Optimization of triple-helix-directed DNA cleavage by benzoquinoquinoxaline-ethylenediaminetetraacetic acid conjugates

The formation of triple-helical structures of DNA is based on sequence-specific recognition of oligopyrimidine.oligopurine stretches of double-helical DNA. Triple-helical structures can be stabilized by DNA-binding ligands. Benzoquinoquinoxaline (BQQ) derivatives are among the most potent intercalating-type agents known to stabilize DNA triple-helical structures. We previously reported the conversion of BQQ into a triplex-directed DNA cleaving agent, namely BQQ-ethylenediaminetetraacetic acid (EDTA), by coupling of 6-(3-aminopropylamino)BQQ to a suitable ethylenediaminetetraacetic acid derivative, and we demonstrated the ability of this conjugate to cause double-stranded cleavage of DNA at the triplex site. However, this prototype derivative BQQ-EDTA conjugate showed lower affinity towards triplex DNA than BQQ itself. In the light of this observation, and guided by molecular modeling studies, we synthesized a second generation of BQQ-EDTA conjugates based on 6-[bis(2-aminoethyl)amino]- and 6-(3,3'-diamino-N-methyldipropylamino)-BQQ derivatives. We confirmed by DNA melting experiments that the new conjugates displayed an increased specific affinity towards triple helices when compared to the previously synthesized BQQ-EDTA. In addition, the efficiency of these new agents in triplex-specific binding and cleavage was demonstrated by triplex-directed double-stranded cleavage of plasmid DNA.     

Application of DNA-Alkylating Pyrrole-Imidazole Polyamides for Cancer Treatment

Pyrrole-imidazole (PI) polyamides, which target specific DNA sequences, have been studied as a class of DNA minor-groove-binding molecules. To investigate the potential of compounds for cancer treatment, PI polyamides were conjugated with DNA-alkylating agents, such as seco-CBI and chlorambucil. DNA-alkylating PI polyamides have attracted attention because of their sequence-specific alkylating activities, which contribute to reducing the severe side effects of current DNA-damaging drugs. Many of these types of conjugates have been developed as new candidates for anticancer drugs. Herein, we review recent progress into research on DNA-alkylating PI polyamides and their sequence-specific action on targets associated with cancer development.     

"Parallel" and "antiparallel tail-clamps" increase the efficiency of triplex formation with structured DNA and RNA targets

Sequence-specific triple-helix structures can be formed by parallel and antiparallel DNA clamps interacting with single-stranded DNA or RNA targets. Single-stranded nucleic acid molecules are known to adopt secondary structures that might interfere with intermolecular interactions. We demonstrate the correlation between a secondary structure involving the target--a stable stem predicted by in silico folding and experimentally confirmed by thermal stability and competition analyses--and an inhibitory effect on triplex formation. We overcame structural impediments by designing a new type of clamp: "tail-clamps". A combination of gel-shift, kinetic analysis, UV thermal melting and thermodynamic techniques was used to demonstrate that tail-clamps efficiently form triple helices with a structured target sequence. The performance of parallel and antiparallel tail-clamps was compared: antiparallel tail-clamps had higher binding efficiencies than parallel tail-clamps both with structured DNA and RNA targets. In addition, the reported triplex-stabilizing property of 8-aminopurine residues was confirmed for tail-clamps. Finally, we discuss the possible use of this improved triplex technology as a new tool for applications in molecular biology.     

Site-specific cleavage of MS2 RNA by a thermostable DNA-linked RNase H

A series of DNA-linked RNases H, in which the 15-mer DNA iscross-linked to the Thermus thermophilus RNase HI (TRNH) variantsat positions 135, 136, 137 and 138, were constructed and analyzedfor their abilities to cleave the complementary 15-mer RNA.Of these, that with the DNA adduct at position 135 most efficientlycleaved the RNA substrate, indicating that position 135 is themost appropriate cross-linking site among those examined. Toexamine whether DNA-linked RNase H also site-specifically cleavesa highly structured natural RNA, DNA-linked TRNHs with a seriesof DNA adducts varying in size at position 135 were constructedand analyzed for their abilities to cleave MS2 RNA. These DNAadducts were designed such that DNA-linked enzymes cleave MS2RNA at a loop around residue 2790. Of the four DNA-linked TRNHswith the 8-, 12-, 16- and 20-mer DNA adducts, only that withthe 16-mer DNA adduct efficiently and site-specifically cleavedMS2 RNA. Primer extension revealed that this DNA-linked TRNHcleaved MS2 RNA within the target sequence.     

