Sequence specific alkylation of DNA by hairpin pyrrole-imidazole polyamide conjugates

BACKGROUND: Pyrrole-imidazole polyamides are synthetic ligands that recognize predetermined sequences in the minor groove of DNA with affinities and specificities comparable to those of DNA-binding proteins. As a result of their DNA-binding properties, polyamides could deliver reactive moieties for covalent reaction at specific DNA sequences and thereby inhibit DNA-protein interactions. Site-specific alkylation of DNA could be a useful tool for regulating gene expression. As a minimal first step, we set out to design and synthesize a class of hairpin polyamides equipped with DNA alkylating agents and characterize the specificity and yield of covalent modification. RESULTS: Bis(dichloroethylamino)benzene derivatives of the well-characterized chlorambucil (CHL) were attached to the gamma turn of an eight-ring hairpin polyamide targeted to the HIV-1 promoter. We found that a hairpin polyamide-CHL conjugate binds and selectively alkylates predetermined sites in the HIV promoter at subnanomolar concentrations. Cleavage sites were determined on both strands of a restriction fragment containing the HIV-1 promoter, revealing good specificity and a high yield of alkylation. CONCLUSIONS: The ability of polyamide-CHL conjugates to sequence specifically alkylate double-stranded DNA in high yield and at low concentrations sets the stage for testing their use as regulators of gene expression in cell culture and ultimately in complex organisms.     

Sequence-specific alkylation of double-strand human telomere repeat sequence by pyrrole-imidazole polyamides with indole linkers

We designed and synthesized pyrrole (Py)-imidazole (Im) hairpin polyamide 1-(chloromethyl)-5-hydroxy-1,2-dihydro-3H-benz[e]indole (seco-CBI) conjugates 1 and 2, which target both strands of the double-stranded region of the human telomere repeat sequences, 5'-d(TTAGGG)(n)-3'/5'-d(CCCTAA)(n)-3'. High-resolution denaturing polyacrylamide gel electrophoresis demonstrated that conjugates 1 and 2 alkylated DNA at the 3' A of 5'-ACCCTA-3' and 5'-AGGGTTA-3', respectively. Cytotoxicities of conjugates 1 and 2 were evaluated using 39 human cancer cell lines; averages of log IC(50) values for conjugates 1 and 2 were -6.96 (110 nM) and -7.24 (57.5 nM), respectively. Conjugates 1 and 2 have potential as antitumor drugs capable of targeting telomere repeat sequence.     

G-rich sequence-specific recognition and scission of human genome by PNA/DNA hybrid G-quadruplex formation

Hole in one: A single peptide nucleic acid (PNA) effectively targets the G-rich region in double-stranded DNA through formation of a PNA/DNA hybrid G-quadruplex. Only one target site in the whole human genome was selectively cleaved by the hybrid G-quadruplex. Such site-selective scission of DNA is central to gene manipulation for molecular biology, biotechnology, and therapy.     

Synthesis of an adenine N-3 substituted CBI adduct by alkylation of adenine with a 1-iodomethylindoline seco-CBI precursor

The synthesis of a 1,2,9,9a-tetrahydrocyclopropa[c]benz[e]indol-4-one (CBI)-adenine adduct via regioselective N-3 alkylation of adenine with a 1-(iodomethyl)-2,3-dihydro-1H-benzo[e]indol-5-ol (I-seco-CBI)-containing precursor is described. Spectroscopic analyses of the unlabeled and adenine-C8 carbon-13 labeled adducts utilizing ROESY NMR techniques allowed structural assignment of the alkylation product as the adenine N-3 substituted regioisomer. A stable-isotopically labeled version of the N-3 adduct incorporating six carbon-13 labels was also prepared by this method for use as an LC-MS internal standard. The cyclized CBI-containing compound was also found to alkylate adenine at elevated temperatures to produce the N-3 adduct albeit at a significantly slower rate than that observed for the I-seco-CBI precursor. Adenine alkylation with an I-seco-CBI precursor offers scalable and facile access to a CBI-adenine adduct facilitating its use as an efficacy marker for the development of duocarmycin-based ADCs.     

