Fluorescent aptasensors based on conformational adaptability of abasic site-containing aptamers in combination with abasic site-binding ligands

Aptamers are nucleic acids that can selectively bind to a variety of targets. Aptamers usually undergo conformational transitions from a flexible or disordered structure into a rigid or ordered structure upon target-binding. This study describes a detection method for l-argininamide (l-Arm) and adenosine based on the conformational adaptability of nucleic acid aptamers. An abasic site (AP site) was formed in the stem and close to the target-binding site of a stem-loop aptamer as an anchoring pocket for a fluorescent ligand. 3,5-Diamino-6-chloro-2-pyrazine carbonitrile (DCPC), which can bind to AP site-containing DNA duplexes by pseudo-base pairing, was utilized as a signaling reporter for the target-binding. The binding of a target to an aptamer induces the tight pairing of bases flanking the AP site, so that DCPC can effectively bind to the stem. The binding of DCPC is accompanied by a significant enhancement of its fluorescence. This new sensing method without an antisense DNA strand was demonstrated by using l-Arm and its aptamer as a model. It was confirmed that the method can sensitively detect l-Arm with a detection limit of 2.1 μM. The proposed method was also applied to adenosine detection, where the reported sequence of an adenosine aptamer was slightly modified. The method based on an AP site-containing aptamer and an AP site-binding ligand was applicable to detection of a target in horse serum.     

Simultaneous recognition of nucleobase and sites of DNA damage: effect of tethered cation on the binding affinity

BACKGROUND: The 3,5-diamino-N-(3-aminopropyl)-6-chloropyrazine-2-carboxamide (DCPC-NH(2)) has been synthesized and characterized by Mass and (1)H NMR. The selective binding of the ligand to thymine (T) target base is investigated by the melting temperature (T(m)) and fluorescence measurements. METHODS: Thermal denaturation study of DNA duplex containing T target base revealed the DeltaT(m) of 5.1 degrees C, while least influence was observed for other target bases. The fluorescence of the ligand DCPC-NH(2) is quenched only upon adding the DNA containing T target base. RESULTS: The binding constant for the interaction of the ligand to T target base containing DNA duplex was determined to be 4.7 (+/-0.3)x10(6) M(-1). The tethered cation in the ligand is found to enhance the binding constant. The ligand binds to both a target nucleotide and an AP site on the complimentary strand for the target strand in a DNA duplex. GENERAL SIGNIFICANCE: Interestingly, the electronic behavior of the ligand depends on the bases flanking the AP site. Its fluorescence is quenched with guanine flanking bases, while it is enhanced with DNA duplex containing T bases flanking an AP site. Finally, the binding modes were visualized by molecular modeling.     

Dinuclear copper-dioxygen intermediates supported by polyamine ligands

Reactivity of the dicopper(I) and dicopper(II) complexes supported by novel polyamine ligands L1 (1,11-bis(6-methylpyridin-2-yl)-2,6,10-triaza-2,6,10-tribenzylundecane) and L2 (5-benzyl-1,9-bis(6-methylpyridin-2-yl)-2,8-bis(6-methylpyridin-2-ylmethyl)-2,5,8-triazanonane) towards O(2) and H(2)O(2), respectively, has been investigated in order to shed light on the ligand effects on Cu(2)/O(2) chemistry. The dicopper(I) complex of L1 (1a) readily reacted with O(2) in a 2:1 ratio at a low temperature (-94 degrees C) in acetone to afford a mixture of (mu-eta2.eta2-peroxo)dicopper(II) and bis(mu-oxo)dicopper(III) complexes. The formation of these species has been confirmed by the electron spin resonance (ESR) silence of the solution as well as their characteristic absorption bands in the UV-visible region (gammamax= 350 and 510 nm due to the peroxo complex and approximately 400 nm due to the bis(mu-oxo) complex] and the resonance Raman bands at 729 cm(-1) [Deltanu (16(O2)-18(O2)) = 38 cm(-1)] due to the peroxo complex and at 611 and 571 cm(-1) [Deltanu(16(O2)-18(O2)) = 22 and 7 cm(-1), respectively] due to the bis(mu-oxo) complex. The peroxo and bis(mu-oxo) complexes were unstable even at the low temperature, leading to oxidative N-dealkylation at the ligand framework. The dicopper(I) complex of L2 (2a) also reacted with O(2) to give (mu-hydroxo)dicopper(II) complex (2b(OH)) as the product. In this case, however, no active oxygen intermediate was detected even at the low temperature (-94 degrees C). With respect to the copper(II) complexes, treatment of the (mu-hydroxo)dicopper(II) complex of L1 (1b(OH)) with an equimolar amount of H(2)O(2) in acetone at -80 degrees C efficiently gave a (mu-1,1-hydroperoxo)dicopper(II) complex, the formation of which has been supported by its ESR-silence as well as UV-vis (370 and 650 nm) and resonance Raman spectra [881 cm(-1); [Deltanu (16(O2)-18(O2)) = 49 cm(-1)]. The (mu-1,1-hydroperoxo)dicopper(II) intermediate of L1 also decomposed slowly at the low temperature to give similar oxidative N-dealkylation products. Kinetic studies on the oxidative N-dealkylation reactions have been performed to provide insight into the reactivity of the active oxygen intermediates.     