Rational Design,Synthesis, and DNA Binding Properties of Novel Sequence‐Selective Peptidyl Congeners of Ametantrone

Natural and synthetic compounds characterized by an anthraquinone nucleus represent an important class of anti‐neoplastic agents, the mechanism of action of which is related to intercalation into DNA. Ametantrone (AM) is a synthetic 9,10‐anthracenedione bearing two (hydroxyethylamino)ethylamino residues at positions 1 and 4; along with other anthraquinones and anthracyclines, it shares a polycyclic intercalating moiety and charged side chains that stabilize DNA binding. All these drugs elicit adverse side effects, which represent a challenge for antitumor chemotherapy. In the present work the structure of AM was augmented with appropriate groups that target well‐defined base pairs in the major groove. These should endow AM with DNA sequence selectivity. We describe the rationale for the synthesis and the evaluation of activity of a new series of compounds in which the planar anthraquinone is conjugated at positions 1 and 4 through the side chains of AM or other bioisosteric linkers to appropriate dipeptides. The designed novel AM derivatives were shown to selectively stabilize two oligonucleotide duplexes that both have a palindromic GC‐rich hexanucleotide core, but their stabilizing effects on a random DNA sequence was negligible. In the case of the most effective compound, the 1,4‐bis‐[Gly‐(L ‐Lys)] derivative of AM, the experimental results confirm the predictions of earlier theoretical computations. In contrast, AM had equal stabilizing effects on all three sequences and showed no preferential binding. This novel peptide derivative can be classified as a strong binder regarding the sequences that it selectively targets, possibly opening the exploitation of less cytotoxic conjugates of AM to the targeted treatment of oncological and viral diseases.     

Selective Delivery of Doxorubicin to EGFR+ Cancer Cells by Cetuximab–DNA Conjugates

Doxorubicin is a hydrophobic anticancer drug that has poor selectivity, due to the lack of active targeting capability. Here, learning lessons from the success of antibody–drug conjugates, we have designed a new doxorubicin delivery system without conjugating doxorubicin to antibody directly. In this setup, cetuximab, an antibody that targets the epidermal growth factor receptor (EGFR) in cancer cells, was conjugated to a single-stranded DNA with a carefully designed sequence in a site-selective manner by using the DNA-templated protein conjugation (DTPC) method. The DNA duplex in the conjugates serves as a carrier of doxorubicin through noncovalent intercalation, and cetuximab functions as the targeting agent; this could drastically decrease systemic toxicity and potentially avoid under- or overdosing. The size of conjugates loaded with doxorubicin was about 8.77 or 16.61 nm when characterized by dynamic light scattering and atomic force microscopy, respectively. In vitro cytotoxicity and selective cancer cell killing was investigated against two EGFR⁺ cell lines (KB and MDA-MB-231) and one EGFR⁻ cell line (NIH-3T3). Cytotoxicity and flow cytometry data showed that doxorubicin loaded in cetuximab–DNA conjugates was more potent in terms of cell cytotoxicity than free doxorubicin in EGFR-overexpressed cell lines, thus suggesting that the conjugates were more selectively and easily taken up into cells, followed by rapid release of doxorubicin from the system into the cytoplasm from endosomes.     

A PNA-DNA2 Triple-Helix Molecular Switch-Based Colorimetric Sensor for Sensitive and Specific Detection of microRNAs from Cancer Cells

Peptide nucleic acids (PNAs), the synthetic DNA mimics that can bind to oligonucleotides to form duplexes, triplexes, and quadruplexes, could be advantageous as probes for nucleic acid sequences owing to their unique physicochemical and biochemical properties. We have found that a homopurine PNA strand could bind to two homopyrimidine DNA strands to form a PNA-DNA₂ triplex. Moreover, the cyanine dye DiSC₂(5) could bind with high affinity to this triplex and cause a noticeable color change. On the basis of this phenomenon, we have designed a label-free colorimetric sensing platform for miRNAs from cancer cells by using a PNA-DNA₂ triple-helix molecular switch (THMS) and DiSC₂(5). This sensing platform can detect miRNA-21 specifically with a detection limit of 0.18 nM, which is comparable to that of the THMS-mediated fluorescence sensing platform. Moreover, this colorimetric platform does not involve any chemical modification or enzymatic signal amplification, which boosts its applicability and availability at the point of care in resource-limited settings. The universality of this approach can be simply achieved by altering the sequences of the probe DNA for specific targets.     

