Metal–base pairing in DNA

The use of DNA as a molecular wire in nanoscale electronic architectures would greatly benefit from its capability of sequence-specific self-assembly. Although single electrons and positive charges have been shown to be transmitted by natural DNA over a distance of several base pairs, the high ohmic resistance of unmodified oligonucleotides imposes a serious obstacle. Exchanging some or all of the Watson–Crick base pairs in DNA by metal complexes may solve this problem and evolve DNA-like materials with superior conductivity for future nano-electronic applications. The so-called metal–base pairs are formed from suitable transition metal ions and ligand-like nucleosides which are introduced into both of the two pairing strands by automated DNA synthesis. This review illustrates the basic concepts of metal–base pairing and highlights recent developments in the field.     

Polyaniline–DNA microsphere formation by simple electropolymerization

Polyaniline (PANI) microspheres were prepared by electrochemical polymerization. To obtain PANI having novel micro- and nanostructures, by the potential scan technique, aniline was electropolymerized in the presence of DNA using four polymerizing solutions containing different acids: H₂SO₄, C₆H₅SO₃H, HClO₄, and CF₃COOH. The growth rate of the PANI film on the electrode surface decreased by the presence of DNA, suggesting that DNA interacted with the growing PANI molecules during the electropolymerization. The growth rate also depended on the type of acid, i.e., the anion, in the polymerizing solution and was in the order of SO₄ ²⁻ > C₆H₅SO₃ ⁻ > ClO₄ ⁻ > CF₃COO⁻, which significantly coincided with the reverse order of the Hofmeister series representing the lyophilicity of the anion. When aniline was electropolymerized in the CF₃COOH polymerizing solution containing DNA, PANI microspheres were obtained without any templates. This PANI showed a sufficient redox activity in the less acidic solution in which the ordinary PANI has a slight redox activity. On the other hand, the electronic state of the PANI differed from the ordinary ones; a new absorption band was evident at 620 nm. The difference in the redox activity and electronic state suggested that the DNA molecules were incorporated in the PANI and electronically interacted with the PANI molecules.     

Detecting Counterion Dynamics in DNA–Protein Association

Due to a high density of negative charges on its surface, DNA condenses cations as counterions, forming the so-called “ion atmosphere”. Although the release of counterions upon DNA–protein association has been postulated to have a major contribution to the binding thermodynamics, this release remains to be confirmed through a direct observation of the ions. Herein, we report the characterization of the ion atmosphere around DNA using NMR spectroscopy and directly detect the release of counterions upon DNA–protein association. NMR-based diffusion data reveal the highly dynamic nature of counterions within the ion atmosphere around DNA. Counterion release is observed as an increase in the apparent ionic diffusion coefficient, which directly provides the number of counterions released upon DNA–protein association.     

Electrochemical investigations of baicalin and DNA–baicalin interactions

Baicalin is an anti-HIV drug purified from the traditional Chinese medicinal plant Scutellaria Baicalensis Georgi. Baicalin has proven to be electroactive at pyrolytic graphite (PG) electrodes. We thus studied its interaction with DNA via the electrochemical approach. We observed that the peak currents corresponding to the baicalin reduction–oxidation (redox) reaction significantly decrease upon the addition of DNA. With complementary ultraviolet/visible (UV/Vis) spectroscopic evidence, we suggest that baicalin binds to DNA through intercalation. This feature has enabled baicalin to discriminate between double-stranded DNA (dsDNA) and single-stranded DNA (ssDNA).Electronic Supplementary Material Supplementary material is available in the online version of this article at . A link in the frame on the left on that page takes you directly to the supplementary material.     

Separation and identification of trinucleotide–melphalan adducts from enzymatically digested DNA using HPLC–ESI–MS

Melphalan is a bifunctional alkylating agent that covalently binds to the nucleophilic sites present in DNA. In this study we investigated oligonucleotides prepared enzymatically from DNA modified with melphalan. Calf thymus DNA was incubated in-vitro with melphalan and the resulting modifications were enzymatically cleaved by means of benzonase and nuclease S1. Efficient sample preconcentration was achieved by solid-phase extraction, in which phenyl phase cartridges resulted in better recovery of the modified species than C₁₈. The applied enzymatic digestion time resulted in production of trinucleotide adducts which were efficiently separated and detected by use of reversed-phase HPLC coupled to an ion-trap mass spectrometer with electrospray ionization. It was assumed that melphalan could act as both a monofunctional and bifunctional alkylating agent. Mono-alkylated adducts were much more abundant, however, and the alkylation site was located on the nucleobases. On the other hand, we unequivocally identified cross-link formation in DNA, even though at low abundance and only a few adduct types were detected. Figure Different Alkylation reactions of Melphalan with DNA     

Water-mediated interactions in the CRP–cAMP–DNA complex: Does water mediate sequence-specific binding at the DNA primary-kink site?

