Extrahelical damaged base recognition by DNA glycosylase enzymes

The efficient enzymatic detection of damaged bases concealed in the DNA double helix is an essential step during DNA repair in all cells. Emergent structural and mechanistic approaches have provided glimpses into this enigmatic molecular recognition event in several systems. A ubiquitous feature of these essential reactions is the binding of the damaged base in an extrahelical binding mode. The reaction pathway by which this remarkable extrahelical state is achieved is of great interest and even more debate.     

Sequence Dependent Repair of 1,N6-Ethenoadenine by DNA Repair Enzymes ALKBH2, ALKBH3, and AlkB

Mutation patterns of DNA adducts, such as mutational spectra and signatures, are useful tools for diagnostic and prognostic purposes. Mutational spectra of carcinogens derive from three sources: adduct formation, replication bypass, and repair. Here, we consider the repair aspect of 1,N⁶-ethenoadenine (εA) by the 2-oxoglutarate/Fe(II)-dependent AlkB family enzymes. Specifically, we investigated εA repair across 16 possible sequence contexts (5′/3′ flanking base to εA varied as G/A/T/C). The results revealed that repair efficiency is altered according to sequence, enzyme, and strand context (ss- versus ds-DNA). The methods can be used to study other aspects of mutational spectra or other pathways of repair.     

Tuning urea-phenanthridinium conjugates for DNA/RNA and base pair recognition

A series of novel urea-phenanthridine conjugates was prepared. The variation of linker length connecting two urea-phenanthridinium conjugates regulated their binding mode toward double stranded polynucleotides, consequently controlling selectivity of compounds toward ds-RNA over ds-DNA stabilization as well as selective fluorescence response toward addition of G-C base pair and A-U(T) base pair containing polynucleotides.     

Switching Demethylation Activities between AlkB Family RNA/DNA Demethylases through Exchange of Active‐Site Residues

The AlkB family demethylases AlkB, FTO, and ALKBH5 recognize differentially methylated RNA/DNA substrates, which results in their distinct biological roles. Here we identify key active‐site residues that contribute to their substrate specificity. Swapping such active‐site residues between the demethylases leads to partially switched demethylation activities. Combined evidence from X‐ray structures and enzyme kinetics suggests a role of the active‐site residues in substrate recognition. Such a divergent active‐site sequence may aid the design of selective inhibitors that can discriminate these homologue RNA/DNA demethylases.     

Estimation of the optimal electrophoretic temperature of DNA single-strand conformation polymorphism by DNA base composition

To explore the relation between DNA base composition and the optimal single-strand conformation polymorphism (SSCP) electrophoretic temperature (T(s)), we analyzed DNA base composition and T(s) of 24 DNA fragments from different genes and found that T(s) was positively correlative with the ratio of base C/base A. T(s) could be estimated by the formula T(s) = [80 x C/(A+1)]/[2.71 + [C/(A+1)]]. T(s) could be increased dramatically by the complementary sequences in both 5'-and 3'-ends of a DNA single-strand.     

Quantum chemical characterization of the cytosine: 2‐Aminopurine base pair

The nature of the base pairing between cytosine and 2‐aminopurine is investigated by means of quantum mechanical calculations including electron correlation and accounting for the effects of aqueous solvation. At neutral pH, both a neutral wobble base pair and a Watson–Crick‐like base pair having a protonated 2‐aminopurine are predicted to be close to one another in energy; other previously proposed forms are found to be too high in energy to be of significant chemical interest. Accounting for the energetics of helix embedding suggests that the equilibrium between the two low‐energy motifs is quite sensitive to local environment. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1167–1179, 2001     

Qualitative study of in vivo melphalan adduct formation in the rat by miniaturized column-switching liquid chromatography coupled with electrospray mass spectrometry

In a general study of DNA adduct formation with melphalan, rats were intravenously injected with a single high dose (10 mg kg(-1)). Adduct formation was studied at the nucleoside level in the target organs liver, bone marrow, kidney and blood with the use of 2D liquid chromatography/tandem mass spectrometry (LC/MS/MS). Adducts of dGuo and dAdo were detected under selected reaction monitoring in liver and bone marrow 10 h after administration of melphalan. In the DNA hydrolysates from kidney and blood a Gua-melphalan adduct was found, although in very low abundance. These first results of the search for in vivo-formed melphalan adducts in the rat showed that our miniaturized LC/MS technique is useful for investigating this type of compound. More experiments will be performed in this area to gather more information about the pharmacokinetics and the quantity of adducts formed.     

