•A water-soluble bis-porphyrin-based fluorescent Cu2+-sensing platform was developed.•The platform was much sensitive than mono-porphyrin-based one.•The platform was demonstrated to work well under organic solvent-free conditions.•The platform could achieve sensitive Cu2+ quantitation with a detection limit of 8.8 nM.•The platform was demonstrated to work well for practical water samples.A water-soluble, cationic bis-porphyrin (Bis-TMPipEOPP) was synthesized, characterized, and its optical properties were investigated. Its fluorescence was found to be specifically quenched by paramagnetic Cu2+ ions via a static quenching mechanism. Based on these findings, an organic solvent-free sensing platform was developed for the “turn-off” detection of Cu2+. Such a platform could achieve sensitive Cu2+ quantitation at a detection limit of 8.8 nM. Compared to its monomeric counterpart TMPipEOPP, Bis-TMPipEOPP exhibited a higher tendency to self-aggregate due to the synergy between the two porphine rings. This characteristics conferred the proposed Bis-TMPipEOPP-based Cu2+-sensing platform with a sensitive fluorescent response to low concentrations of Cu2+ in a linear detection range of between 10 nM and 300 nM. However, the TMPipEOPP-based method provided observable changes in the fluorescent signal only at Cu2+ concentrations >200 nM. These results potentially offer a method for improving the performance of fluorescent-dye-based Cu2+ sensors.

•A water-soluble porphyrin was designed, synthesized and used for optical probing of G-quadruplex.•This porphyrin combines the advantages of tworeported cationic porphyrins.•The porphyrin can probe G-quadruplex with high specificity in a wide pH range 5.0–7.5.•Ratiometric signal output might confer G-quadruplex recognition with high accuracy and reliability.•This work paves a way to design G-quadruplex probes suitable for different pH conditions.A new water-soluble cationic porphyrin derivative m-TMPyEOPP (5,10,15,20-tetrakis{4-[2-(O-(N-methylpyridyl)ethoxyl]oxyphenly}porphyrin) has been designed, synthesized, and fully characterized. This porphyrin derivative combines the advantages of two cationic porphyrins used in G-quadruplex recognition and stabilization studies, i.e., the widely investigated G-quadruplex ligand TMPyP4 and TMPipEOPP reported by us. That is to say, the presence of four bulky side-arm substituents endows the m-TMPyEOPP derivative with the capacity for colorimetric and fluorescence-based recognition of G-quadruplexes with high specificity. By virtue of almost negligible pH-dependent self-aggregation, and hence reduced single- and double-stranded DNA-templated aggregation behavior, it can also work well under acidic conditions. By combining the fluorescence signals obtained at different excitation wavelengths (690 or 260 nm), specific G-quadruplex recognition can be achieved by m-TMPyEOPP in the pH range 5.0–7.5, which almost covers the physiological pH range. Ratiometric signal output mode might confer G-quadruplex recognition with high accuracy, reliability and repeatability. This work demonstrates that the aggregation behaviours of water-soluble cationic porphyrins can be controlled by adjusting the nature of the substituents on their side arms, thus endowing them with different G-quadruplex-specific recognition abilities suitable for different pH conditions.

Photodynamic therapy (PDT) has attracted increasing interest as a promising and non-invasive method for cancer treatment. Double-stranded DNA (dsDNA) is one of the potential bio-targets in PDT, and a PDT drug that could photocleave telomeric G-quadruplex might efficiently kill tumor cells by shortening the telomere length. Herein, a water soluble cationic porphyrin derivative 5,10,15,20-tetra-{4-[2-(1-methyl-1-piperidinyl)ethoxy]phenyl} porphyrin (TMPipEOPP) was demonstrated to be a promising PDT agent. It shows no DNA damage ability in the dark, but efficiently cleaves both double-stranded plasmid DNA and telomeric G-quadruplex DNA under irradiation by producing reactive oxygen species 1O2. However, since TMPipEOPP has much higher binding affinity to G-quadruplex than to dsDNA, it can preferentially bind to and specifically photocleave telomeric G-quadruplex in the presence of dsDNA with identical nucleotide concentrations, thus suggesting that it might be used as a human telomere-targeted photosensitizer for PDT of tumors. Correspondingly, almost no cytotoxicity is observed for TMPipEOPP in the dark, but efficient PDT-induced apoptosis is shown towards human colon carcinoma cells (HCT-8).