Evaluating the Catalytic Potential of a General RNA-Cleaving FANA Enzyme

The discovery of synthetic genetic polymers (XNAs) with catalytic activity demonstrates that natural genetic polymers are not unique in their ability to function as enzymes. However, all known examples of in vitro selected XNA enzymes function with lower activity than their natural counterparts, suggesting that XNAs might be limited in their ability to fold into structures with high catalytic activity. To explore this problem, we evaluated the catalytic potential of FANAzyme 12–7, an RNA-cleaving catalyst composed entirely of 2′-fluoroarabino nucleic acid (FANA) that was evolved to cleave RNA at a specific phosphodiester bond located between an unpaired guanine and a paired uracil in the substrate recognition arm. Here, we show that this activity extends to chimeric DNA substrates that contain a central riboguanosine (riboG) residue at the cleavage site. Surprisingly, FANAzyme 12–7 rivals known DNAzymes that were previously evolved to cleave chimeric DNA substrates under physiological conditions. These data provide convincing evidence that FANAzyme 12–7 maintains the catalytic potential of equivalent DNAzymes, which has important implications for the evolution of XNA catalysts and their contributions to future applications in synthetic biology.     

DNA‐Templated Introduction of an Aldehyde Handle in Proteins

Many medical and biotechnological applications rely on protein labeling, but a key challenge is the production of homogeneous and site‐specific conjugates. This can rarely be achieved by simple residue‐specific random labeling, but generally requires genetic engineering. Using site‐selective DNA‐templated reductive amination, we created DNA–protein conjugates with control over labeling stoichiometry and without genetic engineering. A guiding DNA strand with a metal‐binding functionality facilitates site‐selectivity by directing the coupling of a second reactive DNA strand in the vicinity of a protein metal‐binding site. We demonstrate DNA‐templated reductive amination for His₆‐tagged proteins and metal‐binding proteins, including IgG1 antibodies. We also used a cleavable linker between the DNA and the protein to remove the DNA and introduce a single aldehyde on the protein. This functions as a handle for further modifications with desired labels. In addition to directing the aldehyde positioning, the DNA provides a straightforward route for purification between reaction steps.     

Synthesis of metal-carbonyl-dendrimer-antibody immunoconjugates: towards a new format for carbonyl metallo immunoassay

We report the preparation of metal-carbonyl-dendrimer-antibody conjugates. These metal-carbonyl-multilabeled antibodies are designed to be used in a new solid-phase-format carbonyl metallo immunoassay (CMIA). A fourth-generation polyamidoamine dendrimer was labeled with 10-25 (eta5-cyclopentadienyl)iron dicarbonyl (eta1-N-succinimidyl) entities. An antibody was chemically modified at its carbohydrate chains by a site-directed process used to preserve the antigen-antibody binding site. The antibody was then coupled with the dendrimer labeled with 10 metal carbonyl groups. An average of 1.4 labeled dendrimers were grafted per antibody molecule. These metal-carbonyl-dendrimer-antibody conjugates were used as new universal detection reagents that recognize their specific antigens. The antigens were spotted onto nitrocellulose membranes and detected by using the conjugates in combination with Fourier transform infrared spectroscopy. A detection level in the range 5-200 pmol per membrane was achieved. This approach opens the way to a new CMIA format.     

Synthesis and DNA binding behavior of a dipyridocatecholate bridged dicopper(II) complex

1,10-Phenanthroline-5,6-diol (dpcatH₂) was prepared conveniently from 1,10-phenanthroline-5,6-dione using hydrazine sulfate as reductant, and a new bimetallic Cu(II) complex, [(phen)Cu(dpcat)Cu(phen)](ClO₄)₂, where phen denotes 1,10-phenanthroline was synthesized by a “one-pot” method. Presence of calf thymus DNA would result in an evident change in the electronic absorption, quenching effect on the fluorescence, protection from fluorescence quencher ferrocyanide and disappearance of redox process of the complex, and the viscosity of DNA would be enhanced by addition of the complex. All these facts suggest that the dicopper(II) complex binds to double helix DNA by classical intercalation.     

Autocatalytic processing of pro-papaya proteinase IV is prevented by crowding of the active-site cleft

The DNA coding for pro-papaya proteinase IV (PPIV) has beencloned and expressed in Escherichia coli. Heterologous expressionof the protein, followed by refolding in vitro, yields an enzymaticallyactive pro-enzyme which fails to autodigest to form the matureprotein. Mutagenesis of the active site of papain to simulatethat of PPIV yields a proenzyme which also fails to autoactivate.Complementarymutagenesis of the pro-region/mature boundary ofPPIV, to introduce its own substrate recognition sequence, has,however, produced a pro-enzyme that will autocatalytically cleave.This is the first report of enzymatic activity in a recombinantpro-cysteine proteinase, and the first time that such a proteinhas been shown to fail to autocatalytically cleave because ofits stringent substrate specificity.     

