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The grooves of DNA provide recognition sites for many nucleic acid binding proteins and anticancer drugs such as the covalently binding cisplatin. Here we report a crystal structure showing, for the first time, groove selectivity by an intercalating ruthenium complex. The complex Λ‐[Ru(phen)2phi]2+, where phi=9,10‐phenanthrenediimine, is bound to the DNA decamer duplex d(CCGGTACCGG)2. The structure shows that the metal complex is symmetrically bound in the major groove at the central TA/TA step, and asymmetrically bound in the minor groove at the adjacent GG/CC steps. A third type of binding links the strands, in which each terminal cytosine base stacks with one phen ligand. The overall binding stoichiometry is four Ru complexes per duplex. Complementary biophysical measurements confirm the binding preference for the Λ‐enantiomer and show a high affinity for TA/TA steps and, more generally, TA‐rich sequences. A striking enantiospecific elevation of melting temperatures is found for oligonucleotides which include the TATA box sequence. [ABSTRACT FROM AUTHOR]

The grooves of DNA provide recognition sites for many nucleic acid binding proteins and anticancer drugs such as the covalently binding cisplatin. Here we report a crystal structure showing, for the first time, groove selectivity by an intercalating ruthenium complex. The complex Λ‐[Ru(phen)2phi]2+, where phi=9,10‐phenanthrenediimine, is bound to the DNA decamer duplex d(CCGGTACCGG)2. The structure shows that the metal complex is symmetrically bound in the major groove at the central TA/TA step, and asymmetrically bound in the minor groove at the adjacent GG/CC steps. A third type of binding links the strands, in which each terminal cytosine base stacks with one phen ligand. The overall binding stoichiometry is four Ru complexes per duplex. Complementary biophysical measurements confirm the binding preference for the Λ‐enantiomer and show a high affinity for TA/TA steps and, more generally, TA‐rich sequences. A striking enantiospecific elevation of melting temperatures is found for oligonucleotides which include the TATA box sequence. [ABSTRACT FROM AUTHOR]

The grooves of DNA provide recognition sites for many nucleic acid binding proteins and anticancer drugs such as the covalently binding cisplatin. Here we report a crystal structure showing, for the first time, groove selectivity by an intercalating ruthenium complex. The complex Λ‐[Ru(phen)2phi]2+, where phi=9,10‐phenanthrenediimine, is bound to the DNA decamer duplex d(CCGGTACCGG)2. The structure shows that the metal complex is symmetrically bound in the major groove at the central TA/TA step, and asymmetrically bound in the minor groove at the adjacent GG/CC steps. A third type of binding links the strands, in which each terminal cytosine base stacks with one phen ligand. The overall binding stoichiometry is four Ru complexes per duplex. Complementary biophysical measurements confirm the binding preference for the Λ‐enantiomer and show a high affinity for TA/TA steps and, more generally, TA‐rich sequences. A striking enantiospecific elevation of melting temperatures is found for oligonucleotides which include the TATA box sequence. [ABSTRACT FROM AUTHOR]

The grooves of DNA provide recognition sites for many nucleic acid binding proteins and anticancer drugs such as the covalently binding cisplatin. Here we report a crystal structure showing, for the first time, groove selectivity by an intercalating ruthenium complex. The complex Λ‐[Ru(phen)2phi]2+, where phi=9,10‐phenanthrenediimine, is bound to the DNA decamer duplex d(CCGGTACCGG)2. The structure shows that the metal complex is symmetrically bound in the major groove at the central TA/TA step, and asymmetrically bound in the minor groove at the adjacent GG/CC steps. A third type of binding links the strands, in which each terminal cytosine base stacks with one phen ligand. The overall binding stoichiometry is four Ru complexes per duplex. Complementary biophysical measurements confirm the binding preference for the Λ‐enantiomer and show a high affinity for TA/TA steps and, more generally, TA‐rich sequences. A striking enantiospecific elevation of melting temperatures is found for oligonucleotides which include the TATA box sequence. [ABSTRACT FROM AUTHOR]

