The Utility of Capped Duplex DNA (σ-DNA) in Triplex Interaction Studies

Two optimally capped duplex DNA molecules (σ-DNA; see 1 and 4 ) were synthesized and their utility demonstrated for triplex investigations with their corresponding homopyrimidine DNA and RNA single strands in the D⋅(D⋅D) and R⋅(D⋅D) Hoogsteen mode. Furthermore, it was established that σ-DNA is an ideal tool to study the pH dependency of triplex formation.     

Selective,pH-Dependent Colorimetric and Fluorimetric Detection of Quadruplex DNA with 4-Dimethylamino(phenyl)-Substituted Berberine Derivatives

The 9- and 12-dimethylaminophenyl-substituted berberine derivatives 3 a and 3 b were readily synthesized by Suzuki-Miyaura reactions and shown to be useful fluorescent probes for the optical detection of quadruplex DNA (G4-DNA). Their association with the nucleic acids was investigated by spectrometric titrations, CD and LD spectroscopy, and with DNA-melting analysis. Both ligands bind to duplex DNA by intercalation and to G4-DNA by terminal π stacking. At neutral conditions, they bind with higher affinity (K_b=10⁵−10⁶ M⁻¹) to representative quadruplex forming oligonucleotides 22AG , c-myc , c-kit , and a2 , than to duplex calf thymus (ct) DNA (K_b=5-7×10⁴ M⁻¹). At pH 5, however, the affinity of 3 a towards G4-DNA 22AG is higher (K_b=1.2×10⁶ M⁻¹), whereas the binding constant towards ct DNA is lower (K_b=3.9×10³ M⁻¹) than under neutral conditions. Notably, the association of the ligand with DNA results in characteristic changes of the absorption and emission properties under specific conditions, which may be used for optical DNA detection. Other than the parent berberine, the ligands do not show a noticeable increase of their very low intrinsic emission intensity upon association with DNA at neutral conditions. In contrast, a fluorescence light-up effect was observed upon association to duplex (Φ_fl=0.01) and quadruplex DNA (Φ_fl=0.04) at pH 5. This fluorimetric response to G4-DNA association in combination with the distinct, red-shifted absorption under these conditions provides a simple and conclusive optical detection of G4-DNA at lower pH.     

Interaction of Cu(II) and Cd(II) ions with DNA from Spirulina platensis

Equilibrium dialysis and atomic absorption analysis were used to obtain adsorption isotherms and determine the stoichiometric binding constants of Cu(II) and Cd(II) ions to DNA from Spirulina platensis in solutions. The stoichiometric constants of Cu(II) and Cd(II) ions with DNA from S. platensis in 3 mM NaCI are 15.56⋅10⁴ and 14.40⋅10⁴, respectively. Effect of ionic strength and DNA GC content on binding constants of Cu(II)- and Cd(II)-DNA complexes were studied out. It was showed that the binding constants of Cu(II)- and Cd(II)-DNA complexes decrease with increase of ionic strength. The empirical dependences of logK on the GC content has been derived for Cd(II)- and Cu(II)-DNA complexes.     

Interaction of water with DNA single and double helix in the B conformation

The interaction energy between water and B-DNA in the single and double helix is computed at a number of planar cross sections perpendicular to the helix long axis and for a few cylindrical surfaces enclosing the helix. In addition, Monte Carlo simulations are presented for a small cluster of water around regions of energy minima. On the base of these simulations the structure of water for B-DNA in solution, the quaternary structure of B-DNA, is proposed and discussed. The intermolecular interaction used in the Monte Carlo computation has been derived from ab initio computations of complexes between water and the DNA bases, diethylphosphate, a ribose derivative, and other model compounds.     

Berberrubine Phosphate: A Selective Fluorescent Probe for Quadruplex DNA

A phosphate-substituted, zwitterionic berberine derivative was synthesized and its binding properties with duplex DNA and G4-DNA were studied using photometric, fluorimetric and polarimetric titrations and thermal DNA denaturation experiments. The ligand binds with high affinity toward both DNA forms (K_b = 2–7 × 10⁵ M⁻¹) and induces a slight stabilization of G4-DNA toward thermally induced unfolding, mostly pronounced for the telomeric quadruplex 22AG. The ligand likely binds by aggregation and intercalation with ct DNA and by terminal stacking with G4-DNA. Thus, this compound represents one of the rare examples of phosphate-substituted DNA binders. In an aqueous solution, the title compound has a very weak fluorescence intensity (Φ_fl < 0.01) that increases significantly upon binding to G4-DNA (Φ_fl = 0.01). In contrast, the association with duplex DNA was not accompanied by such a strong fluorescence light-up effect (Φ_fl < 0.01). These different fluorimetric responses upon binding to particular DNA forms are proposed to be caused by the different binding modes and may be used for the selective fluorimetric detection of G4-DNA.     