A water soluble cationic porphyrin derivative 5,10,15,20-tetra-{4-[3-(1-methyl-1-piperidinyl) propoxy]phenyl}porphyrin (TMPipPrOPP), which showed attractive pH-dependent optical responses to G-quadruplexes, was synthesized and characterized. Under molecular crowding conditions, a stable TMPipPrOPP/G-quadruplex complex was formed in acidic pH range. Alkalization of the system to neutral and basic pH caused destruction of the complex due to reduced electrostatic interactions. The formation and destruction of the TMPipPrOPP/G-quadruplex complex was reversibly adjusted by pH, accompanied by repeated on-off switching of the colorimetric and fluorescent responses of TMPipPrOPP to G-quadruplexes. In comparison, no optical responses were observed for single-stranded, duplex and i-motif DNAs in the tested pH range (5.0–8.5). Besides highlighting the importance of designing novel drugs targeting G-quadruplexes in specific genome regions, this work may also provide a useful tool for G-quadruplex-based biosensing and nanomachine construction. One example is the design of colorimetric and fluorescent sensors for ratiometric pH-sensing. The proposed sensing platform can be used not only for highly sensitive pH-sensing in a narrow biological pH range, but also for pH detection in a broad range. Another example is the construction of DNA-based dual-output all-optical molecular logic gates that can perform basic AND, NAND, OR, NOR, INHIBIT and IMPLICATION logic operations.A water soluble cationic porphyrin derivative, which showed highly specific and pH-dependent colorimetric and fluorescent responses to G-quadruplexes under molecular crowding conditions, was synthesized and characterized. Such optical responses can be switched on-off repeatedly by pH stimuli. Besides highlighting the importance of designing novel drugs targeting G-quadruplexes in specific genome regions, this finding may also provide a useful tool for G-quadruplex-based biosensing and nanomachine construction. As examples, colorimetric and fluorescent sensors for ratiometric pH-sensing were designed and DNA-based dual-output all-optical molecular logic gates that can perform several basic logic operations were constructed.

G-rich sequences that might form G-quadruplexes are common in some regions of the human genome. Most of these G-rich sequences are embedded in flanking duplex-forming sequences and coexist with complementary C-rich sequences. Therefore, the competition between G-quadruplexes and the duplex structures in flanking duplex DNAs must be considered in the corresponding G-quadruplex studies. Based on the high specificity of a porphyrin derivative (TMPipEOPP) for G-quadruplexes over duplexes and single-stranded DNAs, a simple method was developed for studying the competition between G-quadruplexes and duplexes in flanking duplex structures. In the presence of a complementary sequence, the core G-rich region of a long DNA sequence tended to form a duplex under dilute conditions and form a G-quadruplex under molecular crowding conditions. The method could also be used to monitor conversion between G-quadruplexes and duplexes in real time. Under dilute conditions, G-rich sequences rapidly hybridized with complementary strands to form stable duplexes that did not disassociate with time. If the G-rich sequences have been folded into G-quadruplexes, addition of a complementary sequence promoted slow conversion from G-quadruplexes to duplexes. However, under molecular crowding conditions, stable G-quadruplexes formed regardless of the presence of complementary sequences and the formed G-quadruplexes did not disassociate with time. Changing solution conditions from dilute to molecular crowding promoted rapid structural conversion of G-rich sequences from duplexes to G-quadruplexes. This method could be an important tool for G-quadruplex studies.