The triplet metal to ligand charge transfer (3MLCT) luminescence of ruthenium (II) polypyridyl complexes offers attractive imaging properties, specifically towards the development of sensitive and structure-specific DNA probes. However, rapidly-deactivating dark state formation may compete with 3MLCT luminescence depending on different DNA structures. In this work, by combining femtosecond and nanosecond pump-probe spectroscopy, the 3MLCT relaxation dynamics of [Ru(phen)2(dppz)]2+ (phen = 1,10-phenanthroline, dppz = dipyridophenazine) in two iconic G-quadruplexes has been scrutinized. The binding modes of stacking of dppz ligand on the terminal G-quartet fully and partially are clearly identified based on the biexponential decay dynamics of the 3MLCT luminescence at 620 nm. Interestingly, the inhibited dark state channel in ds-DNA is open in G-quadruplex, featuring an ultrafast picosecond depopulation process from 3MLCT to a dark state. The dark state formation rates are found to be sensitive to the content of water molecules in local G-quadruplex structures, indicating different patterns of bound water. The unique excited state dynamics of [Ru(phen)2(dppz)]2+ in G-quadruplex is deciphered, providing mechanistic basis for the rational design of photoactive ruthenium metal complexes in biological applications. Photoactive ruthenium metal complexes are relevant luminescent DNA markers, but deciphering their local excited state dynamics in complex biochemical environments is challenging. Here the authors combine femtosecond and nanosecond pump-probe spectroscopy to elucidate the local hydration effects and 3MLCT relaxation dynamics of [Ru(phen)2(dppz)]2+ in two G-quadruplexes. [ABSTRACT FROM AUTHOR]

The detection of G‐quadruplex is of major interest. Nitro‐substituted ruthenium (II) complexes have attracted much attention due to fluorescent sensitivity to environment change. We report here a new nitro‐substituted ruthenium (II) complex, [Ru (phen)2(hnoip)]2+ (1) (hnoip = 2‐(2‐hydroxyl‐5‐nitrophenyl)imidazo[4,5‐f][1,10‐phenanthroline]), which displays distinct fluorescent properties in aqueous solution and non‐aqueous solvents. This complex exhibits large fluorescence enhancement after binding with G‐quadruplex DNA, and displays good fluorescent selectivity over other DNAs. The limit of detection is 6 nm for 22AG in Na+ and 43 nm for 22AG in K+, respectively. The results demonstrated that nitro‐substituted ruthenium (II) complexes can be utilized to design as G‐quadruplex fluorescent probes by protection of the nitro group on the complex from water. [ABSTRACT FROM AUTHOR]

A novel label-free electrogenerated chemiluminescence (ECL) biosensing method for the determination of DNA methyltransferase (MTase) activity was developed on base of enzyme-linkage reactions and tris(1, 10-phenanthroline) ruthenium-assembled graphene oxide (GO) served as an ECL signal compound. The ECL biosensing electrode was fabricated by self-assembling 5'-thiol modified hairpin-capture DNA probe containing methylation recognition site 5'-GATC-3' on the surface of a gold electrode. When DNA adenine methylation (Dam) MTase and S-adenosyl-L-methionine were introduced, all adenine residues within 5'-GATC-3' of hairpin-capture DNA probe on the biosensing electrode were methylated. After the methylated biosensing electrode was treated by the methylation-sensitive restriction endonuclease Dpn I, the methylated adenines were cleaved, methylation-induced scission of hairpin-capture DNA probe would displace the hairpin section and remain the "capture DNA probe" section on the gold electrode, then a long ssDNA was immobilized via the partial hybridization reaction between long ssDNA and hairpin-capture DNA probe remained section, the more binding site allow tris(1, 10-phenanthroline) ruthenium-assembled GO to be more bound to the long ssDNA on the electrode surface through both hydrophobic and p-p stacking interaction, in conjunction with the generation of a increased ECL signal. The ECL intensity versus the concentration of Dam MTase was linear in the range from 0.02 unit/mL to 10 unit/mL. The detection limit was 0.01 unit/mL. This work demonstrates that using the different affinities of GO for ssDNA and dsDNA for the fabrication of the label-free ECL biosensing method for DNA MTase activity is promising approach. [ABSTRACT FROM AUTHOR]