Oxidative and hydrolytic DNA cleavage by Cu(II) complexes of salicylidene tyrosine schiff base and 1,10 phenanthroline/bipyridine

Ternary Cu(II) complexes [Cu(II)(saltyr)(B)] (1,2), (saltyr = salicylidene tyrosine, B = 1,10 phenanthroline (1) or 2,2′ bipyridine (2)) were synthesized and characterized by various techniques. The complexes exhibit square pyramidal (CuN₃O₂) geometry. CT-DNA binding studies revealed that the complexes show good binding propensity (K_b = 3.47 × 10⁴ M⁻¹ and 3.01 × 10⁴ M⁻¹ for 1 and 2, respectively). The role of these complexes in the oxidative and hydrolytic DNA cleavage was studied. The catalytic ability of 1 and 2 follows the order: 1 > 2. The rate constants for the hydrolysis of phosphodiester bond were determined as 2.80 h⁻¹ and 2.11 h⁻¹ for 1 and 2, respectively. It amounts to (0.58-0.77) × 10⁸ fold rate enhancement compared to non-catalyzed DNA cleavage, which is significant.     

Separation of single‐base sequential isomers of single‐stranded DNA by capillary electrophoresis and its application in the discrimination of single‐base DNA mutations

Separation of single‐base substitution sequential DNA isomers remains one of the most challenging tasks in DNA separation by capillary electrophoresis. We developed a simple, versatile capillary electrophoresis technique for the separation of single‐base sequential isomers of DNA having the same chain length. This technique is based on charge differences resulting from the different protonation (acid dissociation) properties of the four DNA bases. A mixture of 13 single‐base sequential isomers of 12‐mer single‐stranded DNA was separated by using an electrophoretic buffer solution containing 20 mM phosphoric acid (pH 2.0) and 8 M urea. We demonstrated that our method could separate all possible mutation patterns under identical experimental conditions. In addition, application of our method to the separation of the polymerase chain reaction product of a 68‐mer gene fragment and its single‐base isomers indicates that in combination with the appropriate genomic DNA extraction techniques, the method can detect single‐base gene mutations.     

Fluorescent detection of single nucleotide polymorphism utilizing a hairpin DNA containing a nucleotide base analog pyrrolo-deoxycytidine as a fluorescent probe

A novel fluorescent method for the detection of single nucleotide polymorphism (SNP) was developed using a hairpin DNA containing nucleotide base analog pyrrolo-deoxycytidine (P-dC) as a fluorescent probe. This fluorescent probe was designed by incorporating a fluorescent P-dC into a stem of the hairpin DNA, whose sequence of the loop moiety complemented the target single strand DNA (ss-DNA). In the absence of the target ss-DNA, the fluorescent probe stays a closed configuration in which the P-dC is located in the double strand stem of the fluorescent probe, such that there is weak fluorescence, attributed to a more efficient stacking and collisional quenching of neighboring bases. In the presence of target ss-DNA, upon hybridizing the ss-DNA to the loop moiety, a stem-loop of the fluorescent probe is opened and the P-dC is located in the ss-DNA, thus resulting in strong fluorescence. The effective discrimination of the SNP, including single base mismatch ss-DNA (A, T, G) and double mismatch DNA (C, C), against perfect complementary ss-DNA was achieved by increased fluorescence intensity, and verified by thermal denaturation and circular dichroism spectroscopy. Relative fluorescence intensity had a linear relationship with the concentration of perfect complementary ss-DNA and ranged from 50 nM to 3.0 μM. The linear regression equation was F/F₀ = 2.73 C (μM) + 1.14 (R = 0.9961) and the detection limit of perfect complementary ss-DNA was 16 nM (S/N = 3). This study demonstrates that a hairpin DNA containing nucleotide base analog P-dC is a promising fluorescent probe for the effective discrimination of SNP and for highly sensitive detection of perfect complementary DNA.     