A mononuclear macrocyclic complex NiIIL3a (L3a = dianion of 2,3-dioxo-5,6:13,14-dibenzo-9,10-cyclohexyl-7,12-bis(methoxycarbonyl)-1,4,8,11-tetraazacyclotetradeca-7,11-diene), which shows high DNA cleavage activity in the presence of H2O2, was reported in our previous work. Considering that many systems for natural enzyme-mediated DNA cleavage contain two or more metal active sites, two new trinuclear complexes [Cu(NiL3a)2(dca)2]·2CH3OH (abbreviated as Cu(NiL3a)2) and [Ag(NiL3a)2(NO3)]·2CH3OH·0.5H2O (abbreviated as Ag(NiL3a)2) were synthesized in this work, where dca is the dicyanamide. The complexes were structurally characterized by single crystal X-ray analysis. The central Cu(II) or Ag(I) atom is linked to two [NiL3a] ligands by oxamido bridges forming a trinuclear structure. In Cu(NiL3a)2, the central Cu(II) ion is in an octahedral coordination geometry. Whereas in Ag(NiL3a)2, the central Ag(I) ion is in a rarely reported trigonal-prismatic coordination geometry. The DNA cleavage behavior of the complexes in the presence of H2O2 was studied in detail. Comparing with the NiL3a, the trinuclear complex Ag(NiL3a)2 nearly has no ability to cleave DNA, whereas Cu(NiL3a)2 is a much better DNA cleavage agent. Cu(NiL3a)2 can efficiently convert supercoiled DNA to nicked DNA with a rate constant of 0.074 ± 0.002 min−1 when 40 μM Cu(NiL3a)2 and 0.6 mM H2O2 are used. The cleavage mechanism between the complex Cu(NiL3a)2 and plasmid DNA is likely to involve singlet oxygen as reactive oxygen species. Circular dichroism (CD) and fluorescence spectroscopy indicate that both Cu(NiL3a)2 and NiL3a bind to DNA by a groove binding mode, and the binding between Cu(NiL3a)2 and DNA is much stronger than that between NiL3a and DNA. The present results may provide some information for the design of efficient multinuclear artificial nucleases.Graphical abstractTwo new trinuclear complexes ([Cu(NiL3a)2(dca)2]·2CH3OH and [Ag(NiL3a)2(NO3)]·2CH3OH·0.5H2O) have been synthesized and structurally characterized. Ag(I) ion is in a rarely reported trigonal-prismatic coordination geometry. Compared with the mononuclear precursor NiL3a, the Ag(I) complex nearly has no ability to cleave DNA, whereas the Cu(II) complex is a much better DNA cleavage agent in the presence of H2O2. Circular dichroism and fluorescence spectroscopy indicate the Cu(II) complex bind to DNA by a groove binding mode.Highlights► Cu(NiL3a)2 and Ag(NiL3a)2 heterometallic complexes as synthetic nucleases. ► Ag(I) ion in a rarely reported trigonal-prismatic coordination geometry. ► Cu(NiL3a)2 shows obviously higher DNA cleavage activity than NiL3a. ► Kinetics of DNA cleavage by Cu(NiL3a)2 in the present H2O2 was studied. ► Cu(NiL3a)2 binds to DNA by a groove binding mode.

Nickel is considered a weak carcinogen. Some researches have shown that bound proteins or synthetic ligands may increase the toxic effect of nickel ions. A systematic study of ligand effects on the interaction between nickel complexes and DNA is necessary. Here, we compared the interactions between DNA and six closely related Schiff base tetraazamacrocyclic oxamido nickel(II) complexes NiL1−3a,1−3b. The structure of one of the six complexes, NiL3b has been characterized by single crystal X-ray analysis. All of the complexes can cleave plasmid DNA under physiological conditions in the presence of H2O2. NiL3b shows the highest DNA cleavage activity. It can convert supercoiled DNA to nicked DNA then linear DNA in a sequential manner as the complex concentration or reaction time is increased. The cleavage reaction is a typical pseudo-first-order consecutive reaction with the rate constants of 3.27 ± 0.14 h−1 (k1) and 0.0966 ± 0.0042 h−1 (k2), respectively, when a complex concentration of 0.6 mM is used. The cleavage mechanism between the complex and plasmid DNA is likely to involve hydroxyl radicals as reactive oxygen species. Circular dichronism (CD), fluorescence spectroscopy and gel electrophoresis indicate that the complexes bind to DNA by partial intercalative and groove binding modes, but these binding interactions are not the dominant factor in determining the DNA cleavage abilities of the complexes.

