Chemical approaches untangling sequence-specific DNA binding by proteins

Structure-based design of novel DNA-binding proteins provides an ultimate test of our understanding of protein-DNA interactions. A combination of synthetic, organic, biochemical and molecular biological approaches has been developed to study the principle of molecular recognition associated with the protein-DNA interactions. The strategies enabled a specific formation of noncovalent peptide dimers and determination of the preferential DNA-binding sequence of short peptides.     

A designer bleomycin with significantly improved DNA cleavage activity

The bleomycins (BLMs) are used clinically in combination with a number of other agents for the treatment of several types of tumors, and the BLM, etoposide, and cisplatin treatment regimen cures 90-95% of metastatic testicular cancer patients. BLM-induced pneumonitis is the most feared, dose-limiting side effect of BLM in chemotherapy, which can progress into lung fibrosis and affect up to 46% of the total patient population. There have been continued efforts to develop new BLM analogues in the search for anticancer drugs with better clinical efficacy and lower lung toxicity. We have previously cloned and characterized the biosynthetic gene clusters for BLMs from Streptomyces verticillus ATCC15003, tallysomycins from Streptoalloteichus hindustanus E465-94 ATCC31158, and zorbamycin (ZBM) from Streptomyces flavoviridis SB9001. Comparative analysis of the three biosynthetic machineries provided the molecular basis for the formulation of hypotheses to engineer novel analogues. We now report engineered production of three new analogues, 6'-hydroxy-ZBM, BLM Z, and 6'-deoxy-BLM Z and the evaluation of their DNA cleavage activities as a measurement for their potential anticancer activity. Our findings unveiled: (i) the disaccharide moiety plays an important role in the DNA cleavage activity of BLMs and ZBMs, (ii) the ZBM disaccharide significantly enhances the potency of BLM, and (iii) 6'-deoxy-BLM Z represents the most potent BLM analogue known to date. The fact that 6'-deoxy-BLM Z can be produced in reasonable quantities by microbial fermentation should greatly facilitate follow-up mechanistic and preclinical studies to potentially advance this analogue into a clinical drug.     

Identification of strong DNA binding motifs for bleomycin

The bleomycins (BLMs) are clinically used antitumor antibiotics. Their mechanism of action is believed to involve oxidative cleavage of DNA and possibly also RNA degradation. DNA degradation has been studied extensively and shown to involve binding of an activated metallobleomycin to DNA, followed by abstraction of C4'-H from deoxyribose in the rate-limiting step for DNA degradation. It is interesting that while DNA and RNA degradation by activated Fe.BLM has been studied extensively, much less is known about the actual binding selectivity of BLM, that is, the obligatory step that precedes cleavage. Thus it is unclear whether cleavage specificity is defined by the binding event or whether cleavage occurs at a subset of preferred binding sites. With only a few exceptions, NMR binding studies have employed metalloBLMs such as Co.BLM and Zn.BLM whose therapeutic relevance is uncertain. A single biochemical study that compared DNA binding and cleavage directly also employed Co.BLM. It is logical to anticipate that preferred sites of DNA cleavage will occur at sites that are (a subset of) preferred DNA binding sites, but there are currently no data available relevant to this issue. Herein, we describe the development and implementation of a novel strategy to identify DNA motifs that bind BLM strongly.     

RNA cleavage and inhibition of protein synthesis by bleomycin

Bleomycin is a clinically used antitumor antibiotic long thought to function therapeutically at the level of DNA cleavage. Recently, it has become clear that bleomycin can also cleave selected members of all major classes of RNA. Using the computer program COMPARE to search the database established by the Anticancer Drug Screening Program of the National Cancer Institute, a possible mechanism-based correlation was found between onconase, an antitumor ribonuclease currently being evaluated in phase III clinical trials, and the chemotherapeutic agent bleomycin. Following these observations, experimentation revealed that bleomycin caused tRNA cleavage and DNA-independent protein synthesis inhibition in rabbit reticulocyte lysate and when microinjected into Xenopus oocytes. The correlation of protein synthesis inhibition to the previously reported site-specific RNA cleavage caused by bleomycin supports the thesis that RNA cleavage may constitute an important element of the mechanism of action of bleomycin.     

