Studies on the Extension of Sequence‐independence and the Enhancement of DNA Triplex Formation

A more elaborate sequence‐independent triple‐helix formation viability study was carried out and extended from a recombination‐like triple‐helical DNA motif of a previous study (J. Mol. Recognition 14, 122–139 (2001)). The intended triple‐helix was formed by mixing one part of a DNA hairpin duplex and one part of a single (or third) strand identical to one of the duplex strands and complementary to the other strand. In contrast to the common purine and pyrimidine motifs in triple‐stranded DNA, the strands of the recombination‐like motif are not monotonously built from pyrimidine only, or purine only, in the sequence. The stability of the recombination‐like motif triplexes with varying sequences was monitored by UV thermal melting curves. The results showed that the order of the stability of the R‐form DNA base triads (J. Mol. Biol., 239, 181–200 (1994)) is G*(G ○ C) > C*(C ○ G) > A*(A ○ T) >T*(T ○ A) (the Watson‐Crick base pair is denoted in the parentheses) in 200 mM NaCl, at pH 7. In an attempt to increase the stability of the triplex in the recombination‐like motif, we replaced cytidine by 5‐methylcytidine (^mC) of the third strand. There is a general trend that ^mC modification stabilizes the complex (<2 °C per ^mC). The complex is furthermore stabilized by Mg²⁺ ion. The Tm increases from 7 to 2 °C from less stable to highly stable triplex by 20 mM Mg²⁺ ion in solution.     

A H+/Ag+ Dual‐Target Responsive Label‐Free Light‐Up Probe Based on a DNA Triplex

We developed a dual‐target responsive sensor for label‐free light‐up fluorescent detection of protons (H⁺) and silver ions (Ag⁺) using an “OR′′ logic gate. Berberine, a cost‐effective and non‐toxic indicator, partially intercalates the formed triplex DNA in the presence of H⁺ or Ag⁺, generating enhanced fluorescence. The designed Ag⁺ probe has high selectivity and desirable sensitivity, which is necessary for practical use. The robust ”OR“ logic gate is capable of a rapid and reversible response to the H⁺ and/or Ag⁺ inputs.     

Factors Affecting DNA–DNA Interstrand Cross‐Links in the Antiparallel 3′–3′ Sense: A Comparison with the 5′–5′ Directional Isomer

Reported herein is a study of the unusual 3′–3′ 1,4‐GG interstrand cross‐link (IXL) formation in duplex DNA by a series of polynuclear platinum anticancer complexes. To examine the effect of possible preassociation through charge and hydrogen‐bonding effects the closely related compounds [{trans‐PtCl(NH₃)₂}₂(μ‐trans‐Pt(NH₃)₂{NH₂(CH₂)₆NH₂}₂)]⁴⁺ (BBR3464, 1 ), [{trans‐PtCl(NH₃)₂}₂(μ‐NH₂(CH₂)₆NH₂)]²⁺ (BBR3005, 2 ), [{trans‐PtCl(NH₃)₂}₂(μ‐H₂N(CH₂)₃NH₂(CH₂)₄)]³⁺ (BBR3571, 3 ) and [{trans‐PtCl(NH₃)₂}₂{μ‐H₂N(CH₂)₃‐N(COCF₃)(CH₂)₄}]²⁺ (BBR3571‐COCF₃, 4 ) were studied. Two different molecular biology approaches were used to investigate the effect of DNA template upon IXL formation in synthetic 20‐base‐pair duplexes. In the “hybridisation directed” method the monofunctionally adducted top strands were hybridised with their complementary 5′‐end labelled strands; after 24 h the efficiency of interstrand cross‐linking in the 5′–5′ direction was slightly higher than in the 3′–3′ direction. The second method involved “postsynthetic modification” of the intact duplex; significantly less cross‐linking was observed, but again a slight preference for the 5′–5′ duplex was present. 2D [¹H, ¹⁵N] HSQC NMR spectroscopy studies of the reaction of [¹⁵N]‐ 1 with the sequence 5′‐d{TATACATGTATA}₂ allowed direct comparison of the stepwise formation of the 3′–3′ IXL with the previously studied 5′–5′ IXL on the analogous sequence 5′‐d(ATATGTACATAT)₂. Whereas the preassociation and aquation steps were similar, differences were evident at the monofunctional binding step. The reaction did not yield a single distinct 3′–3′ 1,4‐GG IXL, but numerous cross‐linked adducts formed. Similar results were found for the reaction with the dinuclear [¹⁵N]‐ 2 . Molecular dynamics simulations for the 3′–3′ IXLs formed by both 1 and 2 showed a highly distorted structure with evident fraying of the end base pairs and considerable widening of the minor groove.     