A Cytotoxic Bis(1,2,3-triazol-5-ylidene)carbazolide Gold(III) Complex Targets DNA by Partial Intercalation

The syntheses of bis(triazolium)carbazole precursors and their corresponding coinage metal (Au, Ag) complexes are reported. For alkylated triazolium salts, di- or tetranuclear complexes with bridging ligands were isolated, while the bis(aryl) analogue afforded a bis(carbene) Au^I-CNC pincer complex suitable for oxidation to the redox-stable [Au^III(CNC)Cl]⁺ cation. Although the ligand salt and the [Au^III(CNC)Cl]⁺ complex were both notably cytotoxic toward the breast cancer cell line MDA-MB-231, the Au^III complex was somewhat more selective. Electrophoresis, viscometry, UV-vis, CD and LD spectroscopy suggest the cytotoxic [Au^III(CNC)Cl]⁺ complex behaves as a partial DNA intercalator. In silico screening indicated that the [Au^III(CNC)Cl]⁺ complex can target DNA three-way junctions with good specificity, several other regular B-DNA forms, and Z-DNA. Multiple hydrophobic π-type interactions involving T and A bases appear to be important for B-form DNA binding, while phosphate O⋅⋅⋅Au interactions evidently underpin Z-DNA binding. The CNC ligand effectively stabilizes the Au^III ion, preventing reduction in the presence of glutathione. Both the redox stability and DNA affinity of the hit compound might be key factors underpinning its cytotoxicity in vitro.     

Ultrasensitive electrochemical analysis of two analytes by using an autonomous DNA machine that works in a two-cycle mode

We report a novel autonomous DNA machine for amplified electrochemical analysis of two DNAs. The DNA machine operates in a two‐cycle working mode to amplify DNA recognition events; the working mode is assisted by two different nicking endonucleases (NEases). Two bio‐barcode probes, a ZnS nanoparticle (NP)–DNA probe and a CdS NP–DNA probe, were used to trace two target DNAs. The detection system was based on a sensitive differential pulse anodic stripping voltammetry (DPASV) method for the simultaneous detection of Zn^II and Cd^II tracers, which were obtained by dissolving the two probes. Under the optimised conditions, detection limits as low as 5.6×10^?17 (3σ) and 4.1×10^?17 M (3σ) for the two target DNAs were achieved. It has been proven that the DNA machine system can simultaneously amplify two target DNAs by more than four orders of magnitude within 30 min at room temperature. In addition, in combination with an aptamer recognition strategy, the DNA machine was further used in the aptamer‐based amplification analysis of adenosine triphosphate (ATP) and lysozyme. With the amplification of the DNA machine, detection limits as low as 5.6×10^?9 M (3σ) for ATP and 5.2×10^?13 M (3σ) for lysozyme were simultaneously obtained. The satisfactory determination of ATP and lysozyme in Ramos cells reveals the good selectivity and feasibility of this protocol. The DNA machine is a promising tool for ultrasensitive and simultaneous multianalysis because of its remarkable signal amplification and simple machine‐like operation.     

一个嫁接有羧酸羟基乙基酯的二吡啶吩嗪Ru(II)配合物的合成、与DNA的相互作用以及溶剂变色性质的研究

合成并表征了一个新的Ru(II)配合物[Ru(bpy)₂(hedppc)](ClO₄)₂ {bpy＝2,2'-联吡啶, hedppc＝二联吡啶[3,2-a: 2',3'-c]吩嗪-11-羧酸(2-羟乙基)酯}. 通过紫外-可见吸收光谱、与溴化乙锭竞争实验、粘度测量和DNA裂解实验研究了配合物与小牛胸腺DNA的相互作用性质. 结果表明配合物以插入模式与DNA键合,键合常数K_b＝(6.99±1.34)×10⁶ mol^－1•L (s＝2.03±0.04)与母体配合物[Ru(bpy)₂ (dppz)]^2＋相近,但光致发光和溶剂变色等光学性质与[Ru(bpy)₂ (dppz)]^2＋有明显的差别.     

