New nucleotide pairs for stable DNA triplexes stabilized by stacking interaction

New nucleotide pairs applicable to formation of DNA triplexes were developed. We designed oligonucleotides incorporating 5-aryl deoxycytidine derivatives (dC5Ars) and cyclic deoxycytidine derivatives, dCPPP and dCPPI, having an expanded aromatic area, as the second strand. As pairing partners, two types of abasic residues (C3: propylene linker, phi: abasic base) were chosen. It was concluded that, when the 5-aryl-modified cytosine bases paired with the abasic sites in TFOs in a space-fitting manner, the stability of the resulting triplexes significantly increased. The recognition of C3 toward dC5Ars was selective because of the stacking interactions between their aromatic part and the nucleobases flanking the abasic site. These results indicate the potential utility of new nucleotide triplets for DNA triplex formation, which might expand the variety of structures and sequences and might be useful for biorelated fields such as DNA nanotechnologies.     

Flexibility of active-site gorge aromatic residues and non-gorge aromatic residues in acetylcholinesterase

The presence of an unusually large number of aromatic residues in the active site gorge of acetylcholinesterase is a subject of great interest. Flexibility of these residues has been suspected to be a key player in controlling the ligand traversal in the gorge. This raises the question of whether the over-representation of aromatic residues in the gorge implies higher-than-normal flexibility of these residues. The current study suggests that it does not. Large changes in the hydrophobic cross-sectional area due to dihedral oscillations are probably the reason of their presence in the gorge.     

Unfolding thermodynamics of DNA pyrimidine triplexes with different molecularities

Nucleic acid oligonucleotides (ODNs), as drugs, present an exquisite selectivity and affinity that can be used in antigene and antisense strategies for the control of gene expression. In this work we try to answer the following question: How does the molecularity of a DNA triplex affect its overall stability and melting behavior? To this end, we used a combination of temperature-dependent UV spectroscopy and calorimetric (differential scanning calorimetry) techniques to investigate the melting behavior of DNA triplexes with a similar helical stem, TC+TC+TC+T/AGAGAGA/TCTCTCT, but formed with different strand molecularity. We determined standard thermodynamic profiles and the differential binding of protons and counterions accompanying their unfolding. The formation of a triplex is accompanied by a favorable free energy term, resulting from the typical compensation of favorable enthalpy-unfavorable entropy contributions, i.e., the folding of a particular triplex is enthalpy driven. The magnitude of the favorable enthalpy contributions corresponds to the number and strength of the base-triplet stacks formed, which are helped by stacking contributions due to the incorporation of dangling ends or loops. Triplex stability is in the following order: monomolecular > bimolecular > trimolecular; this is explained in terms of additional stacking contributions due to the inclusion of loops. As expected, acidic pH stabilized all triplexes by allowing protonation of the cytosines in the third strand; however, the percentage of protonation increases as the molecularity decreases. The results help to choose adequate solution conditions for the study of triplexes containing different ratios of CGC+ and TAT base triplets and to aid in the design of oligonucleotide sequences as targeting reagents that could effectively react with mRNA sequences involved in human diseases, thereby increasing the feasibility of using the antisense strategy for therapeutic purposes.     

Stabilization of DNA duplexes by covalently-linked peptides

The hybridization properties of various peptide-oligonucleotide hybrids were assessed from UV thermal denaturation experiments. Analysis of these and other published data suggests that peptide chains, both hydrophobic and positively charged, generally have a clear stabilizing effect on short-chain oligonucleotide duplexes.     

A cooperative beads-on-a-string approach to exceptionally stable DNA triplexes

A poly(dT) oligomer can serve as the string on which synthetic hairpins possessing poly(dA) and poly(dT) arms connected by a hydrophobic perylene diimide linker are assembled like beads on a string. The synthetic hairpins form head-to-head dimers and trimers, respectively, in the absence of the poly(dT) string and in the presence of a string with inverted polarity at mid-strand. However, they assemble in cooperative head-to-tail fashion on normal poly(dT) oligomers.     

