Interaction of antitumor drug Sn(CH3)2Cl2 with DNA and RNA

Sn(CH₃)₂Cl₂ exerts its antitumor activity in a specific way. Unlike anticancer cis-Pt(NH₃)₂Cl₂ drug which binds strongly to the nitrogen atoms of DNA bases, Sn(CH₃)₂Cl₂ shows no major affinity towards base binding. Thus, the mechanism of action by which tinorganometallic compounds exert antitumor activity would be different from that of the cisplatin drug. The aim of this study was to examine the binding of Sn(CH₃)₂Cl₂ with calf thymus DNA and yeast RNA in aqueous solutions at pH 7.1–6.6 with constant concentrations of DNA and RNA and various molar ratios of Sn(CH₃)₂Cl₂/DNA (phosphate) and Sn(CH₃)₂Cl₂/RNA of 1/40, 1/20, 1/10, 1/5. Fourier transform infrared (FTIR) and UV–visible difference spectroscopic methods were used to determine the Sn(CH₃)₂Cl₂ binding mode, binding constant, sequence selectivity and structural variations of Sn(CH₃)₂Cl₂/DNA and Sn(CH₃)₂Cl₂/RNA complexes in aqueous solution. Sn(CH₃)₂Cl₂ hydrolyzes in water to give Sn(CH₃)₂(OH)₂ and [Sn(CH₃)₂(OH)(H₂O)_n]⁺ species. Spectroscopic evidence showed that interaction occurred mainly through (CH₃)₂Sn(IV) hydroxide and polynucleotide backbone phosphate group with overall binding constant of K(Sn(CH₃)₂Cl₂–DNA)=1.47×10⁵ M⁻¹ and K(Sn(CH₃)₂Cl₂–RNA)=7.33×10⁵ M⁻¹. Sn(CH₃)₂Cl₂ induced no biopolymer conformational changes with DNA remaining in the B-family structure and RNA in A-conformation upon drug complexation.     

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.     

Voltammetric study of the interaction of lomefloxacin (LMF)–Mg(II) complex with DNA and its analytical application

The voltammetric behavior of the LMF-Mg(II) complex with DNA at a mercury electrode is reported for the first time. In NH₃–NH₄Cl buffer (pH=9.10), the adsorption phenomena of the LMF–Mg(II) complex were observed by linear sweep voltammetry. The mechanism of the electrode reaction was found to be a reduction of LMF in the complex, and the composition of the LMF–Mg(II) complex is 2:1. In the presence of calf thymus DNA (ctDNA), the peak current of LMF–Mg(II) complex decreased considerably, and a new well-defined adsorptive reduction peak appeared at −1.63 V (vs. SCE). The electrochemical kinetic parameters and the binding number of LMF–Mg(II) with ctDNA were also obtained. Moreover, the new peak currents of LMF–Mg(II)–DNA system increased linearly correlated to the concentration of DNA in the 4.00×10⁻⁷–2.60×10⁻⁶ g ml⁻¹ range when the concentrations of LMF–Mg(II) complex was fixed at 5.00×10⁻⁶ mol l⁻¹, with the detection limits of 2.33×10⁻⁷ g ml⁻¹. An electrostatic interaction was suggested by electrochemical method.     

DNA and RNA binding properties of an arginine-based ‘Extended Chiral Box’ Peptide Nucleic Acid

Lys-based ‘chiral box’ Peptide Nucleic Acids (PNAs with three adjacent 2D-Lys-based chiral monomers) have shown unsurpassed specificity in DNA recognition. In this Letter, the binding performances of arginine-based chiral PNAs were evaluated for PNAs containing in the middle part of the strand either a 2D,5L-Arg monomer or three adjacent 2D-; 2D,5L-; 5L-Arg monomers (‘Extended Chiral Box’), a combination never studied before. The binding performances of the PNAs were studied by evaluating the melting temperatures of fullmatch and mismatch PNA-DNA and PNA-RNA hybrids and by studying their structure by circular dichroism (CD). The data indicated that the arginine side chains inserted in the PNA structure are perfectly equivalent to lysine side chains as far as oligonucleotide recognition is concerned. The insertion of an ‘Extended Chiral Box’ into PNA differently influences the binding properties to DNA and RNA: the additional side chains had no observable effect on binding affinity and selectivity toward DNA, whereas, seemed to slightly disturb the binding affinity to RNA but at the same time highly enhancing the recognition selectivity.     