Photosensitization of DNA damage by a new cationic pyropheophorbide derivative: sequence-specific formation of a frank scission

Pyropheophorbides are red-absorbing porphyrin-like photosensitizers that may interact with DNA either by intercalation or by external binding with self-stacking according to the value of the nucleotide to chromophore molar ratio (N/C). This article reports on the nature and sequence selectivity of the DNA damage photoinduced by a water-soluble chlorhydrate of aminopyropheophorbide. First, this pyropheophorbide is shown to induce on irradiation the cleavage of phiX174 DNA by both Type-I and -II mechanisms, suggested by scavengers and D2O effects. These conclusions are then improved by sequencing experiments performed on a 20-mer oligodeoxynucleotide (ODN) irradiated at wavelengths >345 nm in the presence of the dye, N/C varying from 2.5 to 0.5. Oxidation of all guanine residues to the same extent is observed after piperidine treatment on both single- and double-stranded ODN. Moreover, unexpectedly, a remarkable sequence-selective cleavage occurring at a 5'-CG-3' site is detected before alkali treatment. This frank break is clearly predominant for a low nucleotide to chromophore molar ratio, corresponding to a self-stacking of the dye along the DNA helix. The electrophoretic properties of the band suggest that this lesion results from a sugar oxidation, which leads via a base release to a ribonolactone residue. The proposal is supported by high-performance liquid chromatography-matrix-assisted laser desorption-ionization mass spectrometry experiments that also reveal other sequence-selective frank scissions of lower intensity at 5'-GC-3' or other 5'-CG-3' sites. This sequence selectivity is discussed with regard to the binding selectivity of cationic porphyrins.     

Synthesis of C-nucleosides designed to participate in triplex formation with native DNA: specific recognition of an A:T base pair in DNA

[structure: see text] We have previously described a system of 2-aminoquinoline- and 2-aminoquinazoline-based C-deoxynucleosides (TRIPsides) that are designed to be incorporated into oligomers that can specifically bind in the major groove via Hoogsteen base pairing to any sequence of native DNA. The four TRIPsides are termed antiGC, antiCG, antiTA, and antiAT with respect to the Watson-Crick base pair targets that they bind. The first three TRIPsides have been prepared, characterized, and shown to form stable and sequence-specific triplexes. In the present study, we describe the preparation of two molecules, 2-amino-4-(2'-deoxy-beta-D-ribofuranosyl)quinazoline (7) and 2-amino-6-fluoro-4-(2'-deoxy-beta-D-ribofuranosyl)quinoline (14), that can serve as the remaining antiAT TRIPside. The phosphoramidites of 7 and 14 were prepared, but only the latter was successfully incorporated into DNA oligomers. It is demonstrated using UV-visible melting experiments that 14 forms sequence-specific intramolecular triplets with A:T base pairs at physiological pH.     

Stable oligonucleotide-directed triplex formation at target sites with CG interruptions: strong sequence-specific recognition by 2',4'-bridged nucleic-acid-containing 2-pyridones under physiological conditions

A sequence of double-stranded DNA (dsDNA) which can be recognized by a triplex-forming oligonucleotide (TFO) is limited to a homopurine-homopyrimidine sequence. To develop novel nucleoside analogues which recognize CG interruption in homopurine-homopyrimidine dsDNA, we synthesized a novel 2'-O,4'-C-methyleneribonucleic acid (2'-O,4'-C-methylene bridged nucleic acid; 2',4'-BNA) that bears the unnatural nucleobases, 2-pyridone (PB) or its 5-methyl congener (mPB); these analogues were introduced into pyrimidine TFOs using a DNA synthesizer. A TFO with a 2'-deoxy-beta-D-ribofuranosyl-2-pyridone (P) or 2',4'-BNA abasic monomer (HB) was also synthesized. The triplex-forming ability of various synthesized 15-mer TFOs and the corresponding homopurine-homopyrimidine dsDNA, which contained a single pyrimidine-purine (PyPu) interruption, was examined in UV melting experiments. It was found that PB and mPB in the TFOs successfully recognized CG interruption under physiological conditions (7 mM sodium phosphate, 140 mM KCl, 5 mM spermine, pH 7.0). Furthermore, triplex formation between the dsDNA target which contained three CG interruptions and the TFO with three PB units was also confirmed. Additional four-point 2',4'-BNA modifications of the TFO containing three PB units significantly enhanced its triplex-forming ability towards the dsDNA and had a Tm value of 43 degrees C under physiological conditions. These results indicate that a critical inherent problem of TFOs, namely, the sequence limitation of the dsDNA target, may be overcome to a large extent and this should promote antigene applications of TFOs in vitro and in vivo.     