Stabilization of parallel triplexes by twisted intercalating nucleic acids (TINAs) incorporating 1,2,3-triazole units and prepared by microwave-accelerated click chemistry

A highly efficient method for postsynthetic modification of unprotected oligonucleotides incorporating internal insertions of (R)-1-O-(4-ethynylbenzyl)glycerol has been developed through the application of click chemistry with water-insoluble pyren-1-yl azide and water-soluble benzyl azide and acceleration by microwave irradiation. The twisted intercalating nucleic acids (TINAs) obtained in these reactions, possessing bulged insertions of (R)-3-O-{4-[1-(pyren-1-yl)-1H-1,2,3-triazol-4-yl]benzyl}glycerol (7), formed parallel triplexes with thermal stabilities of 20.0, 34.0, and 40.0 degrees C at pH 7.2 in the cases of one, two, or three insertions of 7, respectively, separated by three nucleic bases. An oligonucleotide with four insertions of 7--each between three nucleic bases in the sequence--was unable to form complexes with complementary single- or double-stranded DNAs, as a result of self-aggregation of the pyrene moieties. This assumption was supported by the formation of a very strong excimer band at 460 nm in the fluorescence spectra. Molecular modeling of the parallel triplex with bulged insertion of the monomer 7 in the triplex-forming oligonucleotide (TFO) showed that only the pyrene moiety was stacking between the bases of the dsDNA, whereas 1,2,3-triazole did not participate in the triplex stabilization. Thermal denaturation studies of the duplexes and triplexes, as well as the fluorescence properties of TINA-triazole 7, are discussed and compared with previous studies on TINA.     

Environmentally weathered residues source diagnostic by high-molecular-weight polycyclic aromatic sulphur heterocycles

High-molecular-weight polycyclic aromatic sulphur heterocycles (HMPASH) were applied in a forensic chemical analysis to identify the source(s) of environmentally weathered residues polluting the beaches of the Mediterranean city of Alexandria, Egypt, and to assess their weathering trends. The HMPASH were investigated by Fourier transform ion cyclotron resonance mass spectrometry in residues and an Egyptian crude as a possible source oil. The dibenzothiophenes/naphthenodibenzothiophenes (DBE 9/DBE 10) parameter indicated that two studied residues were likely to have originated from Egyptian crude oils, whereas the third residue could have had a foreign source. The residues displayed different stages of weathering. HMPASH having double bond equivalent (DBE) 1–5 were more influenced by weathering processes than those having DBE 6–17, probably because they are aliphatic sulphides and not aromatic compounds.     

Cationic modified nucleic acids for use in DNA hairpins and parallel triplexes

Non-nucleosidic DNA monomers comprising partially protonated amines at low pH have been designed and synthesized. The modifications were incorporated into DNA oligonucleotides via standard DNA phosphoramidite synthesis. The ability of cationic modifications to stabilize palindromic DNA hairpins and parallel triplexes were evaluated using gel electrophoresis, circular dichroism and thermal denaturation measurements. The non-nucleosidic modifications were found to increase the thermal stability of palindromic hairpins at pH 8.0 as compared with a nucleosidic tetraloop (TCTC). Incorporation of modifications at the 5'-end of a triplex forming oligonucleotide resulted in a significant increase in thermal stability at low pH when the modifications were placed as the 5'-dangling end.     

DNA duplexes and triplex-forming oligodeoxynucleotides incorporating modified nucleosides forming stable and selective triplexes

We have previously reported DNA triplexes containing the unnatural base triad G-PPI·C3, in which PPI is an indole-fused cytosine derivative incorporated into DNA duplexes and C3 is an abasic site in triplex-forming oligonucleotides (TFOs) introduced by a propylene linker. In this study, we developed a new unnatural base triad A-ψ·C(R1) where ψ and C(R1) are base moieties 2'-deoxypseudouridine and 5-substituted deoxycytidine, respectively. We examined several electron-withdrawing substituents for R1 and found that 5-bromocytosine (C(Br)) could selectively recognize ψ. In addition, we developed a new PPI derivative, PPI(Me), having a methyl group on the indole ring in order to achieve selective triplex formation between DNA duplexes incorporating various Watson-Crick base pairs, such as T-A, C-G, A-ψ, and G-PPI(Me), and TFOs containing T, C, C(Br), and C3. We studied the selective triplex formation between these duplexes and TFOs using UV-melting and gel mobility shift assays.     