“Base Flipping”: Photodamaged DNA–RNA Duplexes Are Poor Substrates for Photoreactivating DNA-Repair Enzymes

What is damaged cannot always be readily repaired. This is observed for particular areas in the genome (mutation hot spots), which are repaired with low efficiency. DNA–DNA duplexes that exist in the B-conformation are repaired relatively efficiently by photolyases. DNA–RNA duplexes, which prefer an A-type conformation are only moderately destabilized by DNA photolesions and are slowly repaired. This suggests that the DNA conformation modulates the necessary “flipping” process for the repair of DNA lesions.     

Phosphine‐Free Stille–Migita Chemistry for the Mild and Orthogonal Modification of DNA and RNA

An optimized catalyst system of [Pd₂(dba)₃] and AsPh₃ efficiently catalyzes the Stille reaction between a diverse set of functionalized stannanes and halogenated mono‐, di‐ and oligonucleotides. The methodology allows for the facile conjugation of short and long nucleic acid molecules with moieties that are not compatible with conventional chemical or enzymatic synthesis, among them acid‐, base‐, or fluoride‐labile protecting groups, fluorogenic and synthetically challenging moieties with good to near‐quantitative yields. Notably, even azides can be directly introduced into oligonucleotides and (deoxy)nucleoside triphosphates, thereby giving direct access to “clickable” nucleic acids.     

Donor–acceptor interaction of fullerene C60 with triptycene in molecular complex TPC·C60

A molecular complex of fullerene C₆₀ with triptycene, TPC·C₆₀ is obtained. The complex has a three-dimensional packing of C₆₀ molecules. According to the IR spectra, the freezing of free rotation of C₆₀ molecules in the complex is maintained up to 360 K. The XP-spectra of TPC·C₆₀ show the suppression of π–π^* transitions of TPC phenylene rings. The separation of C₆₀ molecules by TPC ones in TPC·C₆₀ results in low intensity of the C₆₀ transitions in the 420–500 nm range in an optical spectrum. This absorption is assumed as that attributed to intermolecular transitions between adjacent C₆₀ molecules.     

Thin‐Film Properties of DNA and RNA Bases: A Combined Experimental and Theoretical Study

The structures of the DNA and RNA bases cytosine, uracil, and thymine in thin films with a nominal film thickness of about 20 nm are studied by using X‐ray photoemission spectroscopy (XPS) and Fourier‐transform infrared spectroscopy. The molecules are evaporated in situ from powder on a gold foil. The experimental results indicate that cytosine is composed of two energetically close tautomeric forms, whereas uracil and thymine exist in only one tautomeric form. Additionally, quantum chemical calculations are performed to complement the experimental results. The relative energies of the tautomeric forms of cytosine, uracil, and thymine are calculated using Hartree–Fock (HF), density functional theory (DFT), and post‐HF methods. Furthermore, the assignment of the XPS spectra is supported by using simple model considerations employing Koopmans ionization energies and Mulliken net atomic charges.     

Phase Separations in Water–Salt Solutions of Polyelectrolyte Complexes Formed by RNA and Polycations: Comparison with DNA Complexes