The molecular electrostatic potentials of the complementary base pairs of DNA

The perturbations in the molecular electrostatic potentials of the bases of the nucleic acids, brought about by hydrogen-bonding into complementary pairs are evaluated by a superposition procedure.     

Λ-及Δ-[Ru(phen)2dppz]n+对错配DNA的识别作用的分子模拟

本文通过在ESFF(Extensible Systematic Force Field)力场下对其作用中的体系势能进行分子力学计算，分析了手性金属配合物Λ－及Δ-[Ru(phen)2dppz]^n 对错配DNA d(CCGAATGAGG)2的识别机理，并在分子水平上对其做了详细解释。     

DNA-binding,oxidative DNA cleavage,and coordination mode of later 3d transition metal complexes of a Schiff base derived from isatin as antimicrobial agents

A Schiff base, obtained by the condensation of isatin monohydrazone with 2,3,5-trichlorobenzaldehyde, and its Co(II), Ni(II), Cu(II), and Zn(II) complexes have been synthesized and characterized. The interaction of these complexes with DNA is investigated using viscosity, absorption titration, and electrochemical techniques. The results indicate that the complexes bind to Calf thymus DNA through intercalation. Oxidative cleavage activities of the complexes are studied using supercoiled pBR322 DNA by gel electrophoresis. Antimicrobial study reveals that copper and zinc complexes are better antimicrobial agents than the Schiff base and its other complexes.     

Scanning Electrochemical Microscopy for Electrochemical Detection of Single‐base Mismatches by Tagging Ferrocenecarboxylic Acid as a Redox Probe to DNA

Scanning electrochemical microscopy (SECM) was employed for sensitive detection of single base mismatches (SBMs) in a sandwiched dsDNA. Ferrocenecarboxylic acid (Fc), covalently conjugated to the dsDNA, was oxidized to Fc⁺ via the DNA‐mediated charge transfer from the underlying gold substrate, and reduced back to Fc by SECM tip generated ferrocyanide. The electrocatalytic oxidation of SECM tip‐generated ferrocyanide was sensitive to presence, as well as the type of SBMs. Apparent standard rate constants (k⁰_app) values for different SBMs, both near the electrode surface and far from it, were evaluated by SECM. The method can detect SBMs independent of their position in dsDNA.     

Ag(I) ion mediated formation of a C-A mispair by DNA polymerases

Silver turns up the A-C: In the presence of Ag(I) ions, a DNA polymerase incorporated deoxyadenosine (from dATP) at the site opposite cytosine in the template strand to afford the full-length product (see scheme), meaning that DNA polymerases prefer a C-Ag(I)-A base pair to the more thermodynamically stable C-Ag(I)-C base pair.     

Synthesis of 2-aminobenzophenone-based Schiff base Pd(II) complexes: Investigation on crystal structure,biological behavior of DNA/protein-binding,molecular docking,and in vitro anticancer activities

Two new monobasic bidentate ligands and their Pd(II) complexes have been synthesized and characterized by analytical and spectroscopic methods. The structures of the complexes were confirmed by single-crystal X-ray diffraction. The bimolecular binding of the ligands and complexes has been carried out and described. Interestingly, both the bidentate chelating ligands replaced all the triphenyl arsine and chloride ions from the metal precursor in the formation of new complexes and were found to be approximately square planar. The interaction of the ligands and the complexes with calf thymus DNA and bovine serum albumin was studied by electronic and emission spectroscopy techniques, which suggested an intercalation mode of binding. It is well-known that the viscosity of a DNA solution increases if any compound added binds to it through intercalation because this process lengthens the DNA helix due to the increased separation of the DNA base pairs when the compound slides in between, whereas a partial, nonclassical intercalation could bend (or kink) the DNA helix, which leads to a reduction in length and thereby reducing its viscosity. By contrast, there will be no change in the viscosity when the compounds bind with DNA grooves or by partial intercalation, which was further confirmed by viscosity measurements and molecular docking studies. It has been found that the compounds cleaved supercoiled DNA into nicked DNA without any external agent. The in vitro cytotoxicity studies of the ligands and complexes against human lung (A549) and breast (MCF7) cancer cell lines showed significant activity for both species.     