Synthesis,crystal structure,and DNA binding of a new oxalato-bridged binuclear zinc(II) complex

A new binuclear zinc(II) complex bridged by μ-oxalate, and end-capped with 2,2′-bipyridine (bpy), [Zn₂(ox)(bpy)₄](ClO₄)₂ · H₂O, has been synthesized and characterized by elemental analyses, molar conductance, IR, and electronic spectra and single-crystal X-ray diffraction. The single-crystal X-ray analysis reveals that the [Zn₂(ox)(bpy)₄]²⁺ cation has two zinc(II) centers bridged by a planar bis(bidentate) oxalate group with Zn···Zn distance of 5.482(3) Å; each zinc(II) is in a distorted octahedral environment. The crystal structure is stabilized by non-classical C–H···O hydrogen bonds and π–π stacking interactions to form a 3-D supramolecular structure. The interaction of the complex with calf-thymus DNA (CT-DNA) was explored by using electronic and fluorescence spectra and viscosity measurements. The results reveal that the complex intercalates with CT-DNA with intrinsic binding constant of 4.1 × 10⁴ M^?1.     

Calculation of the H2+ rovibrational energies and spectroscopic constants in the 2pπ, 3dσ, 4dσ, 4fπ, 4fσ, 5gσ, and 6iσ electronic states

Starting with the Hamilton‐Jacobi equation, Campos et al. have applied Hylleraas' method along with the series obtained by Wind‐Jaffe to several molecular ions, among which the H₂⁺ system, to determine their electronic energies in different states. In this work, we have fitted the potential energy curves for the 2pπ, 3dσ, 4dσ, 4fπ, 4fσ, 5gσ, and 6iσ electronic states of the H₂⁺ ion employing the Rydberg generalized function. From these fittings, the spectroscopic constants and the rovibrational energies have been determined by two distinct methods: Dunham's and the discrete variable representation. The theoretically obtained results are in a satisfactory agreement and are expected to provide a comparison source to future works in the experimental field. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Nucleic-Acid Analogs with Restricted Conformational Flexibility in the Sugar-Phosphate Backbone (‘Bicyclo-DNA’). Part 5. Synthesis,Characterization, and Pairing Properties of Oligo-α-D-(bicyclodeoxynucleotides) of the Bases Adenine and Thymine (α-Bicyclo-DNA)

A conformational analysis of the (3′S,5′R)-2′-deoxy-3′,5′-ethano-α-D -ribonucleosides (a-D-bicyclodeoxynucleosides) based on the X-ray analysis of N⁴-benzoyl-α-D -(bicyclodeoxycytidine) 6 and on ¹H-NMR analysis of the α-D -bicyclodeoxynucleoside derivatives 1 - 7 reveals a rigid sugar structure with the furanose units in the l′-exo/2′-endo conformation and the secondary OH groups on the carbocyclic ring in the pseudoequatorial orientation. Oligonucleotides consisting of α-D -bicyclothymidine and α-D -bicyclodeoxyadenosine were successfully synthesized from the corresponding nucleosides by phosphoramidite methodology on a DNA synthesizer. An evaluation of their pairing properties with complementary natural RNA and DNA by means of UV/melting curves and CD spectroscopy show the following characteristics: i) α-bcd(A₁₀) and α-bcd(T₁₀) (α = short form of α-D )efficiently form complexes with complementary natural DNA and RNA. The stability of these hybrids is comparable or slightly lower as those with natural β-d(A₁₀) or β-d(T₁₀)( β = short form ofβ-D ). ii) The strand orientation in α-bicyclo-DNA/β-DNA duplexes is parallel as was deduced from UV/melting curves of decamers with nonsymmetric base sequences. iii) CD Spectroscopy shows significant structural differences between α-bicyclo-DNA/β-DNA duplexes compared to α-DNA/β-DNA duplexes. Furthermore, α-bicyclo-DNA is ca. 100-fold more resistant to the enzyme snake-venom phosphodiesterase with respect to β-DNA and about equally resistant as α-DNA.     

