Sequence-specific recognition of the major groove of DNA by oligodeoxynucleotides via triple helix formation. Footprinting studies

Enzymatic Synthesis of Chemical Nuclease Triplex-Forming Oligonucleotides with Gene-Silencing Applications

Triplex-forming oligonucleotides (TFOs) are short, single-stranded oligomers that hybridise to a specific sequence of duplex DNA. TFOs can block transcription and thereby inhibit protein production, making them highly appealing in the field of antigene therapeutics. In this work, a primer extension protocol was developed to enzymatically prepare chemical nuclease TFO hybrid constructs, with gene-silencing applications. Click chemistry was employed to generate novel artificial metallo-nuclease (AMN)-dNTPs, which were selectively incorporated into the TFO strand by a DNA polymerase. This purely enzymatic protocol was then extended to facilitate the construction of 5-methylcytosine (5mC) modified TFOs that displayed increased thermal stability. The utility of the enzymatically synthesised di-(2-picolyl)amine (DPA)-TFOs was assessed and compared to a specifically prepared solid-phase synthesis counterpart through gel electrophoresis, quantitative PCR, and Sanger sequencing, which revealed similar recognition and damage properties to target genes. The specificity was then enhanced through coordinated designer intercalators-DPQ and DPPZ-and high-precision DNA cleavage was achieved. To our knowledge, this is the first example of the enzymatic production of an AMN-TFO hybrid and is the largest base modification incorporated using this method. These results indicate how chemical nuclease-TFOs may overcome limitations associated with non-molecularly targeted metallodrugs and open new avenues for artificial gene-editing technology.

DNA Structural Changes Induced by Intermolecular Triple Helix Formation

DNase I footprints of intermolecular DNA triplexes are often accompanied by enhanced cleavage at the 3'-end of the target site at the triplex-duplex junction. We have systematically studied the sequence dependence of this effect by examining oligonucleotide binding to sites flanked by each base in turn. For complexes with a terminal T.AT triplet, the greatest enhancement is seen with ApC, followed by ApG and ApT, with the weakest enhancement at ApA. Similar DNase I enhancements were observed for a triplex with a terminal C+.GC triplet, though with little difference between the different GpN sites. Enhanced reactivity to diethylpyrocarbonate was observed at As that flank the triplex-duplex junction at AAA or AAC but not AAG or AAT. Fluorescence melting experiments demonstrated that the flanking base affected the stability with a 4 °C difference in T m between a flanking C and G. Sequences that produced the strongest enhancement correlated with those having the lower thermal stability. These results are interpreted in terms of oligonucleotide-induced changes in DNA structure and/or flexibility.

NMR studies on oligonucleotide - Methylene blue conjugates targeting double-helical nucleic acids

Methylene blue (MB) - nucleic acid interactions are of considerable interest due to the photosensitizing activity of the dye with potential applications in medicine and biotechnology. Covalent attachment of the MB to an oligonucleotide through a flexible heptamethylene linker enabled a positioning of the dye moiety to specific sites through triplex formation with a target duplex. NMR studies demonstrated interactions of MB with the nucleic acids. In sequences with the MB moiety facing the triplex-duplex junction with an alternating CG duplex overhang next to a T·A·T triple-helical tract, proton resonances experienced severe linebroadening upon MB binding and point to kinetically labile complexes with exchange among different binding modes. For sequences with the MB moiety facing a terminal T·A·T base triad of the triplex tract, structural heterogeneity decreased when compared to a triplex without MB attached to the third strand. Also, the thermal stability of the latter construct increased significantly in the presence of MB, indicating external end stacking as predominant binding mode. Without any obvious disruptions of sequential imino-imino NOE contacts within the triplex and duplex tracts, a most favorable intercalation between T·A·T base triples or CG base pairs is not supported by the present data under our experimental conditions.

Triplex Forming Oligonucleotides – Tool for Gene Targeting

This review deals with the antigene strategy whereby an oligonucleotide binds to the major or minor groove of double helical DNA where it forms a local triple helix. Preoccupation of this article is triplex-forming oligonucleotides (TFO). These are short, synthetic single-stranded DNAs that recognize polypurine:polypyrimidine regions in double stranded DNA in a sequence-specific manner and form triplex. Therefore, the mechanisms for DNA recognition by triple helix formation are discussed, together with main characteristics of TFO and also major obstacles that remain to be overcome are highlighted. TFOs can selectively inhibit gene expression at the transcriptional level or repair genetic defect by direct genome modification in human cells. These qualities makes TFO potentially powerful therapeutic tool for gene repair and/or expression regulation.