Fluorescent Nucleobase Analogues with Extended Pi Surfaces Stabilize DNA Duplexes Containing O6‐Alkylguanine Adducts

Chemical alkylation of DNA produces potentially toxic and mutagenic damage such as O⁶‐alkylguanine (O⁶‐alkylG) adducts. Non‐natural nucleoside analogues that pair with DNA adducts provide a potential basis for studying damaged DNA. Herein, we evaluated the base pairing properties of elongated nucleoside analogues containing napthalene‐derived tricyclic nucleobases as DNA adduct‐pairing nucleoside analogues in DNA hybridization probes. DNA duplex melting studies revealed that the elongated nucleoside analogs formed more stable base pairs opposite O⁶‐alkylG than G and were better able to distinguish between G, O⁶‐alkylG, and an abasic site than any previously described nucleoside analogue. DNA duplexes containing an elongated base analogue exhibited different fluorescence intensities when paired opposite O⁶‐alkylG vs. G or abasic sites. Their selectivity for stabilizing alkylated DNA make the elongated hydrophobic base analogues improved candidates for incorporating into DNA hybridization probes targeting O⁶‐alkylG.     

Screening and investigation of triplex DNA binders from Stephania tetrandra S. Moore by a combination of peak area‐fading ultra high‐performance liquid chromatography with orbitrap mass spectrometry and optical spectroscopies

The identification and screening of triplex DNA binders are important because these compounds, in many cases, are potential anticancer agents as well as promising drug candidates. Therefore, the ability to screen for these compounds in a high‐throughput mode could dramatically improve the drug screening process. A method involving a combination of 96‐well plate format and peak area‐fading ultra high‐performance liquid chromatography coupled with Orbitrap mass spectrometry was employed for screening bioactive compounds binding to the triplex DNA from the extracts of Stephania tetrandra S. Moore. Two compounds were screened out and identified as fangchinoline and tetrandrine based on the comparison of retention time and tandem mass spectrometry data with those of standards. The binding mechanisms of fangchinoline and tetrandrine at the molecular level were explored using tandem mass spectrometry, fluorescence spectroscopy, ultraviolet‐visible spectroscopy, and circular dichroism. Collision‐induced dissociation experiments showed that the complexes with fangchinoline and tetrandrine were dissociated by ligand elimination. According to these measurements, an intercalating binding is the most appropriate binding mode of these two alkaloids to the triplex DNA. The current work provides not only deep insight into alkaloid‐triplex DNA complexes but also useful guidelines for the design of efficient anticancer agents.     

Electrochemical Synthesis and Characterisation of Alternating Tripyridyl–Dipyrrole Molecular Strands with Multiple Nitrogen‐Based Donor–Acceptor Binding Sites

Synthesis of alternating pyridine–pyrrole molecular strands composed of two electron‐rich pyrrole units (donors) sandwiched between three pyridinic cores (acceptors) is described. The envisioned strategy was a smooth electrosynthesis process involving ring contraction of corresponding tripyridyl–dipyridazine precursors. 2,6‐Bis[6‐(pyridazin‐3‐yl)]pyridine ligands 2 a – c bearing pyridine residues at the terminal positions were prepared in suitable quantities by a Negishi metal cross‐coupling procedure. The yields of heterocyclic coupling between 2‐pyridyl zinc bromide reagents 12 a – c and 2,6‐bis(6‐trifluoromethanesulfonylpyridazin‐3‐yl)pyridine increased from 68 to 95 % following introduction of electron‐donating methyl groups on the metallated halogenopyridine units. Favorable conditions for preparative electrochemical reduction of tripyridyl–dipyridazines 2 b , c were established in THF/acetate buffer (pH 4.6)/acetonitrile to give the targeted 2,6‐bis[5‐(pyridin‐2‐yl)pyrrol‐2‐yl]pyridines 1 b and 1 c in good yields. The absorption behavior of the donor–acceptor tripyridyl–dipyrrole ligands was evaluated and compared to theoretical calculations. Highly fluorescent properties of these chromophores were found (ν_em≈2×10⁴ cm^?1 in MeOH and CH₂Cl₂), and both pyrrolic ligands exhibit a remarkable quantum yield in CH₂Cl₂ (?_f=0.10). Structural studies in the solid state established the preferred cis conformation of the dipyrrolic ligands, which adopting a planar arrangement with an embedded molecule of water having a complexation energy exceeding 10 kcal mol^?1. The ability of the tripyridyl–dipyrrole to complex two copper(II) ions in a pentacoordinate square was investigated.     

