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While 8-oxo-7,8-dihydro-2′-deoxyguanosine (dOG) on DNA G-quadruplex (G4) has been studied, the influence of 8-oxo-7,8-dihydro-guanosine (rOG) lesions on telomeric repeat-containing RNA (TERRA) G4 d...

Prokaryotes use repetitive genomic elements termed CRISPR (clustered regularly interspaced short palindromic repeats) to destroy invading genetic molecules. Although CRISPR systems have been widely used in DNA and RNA technology, certain adverse effects do occur. For example, constitutively active CRISPR systems may lead to a certain risk of off-target effects. Here, we introduce post-synthetic masking and chemical activation of guide RNA (gRNA) to controlling CRISPR systems. An RNA structure profiling probe (2-azidomethylnicotinic acid imidazolide) is used. Moreover, we accomplish conditional control of gene editing in live cells. This proof-of-concept study demonstrates promising potential of chemical activation of gRNAs as a versatile tool for chemical biology., Constituitively active CRISPR systems have the risk of adverse off-target effects. Here the authors use chemical masking and activation of gRNA to control activity.

The identification of hydroxylmethyl- and formylpyrimidines in genomic DNA was a landmark event in epigenetics. Numerous laboratories in related fields are investigating the biology of these and other nucleic acid modifications. However, limitations in the ability to detect and synthesize appropriate modifications are an impediment. Herein, we explored a remarkable development in the selective detection of 5-formyluracil in both single-stranded and double-stranded DNA under mild conditions. The “switch-on” specificity towards 5-formyluracil enabled a high signal-to-noise ratio in qualitatively and quantitatively detecting materials containing 5-formyluracil, which is not affected by the presence of abasic sites and 5-formylcytosine, the modified cytosine counterpart of 5-formyluracil. In summary, the innoxiousness, convenience, and cost-efficiency of the 5-formyluracil phosphoramidite synthetic routine would promote the understanding of the epigenetic role of this natural thymidine modification.

Simultaneous fluorogenic switch-on detection and single-base resolution analysis of 5fC through yielding an intramolecular cyclization nucleobase has been presented., 5-Formylcytosine (5fC), which plays an important role in epigenetic functions, has received widespread attention in many related fields. Here, we demonstrate a new design for both the fluorogenic switch-on detection and single-base resolution analysis of 5fC through selectively reacting a reagent with 5fC to yield an intramolecular cyclization nucleobase. The generated product, bearing a similar benzothiazole-iminocoumarin scaffold, is highly fluorescent and enables us to qualitatively and quantitatively detect 5fC moieties in γ-irradiated calf thymus DNA. Additionally, losing the exocyclic 4-amino group in 5fC causes the incorporation of dATP through base pairing with the generated nucleobase during polymerase extension, which helped us to analyze the 5fC sites in both single- and double-stranded oligonucleotides. Our Sanger and Illumina sequencing results show great potential in single-base resolution analysis of 5fC. It is hopeful that a similar design may be used for more detection targets.