Switching of the enzymatic activity synchronized with signal recognition by an artificial DNA receptor on a liposomal membrane

We constructed a supramolecular system on a liposomal membrane that is capable of activating an enzyme via DNA hybridization. The design of the system was inspired by natural signal transduction systems, in which enzymes amplify external signals to control signal transduction pathways. The liposomal membrane, providing a platform for the system, was prepared by the self-assembly of an oligonucleotide lipid, a phospholipid and a cationic synthetic lipid. The enzyme was immobilized on the liposomal surface through electrostatic interactions. Selective recognition of DNA signals was achieved by hybridizing the DNA signals with the oligonucleotide lipid embedded in the liposome. The hybridized DNA signal was sent to the enzyme by a copper ion acting as a mediator species. The enzyme then amplified the event by the catalytic reaction to generate the output signal. In addition, our system demonstrated potential for the discrimination of single nucleotide polymorphisms.     

Structures and reaction mechanisms of cumene formation via benzene alkylation with propylene in a newly synthesized ITQ-24 zeolite: an embedded ONIOM study

The cumene formation via benzene alkylation with propylene on the new three-dimensional nanoporous catalyst, ITQ-24 zeolite, has been investigated by using the ONIOM2(B3LYP/6-31G(d,p):UFF) method. Both consecutive and associative reaction pathways are examined. The contributions of the short-range van der Waals interactions, which are explicitly included in the ONIOM2 model, and an additional long-range electrostatic potential from the extended zeolite framework to the energy profile are taken into consideration. It is found that benzene alkylation with propylene in the ITQ-24 zeolite prefers to occur through the consecutive reaction mechanism. The benzene alkylation step is the reaction rate-determining step with an estimated activation energy of 35.70 kcal/mol, comparable with an experimental report in beta-zeolite of 34.9 kcal/mol. The electrostatic potential from the extended zeolite framework shows a much more significant contribution to the transition state selectivity than the van der Waals interactions.     

Direct and facile syntheses of heterocyclic vinyl-C-nucleosides for recognition of inverted base pairs by DNA triple helix formation: first report by direct Wittig route

The ability to recognize specific gene sequences canonically would allow precise means for genetic intervention. However, specific recognition of two of the four possible base pairs by triplex-forming oligonucleotides (TFO) as X.T-A and Y.C-G within a triplex currently remains elusive. A series of C1-vinyl nucleosides have been proposed, and their stability and specificity have been evaluated extensively by molecular dynamics simulation. Because most C-nucleoside syntheses extend through direct substitution at the C1-position, a more convenient strategy for their syntheses via a direct Wittig coupling is presented here.     

H-DROP: an SVM based helical domain linker predictor trained with features optimized by combining random forest and stepwise selection

Domain linker prediction is attracting much interest as it can help identifying novel domains suitable for high throughput proteomics analysis. Here, we report H-DROP, an SVM-based Helical Domain linker pRediction using OPtimal features. H-DROP is, to the best of our knowledge, the first predictor for specifically and effectively identifying helical linkers. This was made possible first because a large training dataset became available from IS-Dom, and second because we selected a small number of optimal features from a huge number of potential ones. The training helical linker dataset, which included 261 helical linkers, was constructed by detecting helical residues at the boundary regions of two independent structural domains listed in our previously reported IS-Dom dataset. 45 optimal feature candidates were selected from 3,000 features by random forest, which were further reduced to 26 optimal features by stepwise selection. The prediction sensitivity and precision of H-DROP were 35.2 and 38.8 %, respectively. These values were over 10.7 % higher than those of control methods including our previously developed DROP, which is a coil linker predictor, and PPRODO, which is trained with un-differentiated domain boundary sequences. Overall, these results indicated that helical linkers can be predicted from sequence information alone by using a strictly curated training data set for helical linkers and carefully selected set of optimal features.  H-DROP is available at http://domserv.lab.tuat.ac.jp     