Biological and nanotechnological applications using interactions between ionic liquids and nucleic acids

Nucleic acids have emerged as powerful biological and nanotechnological tools. In biological and nanotechnological experiments, methods of extracting and purifying nucleic acids from various types of cells and their storage are critical for obtaining reproducible experimental results. In nanotechnological experiments, methods for regulating the conformational polymorphism of nucleic acids and increasing sequence selectivity for base pairing of nucleic acids are important for developing nucleic acid-based nanomaterials. However, dearth of media that foster favourable behaviour of nucleic acids has been a bottleneck for promoting the biology and nanotechnology using the nucleic acids. Ionic liquids (ILs) are solvents that may be potentially used for controlling the properties of the nucleic acids. Here, we review researches regarding the behaviour of nucleic acids in ILs. The efficiency of extraction and purification of nucleic acids from biological samples is increased by IL addition. Moreover, nucleic acids in ILs show long-term stability, which maintains their structures and enhances nuclease resistance. Nucleic acids in ILs can be used directly in polymerase chain reaction and gene expression analysis with high efficiency. Moreover, the stabilities of the nucleic acids for duplex, triplex, and quadruplex (G-quadruplex and i-motif) structures change drastically with IL cation-nucleic acid interactions. Highly sensitive DNA sensors have been developed based on the unique changes in the stability of nucleic acids in ILs. The behaviours of nucleic acids in ILs detailed here should be useful in the design of nucleic acids to use as biological and nanotechnological tools.

DNA sensor's selectivity enhancement and protection from contaminating nucleases due to a hydrated ionic liquid

The thermodynamic stability of certain mismatched base pairs has made the development of DNA sequence sensing systems challenging. Thus, the stability of fully matched and mismatched DNA oligonucleotides in the hydrated ionic liquid choline dihydrogen phosphate (choline dhp) was investigated. Mismatched base pairs were significantly destabilized in choline dhp relative to those in aqueous buffer. A molecular beacon that forms a triplex with a conserved HIV-1 sequence was then designed and tested in choline dhp. The molecular beacon specifically detected the target duplex via triplex formation at concentrations as low as 1 pmol per 10 μL with 10,000-fold sequence selectivity. Moreover, the molecular beacon was protected from a contaminating nuclease in choline dhp, and DNAs in aqueous solutions were not sufficiently stable for practical use.

Nucleobase-Modified PNA Suppresses Translation by Forming a Triple Helix with a Hairpin Structure in mRNA In Vitro and in Cells

Compounds that bind specifically to double-stranded regions of RNA have potential as regulators of structure-based RNA function; however, sequence-selective recognition of double-stranded RNA is challenging. The modification of peptide nucleic acid (PNA) with unnatural nucleobases enables the formation of PNA-RNA triplexes. Herein, we demonstrate that a 9-mer PNA forms a sequence-specific PNA-RNA triplex with a dissociation constant of less than 1 nm at physiological pH. The triplex formed within the 5' untranslated region of an mRNA reduces the protein expression levels both in vitro and in cells. A single triplet mismatch destabilizes the complex, and in this case, no translation suppression is observed. The triplex-forming PNAs are unique and potent compounds that hold promise as inhibitors of cellular functions that are controlled by double-stranded RNAs, such as RNA interference, RNA editing, and RNA localization mediated by protein-RNA interactions.

Insight into DNA Minor Groove Unspecific Binding of Pyrrole Polyamide

Chemistry-based approaches have exploited base-pairing for sequence-specific recognition of DNA. A variety of sequence-specific Py-Im hairpin polyamides to target sequences of biological interest have been widely developed. Here we reported that an eight-ring N-methylpyrrole polyamide can induce a strong negative signal when it interacted with ct-DNA in the minor groove, which differs from the typical CD signal induced by hairpin polyamide reported previously. Our current efforts mainly focused on investigating possible reasons and binding mode by CD spectroscopy, singular value decomposition, and atomic force microscopy. The results suggested that partly compacted DNA may form due to the unfolded binding mode that made DNA shrink along the axis of duplex. In addition, this unfolded binding was remarkably restrained in high ionic strength medium where the neutralized phosphate groups in the DNA backbone narrowed the minor groove. The present work might help to understand deeply how the Py-Im polyamides bind to duplex DNA under different conditions and, in particular, be applied to gene manipulation and expression.

Improved bioactivity of G-rich triplex-forming oligonucleotides containing modified guanine bases

Triplex structures generated by sequence-specific triplex-forming oligonucleotides (TFOs) have proven to be promising tools for gene targeting strategies. In addition, triplex technology has been highly utilized to study the molecular mechanisms of DNA repair, recombination and mutagenesis. However, triplex formation utilizing guanine-rich oligonucleotides as third strands can be inhibited by potassium-induced self-association resulting in G-quadruplex formation. We report here that guanine-rich TFOs partially substituted with 8-aza-7-deaza-guanine (PPG) have improved target site binding in potassium compared with TFOs containing the natural guanine base. We designed PPG-substituted TFOs to bind to a polypurine sequence in the supFG1 reporter gene. The binding efficiency of PPG-substituted TFOs to the target sequence was analyzed using electrophoresis mobility gel shift assays. We have determined that in the presence of potassium, the non-substituted TFO, AG30 did not bind to its target sequence, however binding was observed with the PPG-substituted AG30 under conditions with up to 140 mM KCl. The PPG-TFOs were able to maintain their ability to induce genomic modifications as measured by an assay for gene-targeted mutagenesis. In addition, these compounds were capable of triplex-induced DNA double strand breaks, which resulted in activation of apoptosis.