Synthesis of Benzo[α] phenoxazin—5—one Derivatives and Their Interactions with DNA

The spectroscopic properties of benzo[a] phenoxazin-5-one derivatives(3a-3m)including newly synthesized 3k-3m from 4-nitrosoaniline hydrochlorides and ethyl 1,3-dihydroxy-2-naphthoate were studied.Compound 31 was converted into a covalent product with DNA,which had a blue shift of the fluorescence maximum,Compounds 3a-3k were fornd to undergo interation with DNA and their complexes with DNA had a red shift of the fluorescence maximum and showed increasing melting temperature of DNA,compound 3m-DNA had a blue shift of the fluorescence maximum to 3m and showed decreasing melting temperature of DNA.     

Guanidiniocarbonylpyrrole–Aryl Derivatives: Structure Tuning for Spectrophotometric Recognition of Specific DNA and RNA Sequences and for Antiproliferative Activity

We present a systematic study of different guanidiniocarbonylpyrrole‐aryl derivatives designed to interact with DNA or RNA both through intercalation of an aromatic moiety into the base stack of the nucleotide and through groove binding of a guanidiniocarbonylpyrrole cation. We varied 1) the size of the aromatic ring (benzene, naphthalene, pyrene and acridine), 2) the length and flexibility of the linker connecting the two binding groups, and 3) the total number of positive charges present at different pH values. The compounds and their interactions with DNA and RNA were studied by UV/Vis, fluorescence and CD spectroscopy. Antiproliferative activities against human tumour cell lines were also determined. Our studies show that efficient interaction with, for example, DNA requires a significantly large aromatic ring (pyrene) connected through a flexible linker to the pyrrole moiety. However, a positive charge, as in 12 , is also needed. Compound 12 allows for base‐pair‐selective recognition of ds‐DNA at physiological pH values. The antiproliferative activities of these compounds correlate with their binding affinities towards DNA, suggesting that their biological effects are most probably due to DNA binding.     

Spin–Spin Artificial DNA Intercalated with Silver Cations: Theoretical Prediction

The indirect nuclear spin–spin coupling constants of Ag⁺ cation intercalated between imidazole rings in DNA chains are calculated by means of DFT with relativistic effects taken into account by the use of the zeroth‐order regular approximation Hamiltonian (DFT‐ZORA). The calculations model how the ¹J(¹⁵N,¹⁰⁹Ag) coupling constant is affected by different types of geometry deformations and by the presence of water, which is simulated by means of the polarizable continuum model and explicitly present water molecules. Calculations for systems containing two and three imidazole pairs are also carried out to model the influence of stacking interactions. The computed ¹J(¹⁵N,¹⁰⁹Ag) spin–spin coupling constant is in the range of 85–105 Hz (depending on the computational model) and is in good agreement with the experimental value (ca. 92 Hz). This coupling constant is very little affected by the presence of solvent, stacking interactions, and geometry deformations. Such behavior is explained by visualization of the coupling path by means of coupling energy density (CED). Bigger models allow the coupling constant between two adjacent silver ions to be computed, and give a value of approximately 1 Hz, which is probably too small to be of practical interest. The ²J(¹⁵N,¹⁵N) value is calculated to be about 2.5 Hz, and is therefore of measurable magnitude.     