Abstract: In this paper, we reported an ultrasensitive ECL spectrometry for determination of DNA using magnetic streptavidin-coated nanobeads MNBs (SA-MNBs) as the carrier of Ru(bpy)3 2+-NHS, where bpy=2,2′-bipyridyl and NHS=N-hydroxysuccinimide ester, to amplify signal. The SA-MNBs were conjugated to the hybrids consisting of capture DNA, target DNA (t-DNA) and probe DNA immobilized on a substrate, followed by releasing the SA-MNBs and binding a huge number of Ru(bpy)3 2+-NHS to the SA-MNBs. The SA-MNBs with Ru(bpy)3 2+-NHS were immobilized on an Au film electrode by means of a magnet. In the presence of tri-n-propylamine, the ECL spectrum of the Ru(bpy)3 2+-NHS at 1.35V was acquired by using an optical multi-channel analyzer. The maximum emission intensity on the ECL spectrum was used to quantify DNA. Using this method, not only the limit of detection for DNA determination was as low as 1.2×10−15 mol/L, but also the ECL spectrum of Ru(bpy)3 2+-NHS on the surface of the SA-MNBs was obtained. The ultrasensitive ECL spectrometry could be used to measure gene expression level in cells. [Copyright &y& Elsevier]

Abstract: A novel and highly sensitive electrochemiluminescence (ECL) assay based on magnetic beads separation/collection process and thymine–Hg2+–thymine (T–Hg2+–T) coordination chemistry has been designed to detect Hg2+ ions in aqueous solution. In this protocol, two amine-terminated complementary DNA probes with five thymine–thymine (T–T) mismatches were introduced. One was coupled with carboxyl-modified magnetic beads and the other was labeled with tris (2, 2-bipyridine) ruthenium (II) (TBR). The couple of DNA probes, in the presence of Hg2+, can form double-stranded structure via the Hg2+-mediated coordination of T–Hg2+–T base pair. Therefore, they can be collected on the surface of electrode using a magnetic field. On the electrode, TBR labels and tripropylamine (TPA) could react to emit photons, which were detected by a custom-built ECL system. The detection limit for Hg2+ in this assay is 5nM, which is below the upper limit of Hg2+ for drinkable water mandated by United States Environmental Protection Agency (EPA), 10nM. To the best of our knowledge, this is the first example of ECL assay applying to detect Hg2+ with highly sensitivity and selectivity. [ABSTRACT FROM AUTHOR]

We have developed a new fluorescent ensemble probe comprising an ionic conjugate between water-soluble thioglycolic acid (TGA) capped CdTe quantum dots (QDs) and Ru(bpy)2(dppx)2+ for the dual-color detection of complementary double-stranded DNAs (dsDNA). To provide the platform for DNA detection, the Ru-complex was first employed as an effective fluorescence quencher to TGA capped QDs via photoinduced electron transfer process. Because of its strong binding affinity with Ru(bpy)2(dppx)2+, complementary dsDNA can break up the low fluoresced ionic ensemble, set free the luminescent QDs, and concomitantly generate the Ru(bpy)2(dppx)2+ intercalated DNA complex. Thus, the recognition of dsDNA by Ru(bpy)2(dppx)2+ can be realized via both the restoration of QDs fluorescence and the emergence of a new fluorescence emission signal of the quencher-substrate at 609 nm, while single-stranded DNA, ribonucleic acid, bovine albumin serum, and biological relevant metal ions cannot produce the similar results. Therefore, a simple, fast, sensitive, and highly selective assay for dsDNA has been realized. [ABSTRACT FROM AUTHOR]

A highly selective electrogenerated chemiluminescence (ECL) biosensor for the detection of target single-strand DNA (ss-DNA) was developed using hairpin DNA as the recognition element and ruthenium complex as the signal-producing compound. The ECL-based DNA biosensor was fabricated by self-assembling the ECL probe of thiolated hairpin DNA tagged with ruthenium complex on the surface of a gold electrode. In the absence of target ss-DNA, the ECL probe immobilized on the surface of the electrode was in the folded configuration in which its termini were held in close proximity to the electrode, and thus a strong ECL signal could be generated. In the presence of target ss-DNA, a stem-loop of the ECL probe on the electrode was converted into a linear double-helix configuration due to hybridization, resulting in the tag moving away from the electrode surface, which in turn decreased the ECL signal. The ECL intensity of the DNA biosensor generated a "switch off" mode, which decreased with an increase of the concentration of target DNA, and a detection limit of 9 × 10-11 M complementary target ss-DNA was achieved. Single mismatched target ss-DNA was effectively discriminated from complementary target ss-DNA. The effect of different loop lengths of the hairpin DNA on the selectivity of the ECL DNA biosensor has been investigated. This work demonstrated that the sensitivity and specificity of an ECL DNA biosensor could be greatly improved using a hairpin DNA species which has an appropriate stem and loop length as the recognition element. [ABSTRACT FROM AUTHOR]