八羟基喹啉铜(Ⅱ)配合物的DNA结合和切割活性及与牛血清白蛋白相互作用（英文）

利用紫外吸收光谱、荧光光谱、圆二色光谱(CD)和琼脂糖凝胶电泳等手段研究了八羟基喹啉铜(Ⅱ)配合物Cu[8-OHQ]2与DNA和蛋白质的相互作用.实验结果表明,在生理条件下,Cu[8-OHQ]2能通过插入方式较强的与CT-DNA结合,诱导DNA构象的改变.其本征结合常数Kb为1.15(±0.01)×105 L/mol,表观结合常数Kapp为4.21×106 L/mol.再者,琼脂糖凝胶电泳实验表明,在生理条件和抗坏血酸(Vc)存在情况下,Cu[8-OHQ]2能有效地将超螺旋pBR322质粒DNA切割成缺刻和线性,甚至降解为小的片断.机理研究表明扩散的·OH,H2O2和1 O2都不是在切割过程中起作用的活性氧物种(ROS);copper-oxo中间体可能是此切割过程中主要的活性氧物种.另外,Cu[8-OHQ]2也能以适中的结合力与牛血清白蛋白(BSA)结合而猝灭BSA内源荧光,猝灭机理为静态猝灭.所有这些结果表明Cu[8-OHQ]2具有作为潜在化疗试剂的生物活性.     

Spectroscopic studies of the interaction of ferrous bleomycin with DNA

Bleomycin is an antibiotic used in cancer chemotherapy for its ability to achieve both single- and double-strand cleavage of DNA through abstraction of the deoxyribose C4'-H. Magnetic circular dichroism (MCD) and X-ray absorption (XAS) spectroscopies have been used to study the interaction of the biologically relevant FeIIBLM complex with DNA. Calf thymus DNA was used as the substrate as well as short oligonucleotides, including one with a preferred 5'-G-pyrimidine-3' cleavage site [d(GGAAGCTTCC)2] and one without [d(GGAAATTTCC)2]. DNA binding to FeIIBLM significantly perturbs the FeII active site, resulting in a change in intensity ratio of the d d transitions and a decrease in excited-state orbital splitting (5Eg). Although this effect is somewhat dependent on length and composition of the oligonucleotide, it is not correlated to the presence of a 5'-G-pyrimidine-3' cleavage site. No effect is observed on the charge-transfer transitions, indicating that the H-bonding recognition between the pyrimidine and guanine base does not perturb Fe-pyrimidine backbonding. Azide binding studies indicate that FeIIBLM bound to either oligomer has the same affinity for N3-. Parallel studies of BLM structural derivatives indicate that FeIIiso-PEPLM, in which the carbamoyl group is shifted on the mannose sugar, forms the same DNA-bound species as FeIIBLM. In contrast, FeIIDP-PEPLM, in which the -aminoalanine group is absent, forms a new species upon DNA binding. These data are consistent with a model in which the primary amine from the -aminoalanine is an FeII ligand and the mannose carbamoyl provides either a ligand to the FeII or significant second-sphere effects on the FeII site; intercalation of the bithiazole tail into the double helix likely brings the metal-bound complex close enough to the DNA to create steric interactions that remove the sugar groups from interaction with the FeII. The fact that the FeII active site is perturbed regardless of DNA sequence is consistent with the fact that cleavage is observed for both 5'-GC-3' and nonspecific oligomers and indicates that different reaction coordinates may be active, depending on orientation of the deoxyribose C4'-H.     

The interaction of copper-bipyridyl complex with DNA and cleavage to DNA.

The interaction of a copper-bipyridyl (bpy) complex with CT-DNA was investigated by voltammetry, absorption and fluorescence spectrophotometry. The binding constant of the Cu(bpy)2(2+) complex interacting with DNA was 3.24 x 10(4) L/mol and the ability binding of Cu(bpy)2(2+) to DNA was 1.3-times as large as that of Cu(bpy)2+ to DNA. DNA could be efficiently cleaved by a potential-modulated method in the presence of the Cu(bpy)2(2+) complex. The fragments of the cleaved DNA were separated by high-performance liquid chromatography (HPLC). The experimental results revealed that the proposed method for DNA cleavage is highly efficient.     