Enhanced DNA Oxidative Damage by Acrylonitrile and Protecting DNA from Damage with an Outer Catalase Layer: an Electrochemical Study

In the present article, an in vitro model system to mimic the transformation of acrylonitrile (ACN) from nontoxic to toxic in DNA damage and the protective function of catalase (Cat) against DNA damage in real biosystems was investigated electrochemically with (CS/DNA)₃‐AQDS and (CS/DNA)₃‐AQDS‐Cat multilayer films, where CS and AQDS represent chitosan and electroactive probe 9,10‐anthraquinone‐2,6‐disulfonate, respectively. The electroactive AQDS was loaded into (CS/DNA)₃ layer‐by‐layer films mainly by intercalation of AQDS into the double‐helix structure of DNA and acted as the probe to detect the damage of DNA in the films. While only ACN could not induce DNA damage, the enhancement of ACN on DNA damage in the presence of Fenton reagents (Fe(II)/EDTA/H₂O₂) was observed. In addition, Cat in the (CS/DNA)₃‐AQDS‐Cat films could protect DNA from damage to a considerable extent in both Fenton and Fenton+ACN solutions because of the high efficiency of Cat in decomposition of H₂O₂.     

Noncovalent DNA binding drives DNA alkylation by leinamycin: evidence that the Z,E-5-(thiazol-4-yl)-penta-2,4-dienone moiety of the natural product serves as an atypical DNA intercalator

Molecular recognition and chemical modification of DNA are important in medicinal chemistry, toxicology, and biotechnology. Historically, natural products have revealed many interesting and unexpected mechanisms for noncovalent DNA binding and covalent DNA modification. The studies reported here characterize the molecular mechanisms underlying the efficient alkylation of duplex DNA by the Streptomyces-derived natural product leinamycin. Previous studies suggested that alkylation of duplex DNA by activated leinamycin (2) is driven by noncovalent association of the natural product with the double helix. This is striking because leinamycin does not contain a classical noncovalent DNA-binding motif, such as an intercalating unit, a groove binder, or a polycation. The experiments described here provide evidence that leinamycin is an atypical DNA-intercalating agent. A competition binding assay involving daunomycin-mediated inhibition of DNA alkylation by leinamycin provided evidence that activated leinamycin binds to duplex DNA with an apparent binding constant of approximately 4.3 ± 0.4 × 10(3) M(-1). Activated leinamycin caused duplex unwinding and hydrodynamic changes in DNA-containing solutions that are indicative of DNA intercalation. Characterization of the reaction of activated leinamycin with palindromic duplexes containing 5'-CG and 5'-GC target sites, bulge-containing duplexes, and 5-methylcytosine-containing duplexes provided evidence regarding the orientation of leinamycin with respect to target guanine residues. The data allow construction of a model for the leinamycin-DNA complex suggesting how a modest DNA-binding constant combines with proper positioning of the natural product to drive efficient alkylation of guanine residues in the major groove of duplex DNA.     

Living polymerization of alpha-olefins with an alpha-diimine Ni(II) catalyst: formation of well-defined ethylene-propylene copolymers through controlled chain-walking

A C2-symmetric Ni(II) catalyst was found to polymerize alpha-olefins with high levels of omega,2-regiochemistry. The resulting products are ethylene-propylene-type copolymers with methylene sequences of precise length between methyl branches. Modification of reaction conditions can introduce omega,1-enchainments into the polymers which increases the average length of methylene sequences between methyl branches.     

DNA recognition by the anthracycline antibiotic respinomycin D: NMR structure of the intercalation complex with d(AGACGTCT)2

Respinomycin D is a member of the anthracycline family of antitumour antibiotics that interact with double stranded DNA through intercalation. The clinical agents daunomycin and doxorubicin are the most well-studied of this class but have a relatively simple molecular architecture in which the pendant daunosamine sugar resides in the DNA minor groove. Respinomycin D, which belongs to the nogalamycin group of anthracyclines, possesses additional sugar residues at either end of the aglycone chromophore that modulate the biological activity but whose role in molecular recognition is unknown. We report the NMR structure of the respinomycin D-d(AGACGTCT)2 complex in solution derived from NOE restraints and molecular dynamics simulations. We show that the drug threads through the DNA double helix forming stabilising interactions in both the major and minor groove, the latter through a different binding geometry to that previously reported. The bicycloaminoglucose sugar resides in the major groove and makes specific contacts with guanine at the 5'-CpG intercalation site, however, the disaccharide attached at the C4 position plays little part in drug binding and DNA recognition and is largely solvent exposed.     