Triplex-induced DNA damage response

Cellular DNA damage response is critical to preserving genomic integrity following exposure to genotoxic stress. A complex series of networks and signaling pathways become activated after DNA damage and trigger the appropriate cellular response, including cell cycle arrest, DNA repair, and apoptosis. The response elicited is dependent upon the type and extent of damage sustained, with the ultimate goal of preventing propagation of the damaged DNA. A major focus of our studies is to determine the cellular pathways involved in processing damage induced by altered helical structures, specifically triplexes. Our lab has demonstrated that the TFIIH factor XPD occupies a central role in triggering apoptosis in response to triplex-induced DNA strand breaks. We have shown that XPD co-localizes with γH2AX, and its presence is required for the phosphorylation of H2AX tyrosine142, which stimulates the signaling pathway to recruit pro-apoptotic factors to the damage site. Herein, we examine the cellular pathways activated in response to triplex formation and discuss our finding that suggests that XPD-dependent apoptosis plays a role in preserving genomic integrity in the presence of excessive structurally induced DNA damage.

Triplex technology in studies of DNA damage, DNA repair, and mutagenesis

Triplex-forming oligonucleotides (TFOs) can bind to the major groove of homopurine-homopyrimidine stretches of double-stranded DNA in a sequence-specific manner through Hoogsteen hydrogen bonding to form DNA triplexes. TFOs by themselves or conjugated to reactive molecules can be used to direct sequence-specific DNA damage, which in turn results in the induction of several DNA metabolic activities. Triplex technology is highly utilized as a tool to study gene regulation, molecular mechanisms of DNA repair, recombination, and mutagenesis. In addition, TFO targeting of specific genes has been exploited in the development of therapeutic strategies to modulate DNA structure and function. In this review, we discuss advances made in studies of DNA damage, DNA repair, recombination, and mutagenesis by using triplex technology to target specific DNA sequences.

DNA-binding drugs caught in action: the latest 3D pictures of drug-DNA complexes

In this paper, we review recent DNA-binding agents that are expected to influence the field of DNA-targeting. We restrict ourselves to binders for which the three-dimensional structure in complex with DNA or RNA has been determined by X-ray crystallography or NMR. Furthermore, we primarily focus on unprecedented ways of targeting peculiar DNA structures, such as junctions, quadruplexes, and duplex DNAs different from the B-form. Classical binding modes of small molecular weight compounds to DNA, i.e. groove binding, intercalation and covalent addition are discussed in those cases where the structures represent a novelty. In addition, we review 3D structures of triple-stranded DNA, of the so-called Peptide Nucleic Acids (PNAs), which are oligonucleotide bases linked by a polypeptide backbone, and of aptamers, which are DNA or RNA receptors that are designed combinatorially. A discussion on perspectives in the field of DNA-targeting and on sequence recognition is also provided.

Purine twisted-intercalating nucleic acids: a new class of anti-gene molecules resistant to potassium-induced aggregation

Sequence-specific targeting of genomic DNA by triplex-forming oligonucleotides (TFOs) is a promising strategy to modulate in vivo gene expression. Triplex formation involving G-rich oligonucleotides as third strand is, however, strongly inhibited by potassium-induced TFO self-association into G-quartet structures. We report here that G-rich TFOs with bulge insertions of (R)-1-O-[4-(1-pyrenylethynyl)-phenylmethyl] glycerol (called twisted intercalating nucleic acids, TINA) show a much lower tendency to aggregate in potassium than wild-type analogues do. We designed purine-motif TINA–TFOs for binding to a regulatory polypurine-polypyrimidine (pur/pyr) motif present in the promoter of the KRAS proto-oncogene. The binding of TINA–TFOs to the KRAS target has been analysed by electrophoresis mobility shift assays and DNase I footprinting experiments. We discovered that in the presence of potassium the wild-type TFOs did not bind to the KRAS target, differently from the TINA analogues, whose binding was observed up to 140 mM KCl. The designed TINA–TFOs were found to abrogate the formation of a DNA–protein complex at the pur/pyr site and to down-regulate the transcription of CAT driven by the murine KRAS promoter. Molecular modelling of the DNA/TINA–TFO triplexes are also reported. This study provides a new and promising approach to create TFOs to target in vivo the genome.