Synthesis,crystal structure,and interaction with DNA and BSA of a chromium(III) complex with naph-gly Schiff base and 1,10-phenanthroline

A new chromium(III) complex, [CrCl(naph-gly)phen]?H₂O (naph-gly = Schiff base derived from 2-hydroxy-1-naphthaldehyde and glycine, phen = 1,10-phenanthroline), has been synthesized and characterized by elemental analysis, electrospray ionization mass spectroscopy, FT-IR, and X-ray single-crystal diffraction. The chromium(III) complex belongs to the trigonal crystal system, P3(1) space group with crystallographic data: a = b = 1.97017(16) nm, c = 1.02991(7) nm, α?=?β?=?90°, γ =120°, V = 3.4621(5) nm³, D_c = 1.476 g?cm^?3, Z = 6, F(0 0 0)?=?1578, R₁ = 0.0508, wR₂ = 0.0907. There are two independent molecules in the crystallographic asymmetric unit of the chromium(III) complex. Each Cr^III is six-coordinate to form an octahedral geometry. In the crystal, a 3-D structure is formed through intermolecular hydrogen bonds. The calf thymus DNA (CT-DNA)- and bovine serum albumin (BSA)-binding properties of the complex have been studied by UV absorption, fluorescence, and circular dichroism (CD) spectroscopy. Results indicate that the chromium(III) complex binds to CT-DNA in an intercalative mode, and it can bind to BSA and cause conformational changes of BSA.     

Regulated Incorporation of Two Different Metal Ions into Programmed Sites in a Duplex by DNA Polymerase Catalyzed Primer Extension

Metal‐mediated base pairs formed by the coordination of metal ions to natural or artificial bases impart unique chemical and physical properties to nucleic acids and have attracted considerable interest in the field of nanodevices. Ag^I ions were found to mediate DNA polymerase catalyzed primer extension through the formation of a C–Ag^I–T base pair, as well as the previously reported C–Ag^I–A base pair. The comparative susceptibility of dNTPs to Ag^I‐mediated enzymatic incorporation into the site opposite cytosine in the template was shown to be dATP>dTTP?dCTP. Furthermore, two kinds of metal ions, Ag^I and Hg^II, selectively mediate the incorporation of thymidine 5′‐triphosphate into sites opposite cytosine and thymine in the template, respectively. In other words, the regulated incorporation of different metal ions into programmed sites in the duplex by DNA polymerase was successfully achieved.     

Quantum chemical study on enantioselective reduction of keto oxime ether with borane catalyzed by oxazaborolidine. Part 2. Structures of catalyst‐alkoxyborane adduct with a four‐membered ring and succeeding reaction intermediates

Quantum chemical ab initio computations of the structures and properties of oxazaborolidine‐alkoxyborane adduct with a B? N? B? O four‐membered ring and succeeding reaction intermediates are carried out in the current work by means of the Hartree–Fock (HF) and the density functional methods. All the structures are optimized completely at the HF/6‐31G(d) and Becke's three‐parameter exchange functional and the gradient‐corrected functional of Lee, Yang, and Paar (B3LYP)/6‐31G(d) levels. As shown in the obtained results, the oxazaborolidine‐alkoxyborane adduct with a B? N? B? O four‐membered ring may be formed during the reduction of the carbonyl bond of the catalyst‐borane‐keto oxime ether adduct. The breakdown of the B? N? B? O four‐membered ring results in the formation of the adduct with a B? N? B? O? C? C? N seven‐membered ring and an oxime bond. The reduction of the oxime bond leads to the adduct with a chiral oxime carbon. The B(2)? N_{C? N} bond in the B? N? B? O? C? C? N seven‐membered ring of the adduct with a reduced oxime bond is weaker comparatively and thus may be more easily broken down. All the adducts have four stable structures. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem 93: 294–306, 2003