Crystal structures and DNA cleavage activities of two mononuclear nickel(II) complexes

Two new nickel complexes, [Ni(L₁)₂]?·?2(CH₃OH) (1) and [Ni(L₂)₂]?·?2(CH₃OH) (2), where HL₁ is 4-chloro-2-((2-hydroxy-ethylimino)methyl)phenol and HL₂ is 4-fluoro-2-((2-hydroxy-ethylimino)methyl)phenol, have been synthesized and characterized by single-crystal X-ray diffraction and UV-Vis absorption spectra. The coordination polyhedron of nickel(II) in each complex can be described as distorted octahedral. The interactions between the complexes and calf thymus (CT)-DNA/DNA were investigated by UV-Vis spectra and agarose gel electrophoresis. The results show that the complex transforms supercoiled to nicked form and exhibits effective DNA cleavage activity via hydrolytic cleavage mechanism.     

Reaction of α,β-unsaturated ketones with guanidine. Substituent effects on the protonation constants of 2-amino-4,6-diarylpyrimidines

1,3-Diaryl-2-propen-1-ones, I, reacted with guanidine hydrochloride (II) in the presence of 3 moles of sodium hydroxide to give the corresponding 2-amino-4,6-diarylpyrimidines, III. The structure and configuration of the products are based on chemical and spectroscopic evidence. The protonation constants of these compounds (series A and series B) have been determined in 50 volume percent ethanol-water medium. Excellent linear correlations are obtained when pK_a values of the two series of 2-amino-4,6-diarylpyrimidines, IIIa-j and IIIk-r, are plotted against the substituent constant, ^σx, and the polar substituent constant, ^σ* xC₆H₄, for substituted phenyl groups. The pK_a values have also been correlated with the extended Hammett equation. The correlation follows the equations: Series A; pK_a = 3.273 - 0.820σI,X - 0.662σR,X Series B; pK_a = 3.169 - 0.424σI,X - 0.137σR,X     

The spin delocalization substituent parameter σ˙. 7. Meta-substituent effects on the cyclodimerization of trifluorostyrenes. A test for the σ˙JJ approach

Rate constants (k's) of the thermal cyclodimerization of ten meta-substituted trifluorostyrenes (m-Y-TFS's) have been measured in the temperature range 110–160°C. On the basis of these k's and the σ_mb values derived from ¹⁹F NMR data the spin-delocalization substituent constant σ^˙_m values of these ten meta-substituents have been calculated. The averaged σ^˙_m values are: m-Et, 0.09; m-t-Bu, 0.11; m-F, 0.03; m-Cl,?0.05; m-Br, 0.12: m-CF₃, ?0.07; m-OMe, 0.10; m-NO₂, ?0.002; m-CN, 0.11 and m-CO₂Me, 0.08. Both the smallness of these values and the nonexistence of correlation between Hammett-Type polar σ^X and these σ^˙_m values support our belief that the σ_j?J approach is reliable and trustworthy.     

λ3σ3P and λ5σ5P derivatives of (E)-1,2-difluoro-2-(pentafluoro-λ6-sulfanyl)ethylene and (Z)-1,2,3,3,3-pentafluoropropylene

For the first time, the (E)-1,2-difluoro-2-(pentafluoro-λ⁶-sulfanyl)ethenyl group has been bonded to λ³σ³ phosphorus using a Grignard reagent. Similar phosphorus derivatives containing the (Z)-1,2,3,3,3-pentafluoropropenyl moiety were also synthesized for comparison. In three cases, hexafluoroacetone was added to form 4,4,5,5-tetrakis(trifluoromethyl) 1,3,2λ⁵σ⁵-dioxaphospholanes. © 1997 John Wiley & Sons, Inc. Heteroatom Chem 8: 467–471, 1997     

Super-resolution morphological dissemination of intercalating dye in single DNA molecules via binding activated localization microscopy

Super-localization of intercalating dye YOYO-1 in single λ-DNA at super-resolution by binding activation localization microscopy (BALM).     

Spectral properties and G-quadruplex DNA binding selectivities of a series of unsymmetrical perylene diimides