Determination of Cytochrome C with Cellulose – DNA Modified Carbon Paste Electrodes

A sensor for cytochrome c (cyt c) was developed using a carbon paste electrode (CPE) modified with cellulose‐DNA. Cyt c was adsorbed on the cellulose‐DNA modified CPE through the electrostatic interaction between them. Owing to this process, a pair of well‐defined peaks appeared at +48 mV/85 mV (E_pc/E_pa vs. Ag/AgCl). This property of the cellulose‐DNA modified CPE was utilized for the analysis of cyt c in a biological sample. The optimum experimental conditions for analysis were investigated and a calibration plot was obtained between 1.0×10^?4 M and 1.0×10^?6 M (±5% at n=5) at the optimized condition. The detection limit for cyt c at the optimized experimental condition was 5.0×10^?7 M (S/N=3) for 30 min of deposition time with differential pulse voltammetry (DPV). The real sample analysis was carried out with the standard addition method to evaluate the developed method. The content of cyt c in total proteins of 80.0 mg/mL in rat mitocondria fractions was determined to be 0.12 (±0.02) mg/mL.     

Mixed Metal–Organic Framework with Multiple Binding Sites for Efficient C2H2/CO2 Separation

The separation of C₂H₂/CO₂ is particularly challenging owing to their similarities in physical properties and molecular sizes. Reported here is a mixed metal–organic framework (M′MOF), [Fe(pyz)Ni(CN)₄] ( FeNi‐M′MOF , pyz=pyrazine), with multiple functional sites and compact one‐dimensional channels of about 4.0 Å for C₂H₂/CO₂ separation. This MOF shows not only a remarkable volumetric C₂H₂ uptake of 133 cm³ cm^?3, but also an excellent C₂H₂/CO₂ selectivity of 24 under ambient conditions, resulting in the second highest C₂H₂‐capture amount of 4.54 mol L^?1, thus outperforming most previous benchmark materials. The separation performance of this material is driven by π–π stacking and multiple intermolecular interactions between C₂H₂ molecules and the binding sites of FeNi‐M′MOF . This material can be facilely synthesized at room temperature and is water stable, highlighting FeNi‐M′MOF as a promising material for C₂H₂/CO₂ separation.     

Electrochemical Studies for the Interaction of DNA with an Irreversible Redox Compound – Hoechst 33258

An electrochemical equation suitable for examining the interaction of irreversible redox compounds with DNA is established. According to the equation, diffusion coefficients of both free and binding compounds (D_f , D_b), binding constant (K) and binding site size (s) of compounds with DNA could be obtained simultaneously by nonlinear fit analysis of electrochemical data. Bis‐benzimidazole derivative (Hoechst 33258), as an irreversible redox compound, was investigated for its electrochemical behavior and the interaction with natural fish sperm DNA (fsDNA) using cyclic voltammetry, chronocoulometry, bulk electrolysis and scanning electrochemical microscope technique. A nonlinear fit analysis of the experimental data yielded: D_f=8.3×10^?5 cm² s^?1, D_b=6.0×10^?6 cm² s^?1, K=2.1×10⁸ cm³ mol^?1, s=3.9. The overall results suggest that Hoechst 33258 binds tightly to the minor groove of fsDNA and covers four base pairs.     

DNA fragment separations by on‐line combination of capillary isotachophoresis–capillary zone electrophoresis with UV detection

A high‐speed DNA fragment separation system based on an on‐line combination of capillary ITP with CZE (CITP‐CZE) and using UV detection at 260 nm was developed. A novel CITP‐CZE buffer system of pH 6.1 was designed for the separation of ten DNA fragments with sizes ranging from 100 to 1000 bp. An effect of underivatized α‐, β‐ and γ‐cyclodextrins on the resolution of DNA fragments in the CZE step of the CITP‐CZE combination was systematically investigated. Methylhydroxyethylcellulose present in the BGE was used to eliminate the EOF. DNA ladder fragments were separated within 10 min with LODs in the range of 1–5 ng/μL (S/N = 3). The RSDs of the migration time and peak area of individual DNA fragments were in the range of 1–3 and 3–9%, respectively. The developed CITP‐CZE system was further applied to the analysis of digest plasmid DNA samples.