erythroid aminoevulinate synthase and the transferrin receptor is controlled by the binding of two iron regulatory proteins to a family of hairpin-forming RNA sequences called iron-responsive elements (IREs). The determination of higher-solution nuclear magnetic resonance (NMR) structures of IRE variants suggests an unusual hexaloop structure, leading to an intra-loop G-C base pair and a highly exposed loop guanine, and a special internal loop/bulge in the ferritin IRE involving a shift in base pairing not predicted with standard algorithms.Results: Cleavage of synthetic 55- and 30-mer RNA oligonucleotides corresponding to the ferritin IRE with complexes based on oxoruthenium(IV) shows enhanced reactivity at a hexaloop guanine and at a guanine adjacent to the internal loop/bulge with strong protection at a guanine in the internal loop/bulge. These results are consistent with the recent NMR structures. The synthetic 55-mer RNA binds the iron-regulatory protein from rabbit reticulocyte lysates. The DNA analogs of the 55- and 30-mers do not show the same reactivity pattern.Conclusions: The chemical reactivity of the guanines in the ferritin IRE towards oxoruthenium(IV) supports the published NMR structures and the known oxidation chemistry of the metal complexes, The results constitute progress towards developing stand-alone chemical nucleases that reveal significant structural properties and provide results that can ultimately be used to constrain molecular modeling.     

Effect of SIMS ionization probability on depth resolution for organic/inorganic interfaces

Secondary ion mass spectrometry (SIMS) relies on the fact that surface particles ejected from a solid surface are ionized under ion bombardment. By comparing the signal of molecular secondary ions desorbed from an organic film with that of the corresponding sputtered neutral precursor molecules, we investigate the variation of the molecular ionization probability when depth profiling through the film to the substrate interface. As a result, we find notable variations of the ionization probability both at the original surface and in the interface region, leading to a strong distortion of the measured SIMS depth profile. The experiments show that the effect can act in two ways, leading either to an apparent broadening or to an artificial sharpening of the observed film‐substrate transition. As a consequence, we conclude that care must be taken when assessing interface location, width, or depth resolution from a molecular SIMS depth profile.     

Density Functional Theory Study of the Interaction between Guanine and Catechin

The interacting patterns and mechanism of the catechin and guanine have been investigated with the density functional theory B3LYP method by 6‐31G* basis set. Fourteen stable structures for the catechin‐guanine complexes have been found which form two hydrogen bonds at least. The results indicate that the complexes are mainly stabilized by the hydrogen bonding interactions. At the same time, the number and strength of hydrogen bond play a co‐determinant parts in the stability of the complexes which can form two or more hydrogen bonds. Theories of atoms in molecules (AIM) and natural bond orbital (NBO) have been adopted to investigate the hydrogen bonds involved in all systems. The interaction energies of all complexes have been corrected for basis set superposition error (BSSE), ranging from ?38.86 to ?14.56 kJ/mol. The results showed that the hydrogen bonding contributes to the interaction energies dominantly. The corresponding bonds stretching motions in all complexes are red‐shifted relative to that of the monomer, which is in agreement with experimental results.     

镍纳米粒子修饰碳糊电极直接电催化鸟嘌呤的研究

将镍纳米粒子与石蜡、石墨按照一定比例混合制备镍纳米粒子修饰碳糊电极,采用循环伏安法(CV)对修饰碳糊电极进行电化学表征,在0.1 mol/L B-R缓冲溶液(pH4.5)中研究了鸟嘌呤在该修饰电极上的电化学行为。结果表明,与裸碳糊电极相比,以掺杂法制备的镍纳米粒子修饰电极能够明显降低鸟嘌呤的过电位,增大其氧化电流,很好地催化氧化鸟嘌呤。在优化的实验条件下,鸟嘌呤在该修饰电极上的氧化峰电流与其浓度在1.0×10-5~5.0×10-4mol/L范围内呈良好的线性关系,检出限(3σ)为7.5×10-6mol/L。     

纳米金修饰玻碳电极对鸟嘌呤的催化氧化

采用电化学沉积法制备了纳米金修饰玻碳电极,并用循环伏安法和电化学阻抗法进行了表征,以此建立了一种直接测定鸟嘌呤的电分析方法。在磷酸盐缓冲溶液(pH 6.0)中,研究了鸟嘌呤在纳米金修饰电极上的电化学行为,实验结果表明,纳米金修饰电极可以增强鸟嘌呤在电极表面的吸附,并加快鸟嘌呤在电极表面的电子传输,使其电化学信号明显增大,检测灵敏度大大提高,该修饰电极对鸟嘌呤表现出良好的电催化性能。在优化实验条件下对鸟嘌呤进行测定,方法的线性范围为8.0×10-7~6.0×10-5mol/L,检出限为1.0×10-8mol/L,在鸟嘌呤浓度为1.0×10-5mol/L时测得RSD(n=10)为2.5%。     