Synthesis and DNA cleavage activity of a novel bleomycin A(5) glycoconjugate

[structure in text] To explore the possibility of modifying bleomycin in a fashion that could alter its physiological distribution in a therapeutic setting, a new analogue of bleomycin has been prepared. This analogue is intended to target the asialoglycoprotein receptor on liver cells. Critically, despite the large C-substituent, the bleomycin conjugate was found to degrade DNA in the same fashion as bleomycin A(5) itself, and with only modestly decreased efficiency.     

Chlorobenzylidine-herring sperm DNA interaction: binding mode and thermodynamic studies

The interaction of chlorobenzylidine with herring sperm DNA has been investigated by fluorescence, absorption, DNA melting experiment and differential scanning calorimetry (DSC). When bound to DNA, chlorobenzylidine shows hypochromism and red shift in absorption spectra, fluorescence quenching and polarization increasing in fluorescence spectra and increasing in DNA melting temperature. These spectral characteristics strongly support intercalation of chlorobenzylidine into herring sperm DNA. Scatchard plots constructed from fluorescence titration data give a binding constant of 3.2 x 10(4) M(-1) and a binding site size of six base pairs per bound drug molecule. The intercalative interaction is exothermic with a van't Hoff enthalpy of -30.6 kJ mol(-1). This result is obtained from DSC experiment. In addition, DeltaG degrees =-28.5 kJ mol(-1), and DeltaS degrees =-7.1 J mol(-1) K(-1). These results show that the binding of chlorobenzylidine to herring sperm DNA is exothermic.     

Metal-based netropsin mimics showing AT-selective DNA binding and DNA cleavage activity at red light

Copper(II) bis-arginate [Cu(l-arg)2](NO3)2 (1) and [Cu(l-arg)(phen)Cl]Cl (2) as mimics of the minor-groove-binding natural antibiotic netropsin show preferential binding to the AT-rich region of double-stranded DNA. The complexes with a d-d band near 600 nm display oxidative DNA cleavage activity on photoirradiation at UV-A light of 365 nm and at red light of 647.1 nm (Ar-Kr laser) in a metal-assisted photoexcitation process forming singlet oxygen (1O2) species in a type-2 pathway.     

Organoruthenium(II) thiosemicarbazone complexes: synthesis, spectral characterization, DNA binding and DNA cleavage studies

A series of new ruthenium(II) complexes were synthesized with Schiff bases derived from salicylaldehyde / o-hydroxyacetophenone/ o-vanillin / 2-hydroxy-1-naphthaldehyde with thiosemicarbazide and acetyl furan. They are characterized by elemental analysis, IR, electronic, ¹H NMR, ¹³C NMR and mass spectral studies. The elemental analysis suggests the stoichiometry to be 1:1 (metal:ligand). Four of these complexes were tested for its binding with CT-DNA using absorption spectroscopic studies and two of these complexes exhibit efficient DNA cleavage activity.      

Interaction of dinuclear ruthenium(II) supramolecular cylinders with DNA: sequence-specific binding, unwinding, and photocleavage

Metallosupramolecular chemistry was used to design a new class of synthetic agents, namely, tetracationic supramolecular cylinders, that bind strongly and noncovalently in the major groove of DNA. To gain additional information on interactions of the cylinders with DNA we explored DNA unwinding and sequence-specific binding properties, as well as DNA photonuclease activity of ruthenium(II) metallosupramolecular cylinder [Ru(2)L(3)](4+), where L is a bis-pyridylimine ligand. We found that [Ru(2)L(3)](4+) unwinds negatively supercoiled plasmid DNA and exhibits binding preference to regular alternating purine-pyrimidine sequences in a similar way to the [Fe(2)L(3)](4+) analogue. Photocleavage studies showed that, unlike [Fe(2)L(3)](4+), [Ru(2)L(3)](4+) induces single-strand breaks on irradiation by visible and UVA light and cleaves DNA mainly at guanine residues contained preferentially in regularly alternating purine-pyrimidine nucleotides. As [Ru(2)L(3)](4+) binds and cleaves DNA in a sequence-dependent manner, it may provide a useful tool for basic and applied biology, such as for controlled manipulation of the genome.     