The cyclic AMP receptor protein (CRP) of Escherichia coli binds preferentially to DNA sequences possessing a T:A base pair at position 6 (at which the DNA becomes kinked), but with which it does not form any direct interactions. It has been proposed that indirect readout is involved in CRP-DNA binding, in which specificity for this base pair is primarily related to sequence effects on the energetic susceptibility of the DNA to kink formation. In the current study, the possibility of contributions to indirect readout by water-mediated hydrogen bonding of CRP with the T:A base pair was investigated. A 1.0 ns molecular dynamics simulation of the CRP-cAMP-DNA complex in explicit solvent was performed, and assessed for water-mediated CRP-DNA hydrogen bonds; results were compared to several X-ray crystal structures of comparable complexes. While several water-mediated CRP-DNA hydrogen bonds were identified, none of these involved the T:A base pair at position 6. Therefore, the sequence specificity for this base pair is not likely enhanced by water-mediated hydrogen bonding with the CRP.     

Toehold-mediated DNA displacement-based surface-enhanced Raman scattering DNA sensor utilizing an Au–Ag bimetallic nanodendrite substrate

A simple and sensitive surface enhanced Raman scattering (SERS)-based DNA sensor that utilizes the toehold-mediated DNA displacement reaction as a target-capturing scheme has been demonstrated. For a SERS substrate, Au–Ag bimetallic nanodendrites were electrochemically synthesized and used as a sensor platform. The incorporation of both Ag and Au was employed to simultaneously secure high sensitivity and stability of the substrate. An optimal composition of Ag and Au that satisfied these needs was determined. A double-strand composed of ‘a probe DNA (pDNA)’ complementary to ‘a target DNA (tDNA)’ and ‘an indicator DNA tagged with a Raman reporter (iDNA)’ was conjugated on the substrate. The conjugation made the reporter molecule close to the surface and induced generation of the Raman signal. The tDNA released the pre-hybridized iDNA from the pDNA via toehold-mediated displacement, and the displacement of the iDNA resulted in the decrease of Raman intensity. The variation of percent intensity change was sensitive and linear in the concentration range from 200 fM to 20 nM, and the achieved limit of detection (LOD) was 96.3 fM, superior to those reported in previous studies that adopted different signal taggings based on such as fluorescence and electrochemistry.     

Thermodynamic characterization of proflavine–DNA binding through microcalorimetric studies

The interaction of an important acridine dye, proflavine hydrochloride, with double stranded DNA was investigated using isothermal titration calorimetry and differential scanning calorimetry. The equilibrium constant for the binding reaction was calculated to be (1.60 ± 0.04) · 10⁵ · M⁻¹ at T = 298.15 K. The binding of proflavine hydrochloride to DNA was favored by both negative enthalpy and positive entropy contributions to the Gibbs energy. The equilibrium constant for the binding reaction decreased with increasing temperature. The standard molar enthalpy change became increasingly negative while the standard molar entropy change became less positive with rise in temperature. However, the standard molar Gibbs free energy change varied marginally suggesting the occurrence of enthalpy–entropy compensation phenomenon. The binding reaction was dominated by non-polyelectrolytic forces which remained virtually unchanged at all the salt concentrations studied. The binding also significantly increased the thermal stability of DNA against thermal denaturation.     

Screening DNA Adducts by LC–ESI–MS–MS: Application to Screening New Adducts Formed from Acrylamide

A method for screening DNA adducts with unknown chemical structures was developed; it involves the use of liquid chromatography–electrospray ionization-tandem mass spectrometry (LC–ESI–MS–MS). In electrospray ionization (ESI) product ion mass spectra of guanine adducts, fragment ions were observed at m/z 152 and 135. Precursor ion scan analysis of these fragment ions indicated that the screening of DNA adducts would be possible. The developed method was used for the analysis of DNA adducts derived from acrylamide, which is not only a constituent of many commonly consumed foods but also a carcinogenic compound. We successfully discovered new guanine adducts. The results of this study indicate that the developed method is useful for screening new DNA adducts.     