Formation of insoluble polyelectrolyte complexes (PECs) between RNA and polycations was followed by measuring the residual RNA absorbance in the solution after separation of the precipitate. The polycations studied were poly(N,N′‐dimethyldiallylammonium) chloride (pendant type) and 2,5‐ionene bromide (integral type) with quaternary amino groups in every monomer unit. The data obtained were compared with the results of analogous studies of DNA‐containing PECs. This study is a part of a project aimed at the specific separation of plasmid DNA from RNA, a major problem in the preparative isolation of plasmid DNA. We thus deliberately chose a heterogenous RNA sample as it represents the RNA present in a real cell extract. In contrast to the exhaustive precipitation of DNA observed at certain φ values, a significant part of RNA was nonprecipitated at any φ = [+]/[?], that is, at any ratio of positively charged quaternary amino groups and negatively charged phosphate groups. The addition of sodium chloride increased the nonprecipitated fraction of RNA. DNA, on the other hand, was completely precipitated by both polycations at φ > 0.7. The less effective precipitation of RNA was probably due to the presence of a considerable fraction of short‐chained molecules, incapable of forming a sufficient cooperative system of salt bonds with the polycation. This assumption was supported by a separate experiment, in which the precipitation behavior of RNA fractions of different molecular masses was investigated. The same tendency, while less pronounced, was also ascertained for PECs formed by polycations with DNA fractions of different molecular masses. The possibility of using the revealed differences between DNA and RNA behavior for effective precipitation procedure useful in bioseparation is discussed. The difference in the precipitation behavior of nucleic acids of different molecular masses means there is a possibility for developing an enzymatic assay for DNAase and RNAase activity.

The relative residual absorbance of RNA (closed symbols) and DNA (open symbols) remaining in solution after precipitation with 2,5‐ionene bromide as a function of the charge ratio, [+]/[?], determined at different concentrations of sodium chloride (M ).     

Sugar–Edge Interactions in a DNA–RNA G‐Quadruplex: Evidence of Sequential C−H⋅⋅⋅O Hydrogen Bonds Contributing to RNA Quadruplex Folding

DNA G‐quadruplexes were systematically modified by single riboguanosine (rG) substitutions at anti‐dG positions. Circular dichroism and NMR experiments confirmed the conservation of the native quadruplex topology for most of the DNA–RNA hybrid structures. Changes in the C8 NMR chemical shift of guanosines following rG substitution at their 3′‐side within the quadruplex core strongly suggest the presence of C8?H???O hydrogen‐bonding interactions with the O2′ position of the C2′‐endo ribonucleotide. A geometric analysis of reported high‐resolution structures indicates that such interactions are a more general feature in RNA quadruplexes and may contribute to the observed preference for parallel topologies.     

Templated Formation of Discrete RNA and DNA:RNA Hybrid G‐Quadruplexes and Their Interactions with Targeting Ligands

G‐rich RNA and DNA oligonucleotides derived from the human telomeric sequence were assembled onto addressable cyclopeptide platforms through oxime ligations and copper‐catalyzed azide‐alkyne cycloaddition (CuAAc) reactions. The resulting conjugates were able to fold into highly stable RNA and DNA:RNA hybrid G‐quadruplex (G4) architectures as demonstrated by UV, circular dichroism (CD), and NMR spectroscopic analysis. Whereas rationally designed parallel RNA and DNA:RNA hybrid G4 topologies could be obtained, we could not force the formation of an antiparallel RNA G4 structure, thus supporting the idea that this topology is strongly disfavored. The binding affinities of four representative G4 ligands toward the discrete RNA and DNA:RNA hybrid G4 topologies were compared to the one obtained with the corresponding DNA G4 structure. Surface plasmon resonance (SPR) binding analysis suggests that the accessibility to G4 recognition elements is different among the three structures and supports the idea that G4 ligands might be shaped to achieve structure selectivity in a biological context.     

Interaction of dipropyltin(IV) with amino acids,peptides, dicarboxylic acids and DNA constituents