Stabilization of G-quadruplex DNA by highly selective ligands via click chemistry

A series of G-quadruplex stabilizing compounds have been prepared via click chemistry employing the Cu(I)-catalyzed Huisgen reaction. These compounds were shown to bind tightly to G-quadruplex DNA even in the presence of competing high concentrations of duplex DNA. Furthermore, a modified TRAP assay has shown that some of these compounds also inhibit telomerase at low micromolar concentration.     

Charge dependent behavior of PNA/DNA/PNA triplexes in the gas phase

Intact noncovalent complexes were studied in the gas phase using negative ion nano-ESI mass spectrometry. Among various noncovalent systems studied in the gas phase, the interaction of DNA strands with peptide nucleic acids (PNAs) presents a strong interest as biologically relevant systems. PNAs originally described by Nielsen are used as DNA mimics as possible medical agents by imprisoning DNA single strands into stable noncovalent complexes. Two types of PNAs were investigated in the PNA/DNA multiplex: the original Nielsen's PNA and a modified backbone PNA by the introduction of syn- and anti-(aminoethyl)thiazolidine rings. We first investigated the stoichiometry of PNA/DNA multiplexes formed in solution and observed them in the gas phase via qualitative kinetics of complementary strand associations. It resulted in observing PNA2/DNA triplexes (ts) as the multiply deprotonated species, most stable in both the solution and gas phase. Second, charge-dependant decompositions of these species were undertaken under low-energy collision conditions. It appears that covalent bond cleavages (base releasing or skeleton cleavage) occur from lower ts charge states rather than ts unzipping, which takes place from higher charge states. This behavior can be explained by considering the presence of zwitterions depending on the charge state. They result in strong salt-bridge interactions between the positively charged PNA side chain and the negatively charged DNA backbone. We propose a general model to clearly display the involved patterns in the noncovalent triplex decompositions. Third, the relative stability of three PNA2/DNA complexes was scrutinized in the gas phase by acquiring the breakdown curves of their ts(6-) form, corresponding to the ts unzipping. The chemical structures of the studied PNAs were chosen in order to evidence the possible influence of backbone stereochemistry on the rigidity of PNA2/DNA complexes. It provided significantly different stabilities via V(m) measurements. The relative gas-phase stability order obtained was compared to that found in solution by Chassaing et al., and shows qualitative agreement.     

Three's a crowd – stabilisation,structure, and applications of DNA triplexes

DNA is a strikingly flexible molecule and can form a variety of secondary structures, including the triple helix, which is the subject of this review. The DNA triplex may be formed naturally, during homologous recombination, or can be formed by the introduction of a synthetic triplex forming oligonucleotide (TFO) to a DNA duplex. As the TFO will bind to the duplex with sequence specificity, there is significant interest in developing TFOs with potential therapeutic applications, including using TFOs as a delivery mechanism for compounds able to modify or damage DNA. However, to combine triplexes with functionalised compounds, a full understanding of triplex structure and chemical modification strategies, which may increase triplex stability or in vivo degradation, is essential – these areas will be discussed in this review. Ruthenium polypyridyl complexes, which are able to photooxidise DNA and act as luminescent DNA probes, may serve as a suitable photophysical payload for a TFO system and the developments in this area in the context of DNA triplexes will also be reviewed.

Triplex-forming oligonucleotides can target specific DNA sequences by binding in the duplex major groove. Chemical modifications and ligand binding have been explored, for use in a variety of biological applications.     

Reductive electron injection into duplex DNA by aromatic amines

An assay based on photoinduced reaction and subsequent cleavage of duplex DNA containing a bromodeoxyuridine ((Br)U) residue and an abasic site was developed to screen aromatic amines for their ability to initiate charge transfer by reductive electron donation. Two candidates, N,N,N',N'-tetramethyl-1,5-diaminonaphthalene (TMDN) and 1,5-diaminonaphthalene (DAN), expressed the desired activity, and an oligodeoxynucleotide-TMDN conjugate was subsequently prepared to identify additional variables affecting the efficiency of electron injection and transfer into DNA. This system demonstrated only mild sensitivity to molecular oxygen but was strongly inhibited by high concentrations of 2-mercaptoethanol. The nucleobase counter to the attached TMDN strongly modulated charge transfer as evident by a 60-fold decrease in reduction of the distal (Br)U when the counterbase A was substituted for C. An inverse relationship between this reduction and quenching of TMDN fluorescence by the counterbase was also discovered and is consistent with a competition between radical recombination and electron migration away from the initial site of its injection into DNA.     