Photoinduced DNA cleavage by fullerene-lysine conjugate

A novel water-soluble [60] fullerene-substituted lysine derivative 3 has been synthesized and characterized by elemental analysis, ¹H NMR, ¹³C NMR and FAB-MS. The synthetic procedure involved condensation of Boc-protected lysine with terephthaldehyde followed by 1,3-dipolar cycloaddition reaction with C₆₀ in the presence of sarcosine and finally deprotection of the amino group using trifluoroacetic acid. The synthesized compound 3 exhibited high DNA cleavage efficiency upon visible light irradiation in the presence of NADH.     

Novel Schiff base metal complexes: synthesis,characterization, DNA binding,DNA cleavage and molecular docking studies

A novel Schiff base, 3-(((1H-1,2,4-triazol-3-yl)imino)methyl)-4H-chromen-4-one (L) was synthesized and used as ligand for the synthesis of Co(II), Ni(II), Cu(II), Zn(II) and Pd(II) complexes. The structural characterization of the ligand and its metal complexes was determined by using various physicochemical and spectroscopic methods. The IR data show that the Schiff base ligand acts as a bidentate donor coordinating through the oxygen atom of the chromone and nitrogen atom of the imine group. Based on all spectral data, tetrahedral geometry has been proposed for all the metal complexes except Cu(II) and Pd(II) complexes. However, square-planar geometry has been proposed for Cu(II) and Pd(II) complexes. DNA binding interaction of the ligand and its metal complexes was investigated by using UV–visible absorption, fluorescence and molecular docking studies. The binding constants were in the order of 10⁴ M^?1 suggesting good binding affinity towards CT-DNA. The DNA cleavage activity of the synthesized compounds was investigated by using agarose gel electrophoresis. In vitro antimicrobial activity of the synthesized compounds were screened against two gram-positive bacteria (Bacillus subtilis, Staphylococcus aureu) and two gram-negative bacteria (Escherichia coli, Proteus vulgaris) and one fungi strain Candida albicans using disc diffusion method. Antioxidant activity was carried out by DPPH radical scavenging method. In vitro anti-proliferative activity of the ligand and its metal complexes was also carried on the HEK-293, HeLa, IMR-32 and MCF-7 cancer cell lines using MTT assay.     

Deglycobleomycin: solid-phase synthesis and DNA cleavage by the resin-bound ligand

[structure: see text] A greatly improved solid-phase synthesis of deglycobleomycin using a Dde-based linker is reported. The resin-bound deglycobleomycin could be completely deblocked and assayed for DNA plasmid relaxation, sequence-selective DNA cleavage, and light production from a molecular beacon.     

Protein-DNA interaction: impedance study of MutS binding to a DNA mismatch

MutS binding to a double-stranded DNA containing a single nucleotide mismatch can be conveniently monitored by impedance spectroscopy and represents the first step in developing an electrochemical binding essay for single nucleotide mismatch detection.     

Synthesis, DNA binding, photo-induced DNA cleavage and cytotoxicity studies of europium(III) complexes

Two Eu(III) complexes, [Eu(acac)(3)(dpq)] (1) and [Eu(acac)(3)(dppz)] CH(3)OH (2) {viz. acetylacetonate (acac), dipyrido[3,2-d:20,30-f]quinoxaline (dpq), dipyrido[3,2-a:20,30-c] phenazine (dppz)}, have been synthesized and their DNA binding, photo-induced DNA cleavage activity and cell cytotoxicity are studied. The complexes display significant binding propensity to the calf thymus DNA in the order: 2(dppz) >1(dpq). Cleavage experiments using pBR322 supercoiled DNA suggest major groove binding for 2 and minor groove binding for 1. The mechanistic aspects on natural light (natural light in room during the day) and UV-A (365 nm) irradiation are via a mechanistic pathway involving formation of singlet oxygen and hydroxyl radical as the reactive species. The photo-induced DNA cleavage activity of 2 is also stronger than 1. The cytotoxicity of 1 and 2 against HeLa (cervical) cancer cells show that the IC(50) value of 19.11 ± 3.56 μM and 17.95 ± 5.47 μM, respectively.