DNA binding and nuclease activity of a one-dimensional heterometallic nitrosyl complex

The interaction of a structurally characterized Sr-Fe nitrosyl complex with DNA has been studied by UV-vis and fluorescence spectroscopy, viscometric, and gel electrophoresis techniques. From the absorption titration studies the intrinsic binding constant of the complex with DNA was calculated to be 1.6x10(4)M(-1). Fluorimetric studies indicate that the complex compete with EB in binding to DNA. The complex shows nuclease activity on pUC19 supercoiled DNA in presence of H(2)O(2).

Monomeric and Heterodimeric Triple Helical DNA Mimics

The construction of artificial triple helical structures with oligonucleotides containing non-nucleosidic phenanthrenes and pyrenes is described. The polyaromatic building blocks, which are used as connectors between the Hoogsteen strand and the Watson-Crick hairpin, lead to a significant stabilization of intramolecular triple helices. Description of the relative orientation of pyrene building blocks is rendered possible by the observation of exciton coupling in the circular dichroism spectra. In addition, the formation of heterodimeric triple helical constructs is explored. Again, the polyaromatic residues are found to have a positive effect on the stability of these structures. The results are important for the design and construction of nucleic-acid-based, triple helical architectures. Furthermore, they will help in the development of analogues of biologically important, naturally occurring triplex structures.

The potential of oligonucleotides for therapeutic applications

Viral-derived particles have been widely used and described in gene therapy clinical trials. Although substantial results have been achieved, major safety issues have also arisen. For more than a decade, oligonucleotides have been seen as an alternative to gene complementation by viral vectors or DNA plasmids, either to correct the genetic defect or to silence gene expression. The development of RNA interference has strengthened the potential of this approach. Recent clinical trials have also tested the ability of aptamer molecules and decoy oligonucleotides to sequestrate pathogenic proteins. Here, we review the potential of oligonucleotides in gene therapy, outline what has already been accomplished, and consider what remains to be done.

Supramolecular Nanopatterns Self-Assembled by Adenine−Thymine Quartets at the Liquid/Solid Interface

By means of scanning tunneling microscopy (STM), we have observed for the first time well-ordered supramolecular nanopatterns formed by mixing two complementary DNA bases: adenine (A) and thymine (T), respectively, at the liquid/solid interface. By mixing A and T at a specific mixing molar ratio, cyclic structures that were distinctly different from the structures observed by the individual base molecules separately were formed. From an interplay between the STM findings and self-consistent charge density-functional based tight-binding (SCC-DFTB) calculation method, we suggest formation of A-T-A-T quartets constructed on the basis of A-T base pairing. The formation of the A-T-A-T quartets opens new avenues to use DNA base pairing as a way to form nanoscale surface architecture and biocompatible patterned surfaces particularly via host-guest complexation that might be suitable for drug design, where the target can be trapped inside the cavities of the molecular containers.

Gas-Phase Watson-Crick and Hoogsteen Isomers of the Nucleobase Mimic 9-Methyladenine⋅2-Pyridone

2-Pyridone (pyridin-2-one) is a mimic of the uracil and thymine nucleobases, with only one N--H and C==O group. It provides a single H-bonding site, compared to three for the canonical pyrimidine nucleobases. Employing the supersonically cooled 9-methyladenine2-pyridone (9MAd x 2PY) complex, which is the simplest base pair to mimic adenine-uracil or adenine-thymine, we show that its gas-phase UV spectrum consists of contributions from two isomers. Based on the H-bonding sites of 9-methyladenine, these are the Watson-Crick and Hoogsteen forms. Combining two-color two-photon ionisation (2C-R2PI), UV-UV depletion and laser-induced fluorescence spectroscopies allows separation of the two band systems, revealing characteristic intermolecular in-plane vibrations of the two isomers. The calculated S(0) and S(1) intermolecular frequencies are in good agreement with the experimental ones. Ab initio calculations predict the Watson-Crick isomer to be slightly more stable (D(0)=-16.0 kcal mol(-1)) than the Hoogsteen isomer (D(0)=-15.0 kcal mol(-1)). The calculated free energies Delta(f)G(0) of the Watson-Crick and Hoogsteen isomers agree qualitatively with the experimental isomer concentration ratio of 3:1.