Oxidative DNA Cleavage with Clip-Phenanthroline Triplex-Forming Oligonucleotide Hybrids

A systematic study of several new types of hybrids of Cu-chelated clamped phenanthroline artificial metallonuclease (AMN) with triplex-forming oligonucleotides (TFO) for sequence-specific cleavage of double-stranded DNA (dsDNA) is reported. The synthesis of these AMN–TFO hybrids is based on application of the alkyne–azide cycloaddition click reaction as the key step. The AMN was attached through different linkers at either the 5′- or 3′-ends or in the middle of the TFO stretch. The diverse hybrids efficiently formed triplexes with the target purine-rich sequence and their copper complexes were studied for their ability to cleave dsDNA in the presence of ascorbate as a reductant. In all cases, the influence of the nature and length of the AMN–TFO, time, conditions and amounts of ascorbate were studied, and optimum conjugates and a procedure that gave reasonably efficient (up to 34 %) cleavage of the target sequence, while rendering an off-target dsDNA intact, were found. The footprint of cleavage on PAGE was identified only in one case, with low conversion; this means that cleavage does not proceed with single nucleotide precision. On the other hand, these AMN–TFO hybrids are useful for the selective degradation of target dsDNA sequences. Future improvements to this design may provide higher resolution and selectivity.     

Rapid synthesis of new DNMT inhibitors derivatives of procainamide

DNA methyltransferases (DNMTs) are responsible for DNA methylation, an epigenetic modification involved in gene regulation. Families of conjugates of procainamide, an inhibitor of DNMT1, were conceived and produced by rapid synthetic pathways. Six compounds resulted in potent inhibitors of the murine catalytic Dnmt3A/3L complex and of human DNMT1, at least 50 times greater than that of the parent compounds. The inhibitors showed selectivity for C5 DNA methyltransferases. The cytotoxicity of the inhibitors was validated on two tumour cell lines (DU145 and HCT116) and correlated with the DNMT inhibitory potency. The inhibition potency of procainamide conjugated to phthalimide through alkyl linkers depended on the length of the linker; the dodecane linker was the best.     

Reactive polymers in diagnostics: Syntheses and characterizations of nucleic acid probes and maleic anhydride-co-methyl vinyl ether polymers

Maleic anhydride-co-methyl vinyl ether copolymers were used as reactive polymers to link oligodeoxyribonucleotides (ODN) to make oligonucleotide-copolymer conjugates of potential applications in diagnostics. The anhydride moieties of the copolymers were used for the covalent binding, via the formation of a peptide bond, on reaction with DNA probes that were amino modified at the 5′ position. The best coupling yields were obtained by carrying out the reaction in a DMSO-borate buffer (95/5 volume ratio) mixture at high ionic strength. Copolymers and ODN-copolymer conjugates were characterized by size exclusion chromatography and multiangle laser light scattering detection. The average molecular weights of the formed conjugates were relatively high, in the 10⁶ g/mol range, resulting from the crosslinking of several copolymer molecules during coupling. Coupling DNA probes onto smaller molecular weight polymers did not result in the formation of very high molecular weight conjugates showing that copolymer chain interpenetration was a determining factor of the crosslinking process that occurs during the coupling reaction. © 1997 John Wiley & Sons, Inc. J Appl Polym Sci 65: 2567–2577, 1997     

Phospholipid Cyclosporine Prodrugs Targeted at Inflammatory Bowel Disease (IBD) Treatment: Design,Synthesis, and in Vitro Validation

Novel phospholipid (PL)-cyclosporine conjugates were prepared and studied as potential prodrugs for inflammatory bowel disease (IBD). Our approach relies on phospholipase A₂ (PLA₂), which is overexpressed in the inflamed intestinal tissues, as the prodrug activator to potentially release cyclosporine at the site of inflammation. PL-cyclosporine prodrug conjugates with methylene linkers of various lengths between the sn-2 position of the PL and cyclosporine were synthesized and evaluated for in vitro activation. Surprisingly, despite previous work indicating that conjugates with six methylene linkers between the lipid and drug would suffer rapid enzymatic hydrolysis, with cyclosporine this was not observed. However, compounds with longer linkers (n=10, 12 methylene units) display complete release of the drug by PLA₂-catalyzed hydrolysis, thus demonstrating the importance and profound impact of structural fine-tuning. This study represents a proof-of-concept for our hypothesis and a first step towards a truly targeted IBD treatment with cyclosporine that could be administered throughout the GI tract.     