• The ground-state of the light-switch complex reacts with water. • Hydrogen bonded water affects the photophysics and photochemistry of the complex. • Selective excited states are repulsive to the hydrogen-bonded water molecules and expel water. • Subsequent reaction with bulk water deactivates the excited state and quenches the emission. The photophysics of [Ru(1,10-phenanthroline) 2 (dipyrido[3,2−1:2′,3′-c]phenazine)]2+ and [Ru(1,10-phenanthroline) 2 (dipyrido[3,2−1:2′,3′-c]phenazine)]2+•2H 2 O are investigated by Density Functional and Time-Dependent Density Functional methods. Evidence to support the formation of hydrogen bonds with water in the ground state is presented, and the effects of hydrogen-bonded water on the electronic structure of the complex are described. The excited-state energies were calculated along water-loss reaction coordinates in the ground state and these studies identified specific excited states, with n-to-π* character on both the singlet and triplet hypersurfaces. These are repulsive with respect to the hydrogen-bonding interaction with the phenazine nitrogen atoms. These so-called "drain-pipe" states expel water and proceed to form a "dry" state which is quenched by reaction with bulk water which of course also quenches the luminescence. [ABSTRACT FROM AUTHOR]

Based on electrochemiluminescence resonance energy transfer (ERET) from Ru(bpy) 3 2+ to graphene oxide (GO), a novel label-free solid-state ECL sensor for sensitive detection of DNA was proposed. First, Ru(bpy) 3 2+/AuNPs was successfully prepared by using a simple and green method and characterized by transmission electron microscopy (TEM), Energy Dispersive X-ray (EDX), and UV–vis spectroscopy. Then, the Ru(bpy) 3 2+/AuNPs colloid was assembled on the gold electrode surface for solid-state ECL film which also later could be used to immobilize thiol-derivatized, single-stranded DNA (HS-ssDNA) via Au–S interactions. The stepwise modification procedure was characterized by cyclic voltammetry(CV), electrochemical impedance spectroscopy (EIS), probe approach curves (PAC) and ECL, respectively. The resulting modified electrode was tested as ECL biosensor for DNA detection. Upon addition of GO, the strong noncovalent interaction between HS-ssDNA and GO led to ECL quenching because of ERET. When in the presence of target ssDNA (t-ssDNA), the distance between the HS-ssDNA and GO increased, which significantly hindered the ERET and, thus, resulted in the restoration of ECL. The ECL intensity of the biosensor increased linearly with t-ssDNA concentration in the range of 50–1000pM, and the detection limit is 20pM. To the best of our knowledge, this is the first application of solid-state ERET from Ru(bpy) 3 2+ to GO and opens new opportunities for sensitive detection of biorecognition events. First, Ru(bpy) 3 2+/AuNPs was successfully prepared by using a facile and green method. Then, directly coating the as-prepared colloid on the surface of Au electrode surface produces a solid-state ECL film which later was used to label HS-ssDNA indirectly. Upon addition of GO, due to the strong noncovalent interaction between the HS-ssDNA and GO, the ECL of Ru(bpy) 3 2+ was efficiently quenched because of ERET. In the presence of target ssDNA (t-ssDNA), the binding between the HS-ssDNA and t-ssDNA disturbed the interaction between the HS-ssDNA and GO, the distance between the HS-ssDNA and GO increased, which significantly hindered the ERET and, thus, resulted in the restoration of Ru(bpy) 3 2+ ECL. Image 1 • A novel label-free solid-state ERET platform for detection of DNA was proposed. • A facile and green method to synthetize Ru(bpy) 3 2+/AuNPs was proposed for the first time. • Probe DNA and target DNA both do not require prior labeling. • The method has high quenching efficiency, stablity, and good specificity. [ABSTRACT FROM AUTHOR]

RuII complexes with π‐extended, acridine‐based ancillary ligands display high affinity and selectivity for DNA and RNA quadruplexes along with remarkable light‐up properties that enable them to discriminate quadruplexes from genomic DNA. The in vitro and in cellulo results of the most promising candidates {i.e., [Ru(phen)2(Cl‐dpqp)]Cl2 and [Ru(bpy)2(Br‐dpqp)]Cl2} shown here confirm the interest of this new family of luminophores as invaluable molecular tools to track and visualize G‐quadruplexes in cells. More information can be found in the Communication by C. Moucheron, M.  Demeunynck, D. Monchaud, et al. on page 4967 ff. [ABSTRACT FROM AUTHOR]