A polarized-light spectroscopy study of interactions of a hairpin polyamide with DNA

We here study the interactions of a polyamide with large DNA, and compare to those of minor groove binder distamycin (DST), including high ligand/DNA binding ratios. Specific as well as nonspecific binding is probed using polarized-light spectroscopy combined with singular value decomposition analysis. Circular and linear dichroism data confirm binding geometries consistent with minor groove binding for both of the ligands. Interestingly, at high and intermediate ligand/DNA ratios the polyamide exhibits no significant sequence discrimination between mixed-sequence (calf thymus) and AT DNA as compared to DST. Each ligand is concluded to exhibit two different binding modes depending upon ligand/DNA ratio and nucleo-base sequence. At high binding ratios, distinct differences between the ligands are observed: circular dichroism spectra exciton effects provide evidence of bimolecular interactions of the polyamide when bound to AT-DNA, whereas no effects are seen with DST or mixed-sequence DNA. Also linear dichroism indicates that a change in binding geometry occurs at high polyamide/AT ratios, and that the effect occurs only with polyamide in contrast to DST. Since the effect is insignificant with DST, or with calf thymus DNA, it is concluded that it relates to the sizes of the ligands and the minor grooves, becoming critical in the limit of crowding.

Triplex-induced recombination and repair in the pyrimidine motif

Triplex-forming oligonucleotides (TFOs) bind DNA in a sequence-specific manner at polypurine/polypyrimidine sites and mediate targeted genome modification. Triplexes are formed by either pyrimidine TFOs, which bind parallel to the purine strand of the duplex (pyrimidine, parallel motif), or purine TFOs, which bind in an anti-parallel orientation (purine, anti-parallel motif). Both purine and pyrimidine TFOs, when linked to psoralen, have been shown to direct psoralen adduct formation in cells, leading to mutagenesis or recombination. However, only purine TFOs have been shown to mediate genome modification without the need for a targeted DNA-adduct. In this work, we report the ability of a series of pyrimidine TFOs, with selected chemical modifications, to induce repair and recombination in two distinct episomal targets in mammalian cells in the absence of any DNA-reactive conjugate. We find that TFOs containing N3′→P5′ phosphoramidate (amidate), 5-(1-propynyl)-2′-deoxyuridine (pdU), 2′-O-methyl-ribose (2′-O-Me), 2′-O-(2-aminoethyl)-ribose, or 2′-O, 4′-C-methylene bridged or locked nucleic acid (LNA)-modified nucleotides show substantially increased formation of non-covalent triplexes under physiological conditions compared with unmodified DNA TFOs. However, of these modified TFOs, only the amidate and pdU-modified TFOs mediate induced recombination in cells and stimulate repair in cell extracts, at levels comparable to those seen with purine TFOs in similar assays. These results show that amidate and pdU-modified TFOs can be used as reagents to stimulate site-specific gene targeting without the need for conjugation to DNA-reactive molecules. By demonstrating the potential for induced repair and recombination with appropriately modified pyrimidine TFOs, this work expands the options available for triplex-mediated gene targeting.

Formation and stability of a Janus-Wedge type of DNA triplex

A new type of DNA targeting with the formation of a Janus-Wedge (J-W) triple helix is described. The "wedge" residue (W) attached to a PNA backbone is designed to insert itself into double-stranded DNA and base pair with both Watson-Crick faces. To study the stability of such an assembly, we have examined the formation of the J-W triplex with dC8 - T8 target sequence. The use of this target sequence permits the study of this new helix form without competing Watson-Crick interactions between the two target residues. Studies indicate that the W strand binds to both target strands, with defined polarity and a stability (-15.2 kcal/mol) that is roughly the sum of the two independent duplex interactions.

Transcription dependence of chromosomal gene targeting by triplex-forming oligonucleotides

Triplex-forming oligonucleotides (TFOs) recognize and bind to specific DNA sequences and have been used to modify gene function in cells. To study factors that might influence triplex formation at chromosomal sites in mammalian cells, we developed a restriction protection assay to detect triplex-directed psoralen crosslinks in genomic DNA prepared from TFO-transfected cells. Using this assay, we detected binding of a G-rich TFO to a chromosomal site even in the absence of transcription when high concentrations of the TFO were used for transfection. However, experimental induction of transcription at the target site, via an ecdysone-responsive promoter, resulted in substantial increases (3-fold or more) in target site crosslinking, especially at low TFO concentrations. When RNA polymerase activity was inhibited, even in the ecdysone-induced cells, the level of TFO binding was significantly decreased, indicating that transcription through the target region, and not just transcription factor binding, is necessary for the enhanced chromosomal targeting by TFOs. These findings provide evidence that physiologic activity at a chromosomal target site can influence its accessibility to TFOs and suggest that gene targeting by small molecules may be most effective at highly expressed chromosomal loci.

