Structural selectivity of aromatic diamidines

Competition dialysis was used to study the interactions of 13 substituted aromatic diamidine compounds with 13 nucleic acid structures and sequences. The results show a striking selectivity of these compounds for the triplex structure poly dA:(poly dT)(2), a novel aspect of their interaction with nucleic acids not previously described. The triplex selectivity of selected compounds was confirmed by thermal denaturation studies. Triplex selectivity was found to be modulated by the location of amidine substiuents on the core phenyl-furan-phenyl ring scaffold. Molecular models were constructed to rationalize the triplex selectivity of DB359, the most selective compound in the series. Its triplex selectivity was found to arise from optimal ring stacking on base triplets, along with proper positioning of its amidine substituents to occupy the minor and the major-minor grooves of the triplex. New insights into the molecular recognition of nucleic acid structures emerged from these studies, adding to the list of available design principles for selectively targeting DNA and RNA.

Small-molecule-directed assembly: A gold nanoparticle-based strategy for screening of homo-adenine DNA duplex binders

By using AuNP-modified homo-adenine DNA conjugate as a model system, simple colorimetric and resonance Rayleigh scattering assays have been developed for screening small molecules that trigger the formation of the non-Watson-Crick homo-adenine duplexes. The assay presented here is more simplified in format as it involves only one type of ssDNA modified Au-NP, and can be easily adapted to high-throughput screening.

Colorimetric recognition of the coralyne-poly(dA) interaction using unmodified gold nanoparticle probes, and further detection of coralyne based upon this recognition system

Among the functional nucleic acids studied, adenine-rich nucleic acids have attracted attention due to their critical roles in many biological processes and self-assembly-based nanomaterials, especially deoxyribonucleic acids (abbreviated as poly(dA)). Therefore the ligands binding to poly(dA) might serve as potential therapeutic agents. Coralyne, a kind of planar alkaloid, has been firstly found that it could bind strongly to poly(dA). This work herein reports an approach for visual sensing of the coralyne-poly(dA) interaction. This method was based on the coralyne inducing poly(dA) into the homo-adenine DNA duplex and the difference in electrostatic affinity between single-stranded DNA and double-stranded DNA with gold nanoparticles (GNPs). Furthermore, we applied the recognition process of the interaction between coralyne and poly(dA) into specific coralyne detection with the assistance of certain software (such as Photoshop). A linear response from 0 to 728 nM was obtained for coralyne, and a detection limit of 91 nM was achieved.

Spectral and electrochemical detection of protonated triplex formation by a small-molecule anticancer agent

Triplex helical formation has been the focus of considerable interest because of possible applications in developing new molecular biology tools as well as therapeutic agents and the possible relevance of H-DNA structures in biology system. We report here that a small-molecule anticancer agent, coralyne, has binding preference to the less stable protonated triplex d(C+-T)(6):d(A-G)(6).d(C-T)(6) over duplex d(A-G)(6).d(C-T)(6) and shows different spectral and electrochemical characteristics when binding to triplex and duplex DNA, indicating that electrochemical technique can detect the less stable protonated triplex formation.

Triplex selective 2-(2-naphthyl)quinoline compounds: Origins of affinity and new design principles

A novel competition dialysis assay was used to investigate the structural selectivity of a series of substituted 2-(2-naphthyl)quinoline compounds designed to target triplex DNA. The interaction of 14 compounds with 13 different nucleic acid sequences and structures was studied. A striking selectivity for the triplex structure poly dA:[poly dT](2) was found for the majority of compounds studied. Quantitative analysis of the competition dialysis binding data using newly developed metrics revealed that these compounds are among the most selective triplex-binding agents synthesized to date. A quantitative structure-affinity relationship (QSAR) was derived using triplex binding data for all 14 compounds used in these studies. The QSAR revealed that the primary favorable determinant of triplex binding free energy is the solvent accessible surface area. Triplex binding affinity is negatively correlated with compound electron affinity and the number of hydrogen bond donors. The QSAR provides guidelines for the design of improved triplex-binding agents.

Developing molecular identification numbers by an all-paths method

A new topological index is devised from an all-paths method. This molecular topological index has highly discriminating power for various kinds of organic compounds such as alkane trees, complex cyclic or polycyclic graphs, and structures containing heteroatoms and thus can be used as a Molecular IDentification number (MID) for chemical documentation. Some published MIDs derived from an all-paths method and their structural selectivity for alkane trees are also reviewed.

The ion selectivity of monensin incorporated phospholipid/alkanethiol bilayers

Monensin was incorporated into phospholipid/alkanethiol bilayers on the gold electrode surface by a new, paint-freeze method to deposit a lipid monolayer on the self-assembled monolayers (SAMs) of alkanethiol. The advantages of this assembly system with a suitable function for investigating the ion selective transfer across the mimetic biomembrane are based on the characteristics of SAMs of alkanethiols and monensin. On the one hand, the SAMs of alkanethiols bring out their efficiency of packing and coverage of the metal substrate and relatively long-term stability; on the other hand, monensin improves the ion selectivity noticeably. The selectivity coefficients K-Na+,K-K+, K-Na+,K-Rb+ and K-Na+,K-Ag+ are 6 x 10(-2), 7.2 x 10(-3) and 30 respectively. However, the selectivity coefficient K-Na+,K-Li+ could not be obtained by a potentiometric method due to the specific interaction between Li+ and phospholipid and the lower degree of complexion between Li+ and monensin. The potential response of this bilayer system to monovalent ions is fairly good. For example, the slope of the response to Na+ is close to 60 mV per decade and its linearity range is from 10(-1) to 10(-5) M with a detection limit of 2 x 10(-6) M, The bilayer is stable for at least two months without changing its properties. This monensin incorporated lipid/alkanethiol bilayer is a good mimetic biomembrane system, which provides great promise for investigating the ion transfer mechanism across the biomembrane and developing a practical biosensor.

Improvements in the selectivity of electrochemical detectors for liquid chromatography and flow injection analysis using the self-assembled n-alkanethiol monolayer-modified au electrode

4-Aminophenol (4-AP), paracetamol (PRCT), norepinephrine (NE), and dopamine (DA) (all somewhat hydrophobic compounds) were HPLC electrochemically detected while the signals from uric acid (UA) and ascorbic acid (AA) (both hydrophilic compounds at the pH studied) were minimized, taking advantage of the permselectivity of the self-assembled n-alkanethiol monolayer (C-10-SAM)-modified Au electrodes based on solute polarity, The effects of various factors, such as the chain length of the n-alkanethiol modifier, modifying time, and pH value, on the permeability of C-10-SAM coatings were examined, The calibration curves, linear response ranges, detection limits, and reproducibilities of the EC detector for 4-AP, PRCT, NE, and DA were obtained, The result shows that the EC detector can be applied in the chromatographic detection of 4-AP, PRCT, NE, and DA in urine, effectively removing the influence of UA and AA in high concentrations existing in biological samples. As a result, a great improvement in the selectivity of EC detectors has been achieved by using Au electrodes coated with neutral n-alkanethiol monolayer.