DNA modified with metal complexes: Applications in the construction of higher order metal–DNA nanostructures

DNA has recently emerged as a useful building block for higher order nanostructures, such as extended two-dimensional surfaces and discrete two- and three-dimensional structures. Transition metal complexes can introduce functionality to these otherwise passive nanostructures. This review examines the synthetic strategies used to introduce metals in a site-specific manner to DNA: either by attaching preformed metal complexes to DNA, or by metal coordination to unmodified or modified DNA. The applications of metal–DNA complexes in building higher order nanostructures and the utility of attaching luminescent or electrochemical labels are discussed.     

Polyoxometalate cobalt–gatifloxacin complex with DNA binding and antibacterial activity

An unusual inorganic–organic antibacterial complex based on polyoxometalates (POMs) and the cobalt–gatifloxacin (GT), [Co^II(C₁₉FH₂₂N₃O₄)₃][C₁₉FH₂₃N₃O₄][HSiW₁₂O₄₀]·23H₂O (1), has been synthesized. Single-crystal structural analysis shows that 1 represents for the first time an unusual tripodal coordination style with three GT molecules coordinating to cobalt(II) by six carboxylate and hydroxyl oxygens. The biological activity of 1 has been evaluated by investigating its binding ability to calf thymus DNA (CT-DNA). UV spectrum study of 1 has shown that it can bind to CT-DNA by intercalation. The DNA-binding constant K_b was 9.6?×?10⁴?M?L^?1, higher than that of pure GT, 3.8?×?10^4?M?L^?1. Furthermore, the antibacterial activities of 1 were tested against Staphylococcus aureus and Escherichia coli, respectively, and have shown slightly lower antibacterial activity than that of free GT at the same mass concentration. If the GT component in the complexes was controlled at the same molar concentration, 1 generates the biggest antibacterial area during the Kirby–Bauer disc diffusion detection. This result indicates that the integration of heteropolyanions and GT exhibits synergistic effects on the antibacterial activity, which paves a new way to design low-cost antibacterial compound by the introduction of POMs.     

Sequence and linker dependent chiral dimerization of DNA–porphyrin conjugates

Circular dichroism (CD), UV–vis absorption, fluorescence, and resonance light scattering (RLS) spectroscopies were used to elucidate the role of the DNA sequence, linkers between DNA and porphyrin, and metal in the porphyrin coordination center on the self-assembly of DNA–porphyrin conjugates. A series of eight non-self-complementary DNA–porphyrin conjugates have been synthesized with zinc and free-base porphyrins covalently attached to the short ODNs (A₈ or T₈) via amide or phosphate linker. A small structural modification (e.g., amide linker replaced by the phosphate linker) showed a dramatic effect on the aggregation properties of DNA–porphyrin conjugates and greatly altered their spectroscopic properties. At low ionic strength, porphyrin aggregation was not observed for any conjugate. An increase in the ionic strength caused two out of eight conjugates to form chiral porphyrin dimers.     

In situ evaluation of chromium–DNA damage using a DNA-electrochemical biosensor

The in situ evaluation of the direct interaction of chromium species with double-stranded DNA (dsDNA) was studied using differential pulse voltammetry at a glassy carbon electrode. The DNA damage was electrochemically detected following the changes in the oxidation peaks of guanosine and adenosine bases. The results obtained revealed the interaction with dsDNA of the Cr(IV) and Cr(V) reactive intermediates of Cr(III) oxidation by O₂ dissolved in the solution bound to dsDNA. This interaction leads to different modifications and causes oxidative damage in the B-DNA structure. Using polyhomonucleotides of guanine and adenine, it was shown that the interaction between reactive intermediates Cr(IV) and Cr(V)–DNA causes oxidative damage and preferentially takes place at guanine-rich segments, leading to the formation of 8-oxoguanine, the oxidation product of guanine residues and a biomarker of DNA oxidative damage. The interaction of Cr(VI) with dsDNA causes breaking of hydrogen bonds, conformational changes, and unfolding of the double helix, which enables easier access of other oxidative agents to interact with DNA, and the occurrence of oxidative damage to DNA.     