Molecular dynamics simulation study of DNA triplex formed by mixed sequences in solution

The unrestrained molecular dynamics simulation of the triple helical DNA with mix sequences d(GACTGGTGAC).d(CTGACCACTG)*d (GACTGGTGAC), using the particle mesh Ewald sum, is presented here. The Ewald summation method effectively eliminates the usualcut-of of the long range interactions and allowed us to evaluate the full effect of the electrostatic forces. The AMBER5.0 force field has been used during the simulation in solvent. The MD results support a dynamically stable model of DNA triplex over the entire length of the trajectory. The duplex structure assumes the conformation, which is very close to B-DNA. In mixed sequences the purine bases occurs in both strand of DNA duplex. The bases of third strand do not favor the Hoogsteen or/and reverse Hoogsteen type of Hydrogen bonding but they form hydrogen bonds with the bases of both the strand of DNA duplex. The orientation of the third strand is parallel to one of the strand of duplex and all nucleotides (C, A, G & T) show isomorphic behavior with respect to the DNA duplex. The conformation of all the three strands is almost same except few exceptions. Due to interaction of third strand the conformational change in the duplex structure and a finite amount of displacement in the W-C base pairs have been observed. The conformational variation of the back bone torsion angles and helicoidal parameters, groove widths have been discussed. The sequence dependent effects on local conformation, helicoidal and morphological structure, width of the grooves of DNA helix may have important implication for understanding the functional energetics and specificity of interactions of DNA and its triplexes with proteins, pharmaceutical agents and other ligands.

Oxidative cleavage of DNA by a dipyridoquinoxaline copper(II) complex in the presence of ascorbic acid

Complex [Cu(dpq)(2)(H(2)O)](ClO(4))(2).H(2)O (1), where dpq is dipyrido-[3,2-D:2',3'-f]-quinoxaline, has been prepared by reacting copper(II) perchlorate hexahydrate with dpq in methanol and structurally characterized. The complex crystallizes in the triclinic space group P-1 with the unit cell parameters a=8.646(2) A, b=12.290(5) A, c=14.283(4) A, alpha=94.01(2) degrees, beta=91.69(2) degrees,gamma=101.60 (3) degrees, V=1481.7(8) A(3) and Z=2. The structure, refined to R=0.0505 and R(w)=0.1441 for 5212 reflections with I>2sigma (I) using 440 parameters, shows the presence of a CuN(4)O chromophore in an axially compressed distorted trigonal-bipyramidal structure. The Cu-N distances lie in the range 1.969(3)-2.103(3) A. The Cu-OH(2) distance is 2.145(3) A. The complex is one-electron paramagnetic and exhibits a visible spectral d-d band at 718 nm in MeCN. It shows a quasi-reversible cyclic voltammetric response at 0.091 V (DeltaE(p)=229 mV) at 50 mV s(-1) in MeCN-0.1 M TBAP for the Cu(II)/Cu(I) couple. In 50 mM Tris-HCl/0.1 M KCl buffer-DMF mixture (1:4 v/v, pH 7.2), the couple appears at 0.089 V versus SCE. The complex undergoes facile reduction with sodium ascorbate in an aqueous DMF mixture (4:1 v/v) to form an unstable brown Cu(I) species (lambda(max)=440 nm, epsilon=7480 M(-1) cm(-1)) which converts to 1 on exposure to air giving a turnover frequency of ca. 400. Binding studies revealed that 1 is an efficient binder to calf thymus DNA. Complex 1 on reaction with supercoiled (SC) DNA in presence of ascorbic acid in a 50 mM Tris-HCl/50 mM NaCl buffer (pH 7.2) shows nuclease activity which is 4.5 times greater than that of the phen analogue.

Triple-helix formation in the antiparallel binding motif of oligodeoxynucleotides containing N(9)- and N(7)-2-aminopurine deoxynucleosides

Triplex-forming oligodeoxynucleotide 15mers, designed to bind in the antiparallel triple-helical binding motif, containing single substitutions (Z) of the four isomeric alphaN(7)-, betaN(7)-, alphaN(9)- and betaN(9)-2-aminopurine (ap)-deoxyribonucleosides were prepared. Their association with double-stranded DNA targets containing all four natural base pairs (X-Y) opposite the aminopurine residues was determined by quantitative DNase I footprint titration in the absence of monovalent metal cations. The corresponding association constants were found to be in a rather narrow range between 1.0 x 10(6) and 1.3 x 10(8) M(-1). The following relative order in Z x X-Y base-triple stabilities was found: Z = alphaN(7)ap: T-A > A-T> C-G approximately G-C; Z = betaN(7)ap: A-T > C-G > G-C > T-A; Z = alphaN(9)ap: A-T = G-C > T-A > C-G; and Z = betaN(9)ap: G-C > A-T > C-G > T-A.