Stabilization by extra-helical thymines of a DNA duplex with Hoogsteen base pairs

We present the crystal structure of the DNA duplex formed by d(ATATATCT). The crystals contain seven stacked antiparallel duplexes in the asymmetric unit with A.T Hoogsteen base pairs. The terminal CT sequences bend over so that the thymines enter the minor groove and form a hydrogen bond with thymine 2 of the complementary strand in the Hoogsteen duplex. Cytosines occupy extra-helical positions; they contribute to the crystal lattice through various kinds of interactions, including a unique CAA triplet. The presence of thymine in the minor groove apparently contributes to the stability of the DNA duplex in the Hoogsteen conformation. These observations open the way toward finding under what conditions the Hoogsteen duplex may be stabilized in vivo. The present crystal structure also confirms the tendency of A.T-rich oligonucleotides to crystallize as long helical stacks of duplexes.     

Characterization of DNA hybridization on partially aminated diamond by aromatic compounds

Here, we report a novel method of micropatterning oligonucleotides via aromatic groups as linkers on partially amino-terminated diamond and the inherence on subsequent hybridization. The covalent immobilization of probe oligonucleotides and characterization of immobilized probe oligonucleotides with carboxylic compounds were investigated by X-ray photoelectron spectroscopy (XPS). To confirm the effects of linker flexibility in a low amino group on diamond for probe oligonucleotides, three kinds of dicarboxylic compound--adipic acid, terephthalic acid, and trimesic acid--were used for immobilization of probe oligonucleotides, like linkers; and these oligonucleotides were hybridized with target oligonucleotides labeled with Cy 5 on the micropatterned diamond surface. The hybridization intensities determined by epifluorescence microscopy were compared and analyzed.     

Metal ligand aromatic cation-pi interactions in metalloproteins: ligands coordinated to metal interact with aromatic residues

Cation-pi interactions between aromatic residues and cationic amino groups in side chains and have been recognized as noncovalent bonding interactions relevant for molecular recognition and for stabilization and definition of the native structure of proteins. We propose a novel type of cation-pi interaction in metalloproteins; namely interaction between ligands coordinated to a metal cation--which gain positive charge from the metal--and aromatic groups in amino acid side chains. Investigation of crystal structures of metalloproteins in the Protein Data Bank (PDB) has revealed that there exist quite a number of metalloproteins in which aromatic rings of phenylalanine, tyrosine, and tryptophan are situated close to a metal center interacting with coordinated ligands. Among these ligands are amino acids such as asparagine, aspartate, glutamate, histidine, and threonine, but also water and substrates like ethanol. These interactions play a role in the stability and conformation of metalloproteins, and in some cases may also be directly involved in the mechanism of enzymatic reactions, which occur at the metal center. For the enzyme superoxide dismutase, we used quantum chemical computation to calculate that Trp163 has an interaction energy of 10.09 kcal mol(-1) with the ligands coordinated to iron.     

Reversible Covalent Stabilization of Stacking Contacts in DNA Assemblies

Stacking bonds formed between two blunt‐ended DNA double helices can be used to reversibly stabilize higher‐order complexes that are assembled from rigid DNA components. Typically, at low cation concentrations, stacking bonds break and thus higher‐order complexes disassemble. Herein, we present a site‐specific photochemical mechanism for the reversible covalent stabilization of stacking bonds in DNA assemblies. To this end, we modified one blunt end with the 3‐cyanovinylcarbazole (^cnvK) moiety and positioned a thymine residue (T) at the other blunt end. In the bound state, the two blunt‐ended helices are stacked together, resulting in a co‐localization of ^cnvK and T. Such a configuration induces the formation of a covalent bond across the stacking contact upon irradiation with 365 nm light. This bond can also be cleaved upon irradiation with 310 nm light, allowing repeated formation and cleavage of the same covalent bond on the timescale of seconds. Our system will expand the range of conditions under which stacking‐bond‐stabilized objects may be utilized.