•A simple and sensitive DNA methyltransferase (MTase)-sensing method was reported.•High sensitivity is achieved by using a multiple primers-like RCA strategy.•The use of G-quadruplex probe provides a label-free and highly specific mode.•The proposed method can work well in high throughput real-time RCA mode.•The method can also be used for MTase inhibitor screening and evaluation.Sensitive and reliable detection of DNA methyltransferase (MTase) is of great significance for both early tumor diagnosis and therapy. In this study, a simple, label-free and sensitive DNA MTase-sensing method was developed on the basis of a nicking endonuclease-mediated multiple primers-like rolling circle amplification (RCA) strategy. In this method, a dumbbell RCA template was prepared by blunt-end ligation of two molecules of hairpin DNA. In addition to the primer-binding sequence, the dumbbell template contained another three important parts: 5′-CCGG-3′ sequences in double-stranded stems, nicking endonuclease recognition sites and C-rich sequences in single-stranded loops. The introduction of 5′-CCGG-3′ sequences allows the dumbbell template to be destroyed by the restriction endonuclease, HpaII, but is not destroyed in the presence of the target MTase—M.SssI MTase. The introduction of nicking endonuclease recognition sites makes the M.SssI MTase-protected dumbbell template-mediated RCA proceed in a multiple primers-like exponential mode, thus providing the RCA with high amplification efficiency. The introduction of C-rich sequences may promote the folding of amplification products into a G-quadruplex structure, which is specifically recognized by the commercially available fluorescent probe thioflavin T. Improved RCA amplification efficiency and specific fluorescent recognition of RCA products provide the M.SssI MTase-sensing platform with high sensitivity. When a dumbbell template containing four nicking endonuclease sites is used, highly specific M.SssI MTase activity detection can be achieved in the range of 0.008–50 U/mL with a detection limit as low as 0.0011 U/mL. Simple experimental operation and mix-and-detection fluorescent sensing mode ensures that M.SssI MTase quantitation works well in a real-time RCA mode, thus further simplifying the sensing performance and making high throughput detection possible. The proposed MTase-sensing strategy was also demonstrated to be applicable for screening and evaluating the inhibitory activity of MTase inhibitors.

G-rich sequences that might form G-quadruplexes are common in some regions of the human genome. Most of these G-rich sequences are embedded in flanking duplex-forming sequences and coexist with complementary C-rich sequences. Therefore, the competition between G-quadruplexes and the duplex structures in flanking duplex DNAs must be considered in the corresponding G-quadruplex studies. Based on the high specificity of a porphyrin derivative (TMPipEOPP) for G-quadruplexes over duplexes and single-stranded DNAs, a simple method was developed for studying the competition between G-quadruplexes and duplexes in flanking duplex structures. In the presence of a complementary sequence, the core G-rich region of a long DNA sequence tended to form a duplex under dilute conditions and form a G-quadruplex under molecular crowding conditions. The method could also be used to monitor conversion between G-quadruplexes and duplexes in real time. Under dilute conditions, G-rich sequences rapidly hybridized with complementary strands to form stable duplexes that did not disassociate with time. If the G-rich sequences have been folded into G-quadruplexes, addition of a complementary sequence promoted slow conversion from G-quadruplexes to duplexes. However, under molecular crowding conditions, stable G-quadruplexes formed regardless of the presence of complementary sequences and the formed G-quadruplexes did not disassociate with time. Changing solution conditions from dilute to molecular crowding promoted rapid structural conversion of G-rich sequences from duplexes to G-quadruplexes. This method could be an important tool for G-quadruplex studies.