Downregulation of c-Ki-ras promoter activity by triplex-forming oligonucleotides endogenously generated in human 293 cells

Exogenous triplex-forming oligodeoxynucleotides (TFO) have the capacity to modulate in vivo the expression of individual genes. As the administration of TFO to cells is not without problems, we analyzed the possibility of generating them directly in the cell, using specific expression vectors. We constructed three vectors, mU6-GA, mU6-CA, and mU6-CT, that direct the synthesis in human 293 cells of 76-mer CU, GU, and AG motif TFO (rTFO) potentially capable of binding to a critical poly (R x Y) sequence contained in the promoter of the Ki-ras proto-oncogene. The ability of the CU, GU, and AG motif rTFO to interact with the double helix of the c-Ki-ras target was investigated in vitro by footprinting and band-shift experiments, using both synthetic and endogenously synthesized oligoribonucleotides. The human 293 cells were transfected with DNA mixtures containing a plasmid, which bears the reporter chloramphenicol acetyltransferase (CAT) gene downstream from the c-Ki-ras promoter (pKRS-413), as well as an rTFO-generating vector (mU6-GA, mU6-CA, or mU6-CT). As control, the cells were transfected with DNA mixtures containing vector mU6-C1 or mU6-C2. These generated transcripts unable to form triple helices with the poly (R x Y) sequence of the c-Ki-ras promoter. Intracellular synthesis of the 76-mer CU, GU, and AG rTFO by mU6-GA, mU6-CA, and mU6-CT was checked by Northern blot hybridization. Through beta-gal and CAT ELISA immunoassays, we found that the 293 cells transfected with either mU6-GA, mU6-CA, or mU6-CT showed a significant inhibition of CAT expression compared with cells transfected with control plasmids mU6-C1 or mU6-C2. The results of five separate transient transfection experiments showed that endogenous GU and AG rTFO, generated by mU6-CA and mU6-CT, produce, respectively, 40% (+/- 4% SE) and 47% (+/- 8% SE) CAT inhibition, whereas CU rTFO, generated by mU6-GA, produces 38% (+/- 7% SE) CAT inhibition. In conclusion, this study suggests that it is possible to downregulate the expression of an individual gene through the use of recombinant vectors encoding the information for the intracellular synthesis of short triplex-forming RNA strands.

Structure of poly (dT).poly (dA).poly (dT)

The molecular structure of poly (dT).poly (dA).poly (dT) has been determined and refined using the continuous x-ray intensity data on layer lines in the diffraction pattern obtained from an oriented fiber of the DNA. The final R-value for the preferred structure is 0.29 significantly lower than that for plausible alternatives. The molecule forms a 12-fold right-handed triple-helix of pitch 38.4 A and each base triplet is stabilized by a set of four Crick-Watson-Hoogsteen hydrogen bonds. The deoxyribose rings in all the three strands have C2'-endo conformations. The grooveless cylindrical shape of the triple-helix is consistent with the lack of lateral organization in the fiber.

Selective recognition of a C-G base-pair in the parallel DNA triple-helical binding motif

Selective recognition of a C-G base-pair within the parallel DNA triple-helical binding motif was achieved by a third strand containing the base 5-methyl pyrimidin-2-one. The third strand affinities (K(D)) for a representative 15-mer duplex sequence containing all four Watson-Crick base pairs (X-Y) in the center are C-G (26 nM) >> A-T (270 nM) approximately T-A (350 nM) > G-C (ca 700 nM).

Strong, specific, monodentate G-C base pair recognition by N7-inosine derivatives in the pyrimidine.purine-pyrimidine triple-helical binding motif

The nucleoside analogs 7-(2'-deoxy-alpha-D-ribofuranosyl)hypoxanthine (alpha7H,1), 7-(2'-deoxy-beta-D-ribofuranosyl)hypoxanthine (beta7H,2) and 7-7-(2'-O-methyl-beta-D- ribofuranosyl)hypoxanthine (beta7HOMe,3) were prepared and incorporated into triplex forming oligodeoxynucleotides, designed to bind to DNA in the parallel (pyrimidine.purine-pyrimidine) motif. By DNase I footprinting techniques and UV-melting curve analysis it was found that, at pH 7. 0, the 15mer oligonucleotides d(TTTTTMeCTXTMeCTMeCTMeCT) (MeC = 5-methyl-deoxycytidine, X =beta7H,beta7HOMe) bind to a DNA target duplex forming a H.G-C base triple with equal to slightly increased (10-fold) stability compared to a control oligodeoxynucleotide in which the hypoxanthine residue is replaced by MeC. Remarkably, triple-helix formation is specific to G-C base pairs and up to 40 microM third strand concentration, no stable triplex exhibiting H.A-T, H.T-A or H.C-G base arrangements could be found (target duplex concentration approximately 0.1 nM). Multiply substituted sequences containing beta7H residues either in an isolated [d(TTTTTbeta7HTbeta7HTbeta7HTbeta7HTbeta7HT)] or in a contiguous [d(TTTbeta7Hbeta7Hbeta7Hbeta7HTTTTbeta7HTTT)] manner still form triplexes with their targets of comparable stability as the control (MeC-containing) sequences at pH 7.0 and high salt or spermine containing buffers. General considerations lead to a structural model in which the recognition of the G-C base pair by hypoxanthine takes place via only one H-bond of the N-H of hypoxanthine to N7 of guanine. This model is supported by a molecular dynamics simulation. A general comparison of the triplex forming properties of oligonucleotides containing beta7H with those containing MeC or N7-2'-deoxyguanosine (N7G) reveals that monodentate recognition in the former case can energetically compete with bidentate recognition in the latter two cases.