QM/MM calculation of solvent effects on absorption spectra of guanine

Electronic spectra of guanine in the gas phase and in water were studied by quantum mechanical/molecular mechanical (QM/MM) methods. Geometries for the excited‐state calculations were extracted from ground‐state molecular dynamics (MD) simulations using the self‐consistent‐charge density functional tight binding (SCC‐DFTB) method for the QM region and the TIP3P force field for the water environment. Theoretical absorption spectra were generated from excitation energies and oscillator strengths calculated for 50 to 500 MD snapshots of guanine in the gas phase (QM) and in solution (QM/MM). The excited‐state calculations used time‐dependent density functional theory (TDDFT) and the DFT‐based multireference configuration interaction (DFT/MRCI) method of Grimme and Waletzke, in combination with two basis sets. Our investigation covered keto‐N7H and keto‐N9H guanine, with particular focus on solvent effects in the low‐energy spectrum of the keto‐N9H tautomer. When compared with the vertical excitation energies of gas‐phase guanine at the optimized DFT (B3LYP/TZVP) geometry, the maxima in the computed solution spectra are shifted by several tenths of an eV. Three effects contribute: the use of SCC‐DFTB‐based rather than B3LYP‐based geometries in the MD snapshots (red shift of ca. 0.1 eV), explicit inclusion of nuclear motion through the MD snapshots (red shift of ca. 0.1 eV), and intrinsic solvent effects (differences in the absorption maxima in the computed gas‐phase and solution spectra, typically ca. 0.1–0.3 eV). A detailed analysis of the results indicates that the intrinsic solvent effects arise both from solvent‐induced structural changes and from electrostatic solute–solvent interactions, the latter being dominant. © 2009 Wiley Periodicals, Inc. J Comput Chem 2010     

Binding of singlet oxygen with a stacked guanine dimer

Geometry optimization calculations were performed using the B3LYP/6‐31+G* method on the complexes of ¹O₂ and ³O₂ molecules with a stacked dimer of planar guanine, varying the distance (D) between the planes of the guanine molecules. In this process, geometries of the guanine molecules were held fixed, D was fixed at different values, while the bond lengths of ¹O₂ and ³O₂ as well as their orientations with respect to the guanine molecules were optimized for each value of D. The complexes in their most stable geometries were solvated in water using the integral equation formalism of the polarized continuum model of the self‐consistent reaction field theory. In gas phase, the most stable complex between ¹O₂ and the guanine dimer (2G.¹O₂) is formed when D is about 6 Å, while the most stable complex between ³O₂ and the guanine dimer (2G.³O₂) is formed when D is about 3.75 Å. In the minimum total energy geometry of 2G.¹O₂, ¹O₂ is located between the guanine molecules, above the imidazole ring of one of them. However, in the minimum total energy geometry of 2G.³O₂, ³O₂ is located outside the stack of guanine molecules, near the amino group of one of them. The solvation calculations showed that in aqueous media, ¹O₂ would bind with the stacked guanine dimer more strongly than in gas phase, while ³O₂ would not bind with the same. The mode of binding of ¹O₂ with the stacked guanine dimer is such that it seems that ¹O₂ would replace one basepair in DNA, as happens in the intercalative mode of binding of drugs and other molecules, and it can lead to the formation of 8‐oxoguanine that has a mutagenic nature. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Unraveling the Degradation Mechanism of Purine Nucleotides Photosensitized by Pterins: The Role of Charge‐Transfer Steps

Photosensitized reactions contribute to the development of skin cancer and are used in many applications. Photosensitizers can act through different mechanisms. It is currently accepted that if the photosensitizer generates singlet molecular oxygen (¹O₂) upon irradiation, the target molecule can undergo oxidation by this reactive oxygen species and the reaction needs dissolved O₂ to proceed, therefore the reaction is classified as ¹O₂‐mediated oxidation (type II mechanism). However, this assumption is not always correct, and as an example, a study on the degradation of 2′‐deoxyguanosine 5′‐monophosphate photosensitized by pterin is presented. A general mechanism is proposed to explain how the degradation of biological targets, such as nucleotides, photosensitized by pterins, naturally occurring ¹O₂ photosensitizers, takes place through an electron‐transfer‐initiated process (type I mechanism), whereas the contribution of the ¹O₂‐mediated oxidation is almost negligible.