Friedel-Crafts alkylation of a cage enone: synthesis of aralkyl substituted tetracyclo[5.3.1.0.0]undeca-9,11-diones and the formation of fascinating novel cage compounds with pyrrole and thiophene using Montmorillonite K-10

The intrinsic catalytic properties of Montmorillonite K-10 clay have been utilized for Friedel-Crafts alkylation of the polycyclic caged enone 1 using different carbo and heterocyclic aromatic systems leading to novel compounds. Carbon-carbon bond formation between the aromatic compounds and the cage system has led to three different types of products.     

A low-molecular-mass gelator with an electroactive tetrathiafulvalene group: tuning the gel formation by charge-transfer interaction and oxidation

A new low-molecular-mass gelator with one TTF and one urea group is described. It was found that the gel formation can be tuned by formation of CT complexes and oxidation.     

Selective molecular recognition of arginine by anionic salt bridge formation with bis-phosphate crown ethers: implications for gas phase peptide acidity from adduct dissociation

Arginine forms a stable noncovalent anionic salt bridge complex with DP (a crown ether which contains two endocyclic dialkylhydrogenphosphate esters). Abundant adduct formation with DP is observed for complexes with arginine, YAKR, HPPGFSPFR, AAKRKAA, RR, RPPGFSPFR, RYLGYL, RGDS, and YGGFMRGL in electrospray ionization mass spectrometry (ESI-MS) experiments. DFT calculations predict a hydrogen bonded salt bridge structure with a protonated guanidinium flanked by two deprotonated phosphates to be the lowest energy structure. Dissociation of DP/peptide adducts reveals that, in general, the relative gas phase acidity of a peptide is dependent on peptide length, with longer peptides being more acidic. In particular, peptides that are six residues or more in length can stabilize the deprotonated C-terminus by extensive hydrogen bonding with the peptide backbone. Dissociation of DP/peptide complexes often yields the deprotonated peptide, allowing for the facile formation of anionic peptides that otherwise would be difficult to generate in high abundance. Although DP has a preference for binding to arginine residues in peptides, DP is also observed to form less abundant complexes with peptides containing multiple lysines. Lys-Xxx-Lys and Lys-Lys sequences form low abundance anionic adducts with DP. For example, KKKK exclusively forms a double adduct with one net negative charge on the complex.     

Coordination chemistry of bis(2-pyridylimine) ligands with Ag(I): formation of two structurally different coordination polymers and one metallocycle controlled by linker and the solvent system

Reaction of equimolar amounts of AgClO₄ and bis[4-(2-pyridylmethyleneamino)phenyl] methane (L¹) or bis[4-(2-pyridylmethyleneamino)phenyl] ether (L²) in a 1:1 solvent mixture of CH₃CN and CH₂Cl₂ leads to the formation of two infinite coordination polymers of the composition {[Ag(L¹)]ClO₄·CH₃CN}_n (1) and {[Ag(L²)]ClO₄·CH₂Cl₂}_n (2). Whereas 1 represents a homochiral single-stranded helicate the related complex 2 shows a typical zigzag chain arrangement. Both structures are characterized by a distorted tetrahedral coordination environment of the Ag(I) centres each based on a N₄ coordination pattern of two ligand molecules. The resulting strands are connected by a hydrogen bonding network including ClO₄ ^? anions and solvent molecules forming 2-D layers. Additional ?ШC?? and CH?C?? interactions between the aromatic parts of the ligand molecules give a 3-D arrangement of the packing. In contrast, a discrete dinuclear metallocycle, [Ag₂(L²)₂](ClO₄)₂·CH₃OH (3), has been formed by reaction of AgClO₄ with L² when CH₂Cl₂ in the solvent mixture was replaced by CH₃OH. Again each Ag(I) has a distorted tetrahedral geometry and is coordinated to two pyridylimine units of two ligand molecules. Additional weak hydrogen bonds involving perchlorate and solvent molecules as well as edge-to-face and face-to-face ?ШC?? interactions allow a 3-D packing arrangement.