Potassium-resistant triple helix formation and improved intracellular gene targeting by oligodeoxyribonucleotides containing 7-deazaxanthine

Triple helix formation by purine-rich oligonucleotides in the anti-parallel motif is inhibited by physiological concentrations of potassium. Substitution with 7-deazaxanthine (c7X) has been suggested as a strategy to overcome this effect. We have tested this by examining triple helix formation both in vitro and in vivo by a series of triple helix-forming oligonucleotides (TFOs) containing guanine plus either adenine, thymine, or c7X. The TFOs were conjugated to psoralen at the 5'end and were designed to bind to a portion of the supF mutation reporter gene. Using in vitro gel mobility shift assays, we found that triplex formation by the c7X-substituted TFOs was relatively resistant to the presence of 140 mM K+. The c7X-containing TFOs were also superior in gene targeting experiments in mammalian cells, yielding 4- to 5-fold higher mutation frequencies in a shuttle vector-based mutagenesis assay designed to detect mutations induced by third strand-directed psoralen adducts. When the phosphodiester backbone was replaced by a phosphorothioate one, the in vitro binding of the c7X-TFOs was not affected, but the efficiency of in vivo triple helix formation was reduced. These results indicate the utility of the c7X substitution for in vivo gene targeting experiments, and they show that the feasibility of the triplex anti-gene strategy can be significantly enhanced by advances in nucleotide chemistry.

Divalent transition metal cations counteract potassium-induced quadruplex assembly of oligo(dG) sequences

Nucleic acids containing tracts of contiguous guanines tend to self-associate into four-stranded (quadruplex) structures, based on reciprocal non-Watson-Crick (G*G*G*G) hydrogen bonds. The quadruplex structure is induced/stabilized by monovalent cations, particularly potassium. Using circular dichroism, we have determined that the induction/stabilization of quadruplex structure by K+is specifically counteracted by low concentrations of Mn2+(4-10 mM), Co2+(0.3-2 mM) or Ni2+(0.3-0.8 mM). G-Tract-containing single strands are also capable of sequence-specific non-Watson-Crick interaction with d(G. C)-tract-containing (target) sequences within double-stranded DNA. The assembly of these G*G.C-based triple helical structures is supported by magnesium, but is potently inhibited by potassium due to sequestration of the G-tract single strand into quadruplex structure. We have used DNase I protection assays to demonstrate that competition between quadruplex self-association and triplex assembly is altered in the presence of Mn2+, Co2+or Ni2+. By specifically counteracting the induction/stabilization of quadruplex structure by potassium, these divalent transition metal cations allow triplex formation in the presence of K+and shift the position of equilibrium so that a very high proportion of triplex target sites are bound. Thus, variation of the cation environment can differentially promote the assembly of multistranded nucleic acid structural alternatives.

Molecular modelling study of the netropsin complexation with a nucleic acid triple helix

A detailed molecular mechanical study has been made on the complexes of netropsin with the double stranded oligonucleotide (dA)12.(dT)12 and with the triple helix (dA)12.(dT)12.(dT)12. The complexes were built using computer graphics and energy refined using JUMNA program. In agreement with circular dichroism experiments we have shown that 3 netropsins can bind the minor grooves of the triple helix and of the double helix. The groove geometry in the duplex and in the triplex is very similar. However a detailed analysis of the energetic terms shows, in agreement with thermal denaturation studies, that the affinity of netropsin toward the double helices is larger than towards triple helices.

Double hairpin complexes allow accommodation of all four base pairs in triple helices containing both DNA and RNA strands

We investigated the binding of an antisense oligodeoxynucleotide to a stem-loop structure corresponding to the mini-exon sequence of the protozoan parasite Leishmania amazonensis. This oligomer was designed to anneal to the single-stranded region adjacent to the bottom of the hairpin and to fold back on itself, giving rise to a "double-hairpin" complex that involved a local triplex. This imposed the recognition, by the third strand, of a "purine" strand containing 6 interspersed pyrimidines out of 15 nucleic acid bases. The sequence of the complementary oligonucleotide was derived from the so-called pyrimidine motif; the third strand of the anti-mini-exon oligomer was parallel to the purine strand of the target. Electrophoretic mobility shift assays and footprinting studies demonstrated that such an antisense oligomer was able to bind to both the DNA and RNA versions of the Leishmania hairpin. These double hairpin complexes allowed the formation at pH 6.0 of a triple-stranded structure, despite the presence of 4 A:T*G and 2 G:C*T triplets out of 15.