Organometallic DNA–B12 Conjugates as Potential Oligonucleotide Vectors: Synthesis and Structural and Binding Studies with Human Cobalamin-Transport Proteins

The synthesis and structural characterization of Co-(dN)₂₅-Cbl (Cbl: cobalamin; dN: deoxynucleotide) and Co-(dN)₃₉-Cbl, which are organometallic DNA–B₁₂ conjugates with single DNA strands consisting of 25 and 39 deoxynucleotides, respectively, and binding studies of these two DNA–Cbl conjugates to three homologous human Cbl transporting proteins, transcobalamin (TC), intrinsic factor (IF), and haptocorrin (HC), are reported. This investigation tests the suitability of such DNA–Cbls for the task of eventual in vivo oligonucleotide delivery. The binding of DNA–Cbl to TC, IF, and HC was investigated in competition with either a fluorescent Cbl derivative and Co-(dN)₂₅-Cbl, or radiolabeled vitamin B₁₂ (⁵⁷Co-CNCbl) and Co-(dN)₂₅-Cbl or Co-(dN)₃₉-Cbl. Binding of the new DNA–Cbl conjugates was fast and tight with TC, but poorer with HC and IF, which extends a similar original finding with the simpler DNA–Cbl, Co-(dN)₁₈-Cbl. The contrasting affinities of TC versus IF and HC for the DNA–Cbl conjugates are rationalized herein by a stepwise mechanism of Cbl binding. Critical contributions to overall affinity result from gradual conformational adaptations of the Cbl-binding proteins to the DNA–Cbl, which is first bound to the respective β domains. This transition is fast with TC, but slow with IF and HC, with which weaker binding results. The invariably tight interaction of the DNA–Cbl conjugates with TC makes the Cbl moiety a potential natural vector for the specific delivery of oligonucleotide loads from the blood into cells.     

Bleomycin Can Cleave an Oncogenic Noncoding RNA

Noncoding RNAs are pervasive in cells and contribute to diseases such as cancer. A question in biomedical research is whether noncoding RNAs are targets of medicines. Bleomycin is a natural product that cleaves DNA; however, it is known to cleave RNA in vitro. Herein, an in‐depth analysis of the RNA cleavage preferences of bleomycin A5 is presented. Bleomycin A5 prefers to cleave RNAs with stretches of AU base pairs. Based on these preferences and bioinformatic analysis, the microRNA‐10b hairpin precursor was identified as a potential substrate for bleomycin A5. Both in vitro and cellular experiments demonstrated cleavage. Importantly, chemical cleavage by bleomycin A5 in the microRNA‐10b hairpin precursors occurred near the Drosha and Dicer enzymatic processing sites and led to destruction of the microRNA. Evidently, oncogenic noncoding RNAs can be considered targets of cancer medicines and might elicit their pharmacological effects by targeting noncoding RNA.     

The Yersinia adhesin YadA binds to a collagenous triple-helical conformation but without sequence specificity

The Yersinia adhesin A (YadA) is a collagen-binding trimeric autotransporter of Yersinia enterocolitica, an enteropathogen that causes a range of gastroenteric and systemic diseases, and YadA is essential for Y. enterocolitica virulence. Although previous studies suggest a specific binding site in collagen for YadA, we found that recombinant YadA binds to both major cyanogen bromide fragments of collagen type II and the collagen-like model peptide (Pro-Hyp-Gly)(10) [(POG)(10)]. To further characterise the YadA-collagen interaction, we investigated the binding of YadA to (POG)(10) and three other model peptides, (Pro-Pro-Gly)(10) which lacks the hydroxyl groups of (POG)(10), T3-785 which contains a stretch of the collagen type III sequence and Gly(-) which is similar to (POG)(10) but lacks the central glycine. All the peptides except Gly(-) adopt a collagen-like triple-helical conformation at room temperature. All three triple-helical peptides bound to YadA, with (POG)(10) being the tightest, whereas binding of Gly(-) was hardly detectable. The affinity of (POG)(10) for YadA was 0.28 microM by isothermal titration calorimetry and 0.17 microM by surface plasmon resonance (SPR), similar to that of collagen type I. Our results show that a collagen-like triple-helical conformation, strengthened by the presence of hydroxyproline residues, is both necessary and sufficient for YadA binding.