Dense Neuron Clustering Explains Connectivity Statistics in Cortical Microcircuits

Local cortical circuits appear highly non-random, but the underlying connectivity rule remains elusive. Here, we analyze experimental data observed in layer 5 of rat neocortex and suggest a model for connectivity from which emerge essential observed non-random features of both wiring and weighting. These features include lognormal distributions of synaptic connection strength, anatomical clustering, and strong correlations between clustering and connection strength. Our model predicts that cortical microcircuits contain large groups of densely connected neurons which we call clusters. We show that such a cluster contains about one fifth of all excitatory neurons of a circuit which are very densely connected with stronger than average synapses. We demonstrate that such clustering plays an important role in the network dynamics, namely, it creates bistable neural spiking in small cortical circuits. Furthermore, introducing local clustering in large-scale networks leads to the emergence of various patterns of persistent local activity in an ongoing network activity. Thus, our results may bridge a gap between anatomical structure and persistent activity observed during working memory and other cognitive processes.     

Effect of the bases flanking an abasic site on the recognition of nucleobase by amiloride

Background

We explain here the various non-covalent interactions which are responsible for the different binding modes of a small ligand with DNA.

Methods

The combination of experimental and theoretical methods was used.

Results

The interaction of amiloride with thymine was found to depend on the bases flanking the AP site and different binding modes were observed for different flanking bases. Molecular modeling, absorption studies and binding constant measurements support for the different binding patterns. The flanking base dependent recognition of AP site phosphates was investigated by ³¹P NMR experiments. The thermodynamics of the ligand–nucleotide interaction was demonstrated by isothermal titration calorimetry. The emission behavior of amiloride was found to depend on the bases flanking the AP site. Amiloride photophysics in the context of AP-site containing DNA is investigated by time-dependent density functional theory.

Conclusions

Flanking bases affect the ground and excited electronic states of amiloride when binding to AP site, which causes flanking base-dependent fluorescence signaling.

General significance

The various noncovalent interactions have been well characterized for the determination of nucleic acid structure and dynamics, and protein–DNA interactions. However, these are not clear for the DNA–small molecule interactions and we believe that our studies will bring a new insight into such phenomena.     

Influence of substituent modifications on the binding of 2-amino-1,8-naphthyridines to cytosine opposite an AP site in DNA duplexes: thermodynamic characterization

Here, we report on a significant effect of substitutions on the binding affinity of a series of 2-amino-1,8-naphthyridines, i.e., 2-amino-1,8-naphthyridine (AND), 2-amino-7-methyl-1,8-naphthyridine (AMND), 2-amino-5,7-dimethyl-1,8-naphthyridine (ADMND) and 2-amino-5,6,7-trimethyl-1,8-naphthyridine (ATMND), all of which can bind to cytosine opposite an AP site in DNA duplexes. Fluorescence titration experiments show that the binding affinity for cytosine is effectively enhanced by the introduction of methyl groups to the naphthyridine ring, and the 1:1 binding constant (10⁶ M⁻¹) follows in the order of AND (0.30) < AMND (2.7) < ADMND (6.1) < ATMND (19) in solutions containing 110 mM Na⁺ (pH 7.0, at 20°C). The thermodynamic parameters obtained by isothermal titration calorimetry experiments indicate that the introduction of methyl groups effectively reduces the loss of binding entropy, which is indeed responsible for the increase in the binding affinity. The heat capacity change (ΔC_p), as determined from temperature dependence of the binding enthalpy, is found to be significantly different between AND (−161 cal/mol K) and ATMND (−217 cal/mol K). The hydrophobic contribution appears to be a key force to explain the observed effect of substitutions on the binding affinity when the observed binding free energy (ΔG_obs) is dissected into its component terms.