Interaction of dipropyltin(IV) with selected amino acids, peptides, dicarboxylic acids or DNA constituents was investigated using potentiometric techniques. Amino acids form 1?:?1 and 1?:?2 complexes and, in some cases, protonated complexes. The amino acid is bound to dipropyltin(IV) by the amino and carboxylate groups. Serine is complexed to dipropyltin(IV) with ionization of the alcoholic group. A relationship exists between the acid dissociation constant of the amino acids and the formation constants of the corresponding complexes. Dicarboxylic acids form both 1?:?1 and 1?:?2 complexes. Diacids forming five- and six-membered chelate rings are the most stable. Peptides form complexes with stoichiometric coefficients 111(MLH), 110(ML) and 11-1(MLH_?1)(tin: peptide: H⁺). The mode of coordination is discussed based on existing data and previous investigations. DNA constituents inosine, adenosine, uracil, uridine, and thymine form 1?:?1 and 1?:?2 complexes and the binding sites are assigned. Inosine 5′-monophosphate, guanosine 5′-monophosphate, adenosine 5′-monophosphate and adenine form protonated species in addition to 1?:?1 and 1?:?2 complexes. The protonation sites and tin-binding sites were elucidated. Cytosine and cytidine do not form complexes with dipropyltin(IV) due to low basicity of the donor sites. The stepwise formation constants of the complexes formed in solution were calculated using the non-linear least-square program MINIQUAD-75. The concentration distribution of the various complex species was evaluated as a function of pH.     

A new derivatization procedure for the determination of cephalexin with 1,2-naphthoquinone 4-sulphonate in pharmaceutical and urine samples using solid-phase extraction cartridges and UV–visible detection

The present report shows how to derivatize cephalexin with 1,2-naphthoquinone-4-sulphonate (NQS) into solid-phase extraction cartridges (C₁₈) using UV–visible detection. Optimum conditions for this new procedure are: hydrogen carbonate/carbonate buffer pH=10.5, 5 min reaction time at 25°C and NQS concentration of 7.1×10⁻³ mol l⁻¹. The accuracy and the precision of the method were tested. The procedure was used to measure cephalexin in pharmaceutical and urine samples. The results obtained were contrasted with those reported by UV-spectrophotometric and HPLC methods for pharmaceutical samples and with HPLC method for urine samples. The H-point standard additions method was used to measure cephalexin in pharmaceutical samples, and the generalized H-point standard additions method was used to measure cephalexin in urine samples.     

X-ray crystal structure of a Cu(II) complex with the antiparasitic drug tinidazole,interaction with calf thymus DNA and evidence for antibacterial activity

Interaction of metal ions with biologically active molecules like 5-nitroimidazoles modulates their electronic environment and therefore influences their biological function. In the present work, an antiparasitic drug tinidazole (tnz) was selected and a Cu(II) complex of tnz [Cu₂(OAc)₄(tnz)₂] was prepared. A dinuclear paddle-wheel [Cu₂(OAc)₄(tnz)₂] was obtained by single-crystal XRD and further characterized by spectroscopic techniques and cyclic voltammetry. To understand the biological implications of complex formation, interaction of tnz and its complex was studied with calf thymus DNA, bacterial and fungal cell lines. Results of calf thymus DNA interaction using cyclic voltammetry indicate the overall binding constant (K^*) of Cu₂(OAc)₄(tnz)₂ [(59?±?6)?×?10⁴?M^?1] is ~17 times greater than that of tnz [(3.3?±?0.4)?×?10⁴?M^?1]. Minimum inhibitory concentration values suggest that [Cu₂(OAc)₄(tnz)₂] possesses better antibacterial activity than tnz on both bacterial strains, while the activity on a fungal strain was comparable.     

Opposite Orientation of Backbone Inclination in Pyranosyl‐RNA and Homo‐DNA Correlates with Opposite Directionality of Duplex Properties

Backbone inclination is a parameter which can be used for the classification of the structure type of oligonucleotide duplexes. Its significance for the interpretation of the sequence dependence of duplex stability is illustrated based on examples of the p‐RNA and homo‐DNA series.     

Click Chemistry for the Identification of G‐Quadruplex Structures: Discovery of a DNA–RNA G‐Quadruplex

A trap that closes with a “click” : The copper‐catalyzed azide–alkyne cycloaddition can occur in different G‐quadruplex structures (see scheme). The species trapped by the click reaction can then be separated and analyzed. By using this approach, a DNA–RNA hybrid‐type G‐quadruplex structure formed by human telomeric DNA and RNA sequences was detected.