A supramolecular polymerisation model for the structurisation of DNA–lipid complexes

Complexes formed by DNA and lipid mixtures have great interest for the assessment of self-assembling mechanisms in open biological systems. X-ray diffraction has revealed that minor alterations of the cationic/neutral lipid composition produced major alterations to the liquid crystalline structure and the hydration of the complexes. We have extended to these systems by an approach based on the identification of a fundamental repeating unit that grows according to the general principles of supramolecular polymerisation and liquid crystallinity. Structural reorganisations that optimise the electrostatic and hydrophobic compensation are enhanced by competition between the rigidity of the polyelectrolyte and the cohesion of the lipid assembly. The non-hydrated hexagonal structure revealed by X-ray examination is represented by a dendritic-type supramolecular polymerisation of DNA units decorated by the aliphatic tails of dissociated liposomes. An increase in the cationic/neutral lipid component ratio enhances the stability of planar bilayers, favouring the formation of the partly hydrated lamellar structure revealed by X-ray diffraction.     

Extending the applicability of the O-ring theory to protein–DNA complexes

Many biological processes depend on protein-based interactions, which are governed by central regions with higher binding affinities, the hot-spots. The O-ring theory or the “Water Exclusion” hypothesis states that the more deeply buried central regions are surrounded by areas, the null-spots, whose role would be to shelter the hot-spots from the bulk solvent. Although this theory is well-established for protein–protein interfaces, its applicability to other protein interfaces remains unclear. Our goal was to verify its applicability to protein–DNA interfaces. We performed Molecular Dynamics simulations in explicit solvent of several protein–DNA complexes and measured a variety of solvent accessible surface area (SASA) features, as well as, radial distribution functions of hot-spots and null-spots. Our aim was to test the influence of water in their coordination sphere. Our results show that hot-spots tend to have fewer water molecules in their neighborhood when compared to null-spots, and higher values of ΔSASA, which confirms their occlusion from solvent. This study provides evidence in support of the O-ring theory with its applicability to a new type of protein-based interface: protein–DNA.     

Preparation of N3-thymidine–butylene–N3-thymidine interstrand cross-linked DNA via an orthogonal deprotection strategy

A DNA duplex containing an N3-thymidine–butylene–N3-thymidine interstrand cross-link (ICL) was prepared using an on-column orthogonal deprotection strategy to permit different nucleotide sequence composition around the cross-linked site. The conditions used to remove 5′-O-allyloxycarbonyl and 3′-O-tert-butyldimethylsilyl protective groups for various on-column oligonucleotide intermediates did not affect the cross-linked lesion. Efficient removal of these groups enabled successful coupling of 2′-deoxyphosphoramidites to produce the desired duplex with a 31% yield after deprotection and purification.     

Self-Assembled L–DNA Linkers for Rapid Construction of Multi-Specific Antibody-Drug Conjugates Library

One of the key challenges of improving clinical outcomes of antibody drug conjugates (ADCs) is overcoming cancer resistance to the antibody and/or drug components of ADCs, and hence the need for ADC platforms with high combinatory flexibility. Here, we introduce the use of self-assembled left-handed DNA (L–DNA) oligonucleotides to link combinatory single-domain antibodies and toxin payloads for tunable and adaptive delivery of ADCs. We demonstrate that the method allows convenient construction of a library of ADCs with multi-specific targeting, multi-specific payloads, and exact drug-antibody ratio. The newly constructed ADCs with L–DNA scaffold showed favorable properties of in vitro cell cytotoxicity and in vivo suppression and eradication of solid tumors. Collectively, our data suggest that the L–DNA based modular ADC (MADC) platform is a viable option for generating therapeutic ADCs and for potentially expanding ADC therapeutic window via multi-specificity.     

Metal complexes of porphyrin–anthraquinone hybrids: DNA binding and photocleavage specificities

A cationic porphyrin–anthraquinone hybrid and its Zn(II), Cu(II), Co(III), and Mn(III) complexes were synthesized and their interactions with duplex DNA were studied using a combination of absorption, fluorescence titration, circular dichroism spectroscopy, thermal DNA denaturation, viscosity measurements, gel electrophoresis, and gas chromatography. Metal coordination induces intermolecular steric hindrance and thus the metal hybrids have smaller DNA binding affinities than the free base hybrid; the steric hindrance could relax the intermolecular aggregation and increase ¹O₂ generation of the metal hybrids. The DNA photocleavage abilities of these hybrids were investigated.