A series of new unsymmetrical perylene diimides have been synthesized to investigate their binding selectivities to G-quadruplex DNA structure, a unique four-stranded DNA motif, which is significant to the regulation of telomerase activity. The structures of the perylene diimides have been characterized by IR spectrophotometer, ¹H NMR, ¹³C NMR, MS, TGA and time-resolved instruments. Spectrochemical behaviors have been investigated by visible absorption and fluorescence emission spectra. The spectral characterization of the compounds has been investigated in five common organic solvents of different polarity and in water (in 170 mM phosphate buffer at pH 6). Marked red shifts of absorbance and fluorescence emission bands of the compounds in aqueous solution are compared with the other organic solutions. The fluorescence quantum yields are determined low in more polar solvents and also calculated to be about less than about 0.05 in aqueous solution because of the aggregation effects. Photodegradation rate constants (k_p) of the synthesized compounds have been compared under xenon lamp irradiation in acetonitrile solution.Binding abilities of the synthesized perylene diimides to different form of DNA strands have been investigated by visible absorption and fluorescence spectroscopy in the phosphate buffer solutions. Also, pH-dependent aggregation and G-quadruplex DNA binding selectivity of these ligands have been compared. Among these ligands, N-(2,6-diisopropylphenyl)-N′-(4-pyridyl)-perylene-3,4,9,10-tetracarboxylic diimide (PYPER) has been found to be the most selective interactive ligand for G-quadruplex formed in the G4′-DNA structure. PYPER has shown a significant selectivity to G4′-DNA which is comprised of d(TTAGGG) repeats, known as human telomeres, in the phosphate buffer at pH 6. The absorption maximum of the PYPER/G4′-DNA complex has given bathochromic shift of 7 nm with respect to the absorption maximum of DNA-free solution of PYPER in phosphate buffer at pH 6. Fluorescence quenching experiments between PYPER and G4′-DNA show that PYPER demonstrates about a 9.3-fold selectivity for binding to G4′-DNA versus ds-DNA base pairs with the bimolecular rate constant of 0.95 × 10¹² M⁻¹ s⁻¹.     

PKa of cytosine on the third strand of triplex DNA: Preliminary Poisson–Boltzmann calculations

The energetics of formation of a triple-helical structure in homopurine–homopyrimidine mixtures has been modeled using Poisson–Boltzmann calculations. Oligomers with the sequence d(TC)_n and d(AG)_n form hydrogen-bonded triple-helical structures of the form d(TC)_n⋅d(AG)_n⋅d(TC⁺)_n. The third base, a pyrimidine in this case, forms Hoogsteen-type hydrogen bonds with the purine, requiring that the cytosine residues of the third strand protonate at N3. The pK_a of cytosine, 4.3 in the isolated solvated molecule, is raised by the strong electrostatic field in the triple helix. We have done calculations of the effective pK_a of this cytosine and compared the results with experimental studies of triple-helix formation as a function of pH. This provides a test of various models of the dielectric constant for triplex DNA and its local environment. © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 1177–1184, 1998     

O6-Alkylguanine DNA Alkyltransferase Mediated Disassembly of a DNA Tetrahedron

Tetrahedron DNA structures were formed by the assembly of three-way junction ( TWJ ) oligonucleotides containing O⁶-2′-deoxyguanosine-alkylene-O⁶-2′-deoxyguanosine (butylene and heptylene linked) intrastrand cross-links (IaCLs) lacking a phosphodiester group between the 2′-deoxyribose residues. The DNA tetrahedra containing TWJs were shown to undergo an unhooking reaction by the human DNA repair protein O⁶-alkylguanine DNA alkyltransferase (hAGT) resulting in structure disassembly. The unhooking reaction of hAGT towards the DNA tetrahedra was observed to be moderate to virtually complete depending on the protein equivalents. DNA tetrahedron structures have been explored as drug delivery platforms that release their payload in response to triggers, such as light, chemical agents or hybridization of release strands. The dismantling of DNA tetrahedron structures by a DNA repair protein contributes to the armamentarium of approaches for drug release employing DNA nanostructures.     

Mobility of single DNA chain under electric field during its transient contact with solid surfaces

The motion of DNA chain under electric field when it is in transient contact with the solid surfaces in aqueous solution was studied by single molecule fluorescence microscopy at the total internal reflection geometry (TIRFM). In situ observation discovered that single λ-DNA chains driven by electric field made transient contact with the solid surface and made hitting–sliding–leaving-like motion along the surface. By varying the surface chemistry, from the negative-charged silanol group-rich surface to positive-charged amino group-rich surface, as well as hydrophobic surfaces, the dependence of DNA mobility on the surface–DNA interaction was studied. The results show that a dependence of the mobility of DNA on the surface polarity with respect to DNA itself. The study on different surfaces rich of silanol, amide, amino, and methyl groups show a sequence of DNA mobility of silanol > amide > amino. The mobility of DNA on methyl terminated surface was found to be similar to that on amino surface. © 2009 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 47: 2541–2546, 2009