Natural nucleic acid bases can form Watson–Crick (WC) or Hoogsteen (HG) base pairs. Importantly, 8-oxo-2′-deoxyguanosine (8-oxo-dG) in DNA or 8-oxo-dG 5′-triphosphate (8-oxo-dGTP) favors a syn conformation because of the steric repulsion between O8 and O4′ of the deoxyribose ring. 8-oxo-dGTP can be incorporated into DNA opposite the templating adenine (A) using HG pairing as the dominant mechanism. Both RNA and DNA can be methylated at the N6 position of A to form N6-methyladenine (m6A). It has been found that certain viral infections may trigger an increase in the production of both 8-oxo-dGTP and m6A. The current study aims to systematically explore the effects of m6A methylation on HG base pairs and the consequent nucleotide incorporation. Our thermodynamic melting study shows that the m6A·8-oxo-dG is significantly less stable than the A·8-oxo-dG base pair in the paired region of a DNA duplex. Moreover, we have used pre-steady-state kinetics to examine the incorporation of 8-oxo-dGTP opposite m6A relative to A by a variety of reverse transcriptase (RT) enzymes and DNA polymerase (DNA pol) enzymes such as the human immunodeficiency virus type 1 (HIV-1) RT and human DNA pol β. The results demonstrate that all of these enzymes incorporate 8-oxo-dGTP less efficiently opposite m6A relative to A. Considering the steric bulk of the purine–purine pair between 8-oxo-dG and A, m6A methylation may affect the HG pairing to a great extent. Hence, it will be unfavorable to incorporate 8-oxo-dGTP into the growing strand opposite m6A. Moreover, the impeded incorporation of 8-oxo-dGTP opposite m6A has been extended to determine m6A at pre-defined positions in human rRNA. Our study may provide new insights into the roles of m6A in reducing the mutagenic potential of cellular 8-oxo-dGTP.

Biotinylated o-phenylenediamine directly tethered to naphthalimide can both enrich and fluorogenically label 5-formyluracil in DNA under physiological conditions., Recently, the detection of natural thymine modified 5-formyluracil has attracted widespread attention. Herein, we introduce a new insight into designing reagents for both the selective biotin enrichment and fluorogenic labelling of 5-formyluracil in DNA. Biotinylated o-phenylenediamine directly tethered to naphthalimide can switch on 5-formyluracil, under physiological conditions, which can then be used in cell imaging after exposure to γ-irradiation. In addition, its labelling property caused the polymerase extension to stop in the 5-formyluracil site, which gave us more information than the fluorescence did itself. The idea of detecting 5-formyluracil might be used in the synthesis of other modified diaminofluoresceins.

In this study, a resorufin derivative RTP-1, which is a novel fluorescent “turn-on” probe for sensitive detection of hydrazine within 30 min, is designed and synthesized. The selective deprotection of the ester group of the probe by hydrazine led to a prominent enhancement of fluorescent intensity, as well as a remarkable color change from colorless to pink, which could be distinguished by naked eye. The fluorescence enhancement showed decent linear relationship with hydrazine concentration ranging from 0 to 50 μmol/L, with a detection limit of 0.84 μmol/L. The specificity of RTP-1 for hydrazine to a number of metal ions, anions and amines is satisfactory. The sensing mechanism of RTP-1 and hydrazine was evaluated by HPLC, ESI mass spectrometry and density functional theory (DFT). Moreover, we have utilized this fluorescent probe for imaging hydrazine in living cells, and the fluorescence was clearly observed when the cells were incubated with hydrazine (100 μmol/L) for 30 min.

Herein, we report two distinct G-quadruplex conformations of the same G-rich oligonucleotide, regulated by a small molecule. This is the first report in which both right- and left-handed G-quadruplex conformations have been obtained from the same sequence. We discriminated these two distinct conformations and investigated their kinetics and thermodynamics.

The ability to detect and quantify microRNA (miRNA) could greatly facilitate the comprehension of miRNA-mediated biological process and related disease in more detail. We developed, for the first time, a convenient and efficient strategy for miRNA detection based on direct molecular recognition between initially quenched DNA probes and miRNA targets. The loop region of dual labeled DNA probe with hairpin shape was complementary to target miRNA, which could induce a corresponding conformational switch, a DNA:RNA hybrid duplex was formed with a single-strand DNA overhang, which could be recognized and degraded by various exonucleases, including Exonuclease I (Exo I) and T4 DNA polymerase. Fluorescence enhancement was generated by the degradation, which occurred in the 3′–5′ direction. This method represented a reliable way to distinguish different miRNAs with high homology, such as different members of the miR-200 family. Furthermore, multiplexed miRNAs detection could be achieved with our developed approach. More importantly, this proposed method can distinguish the expression level of miR-21 in human liver tissues between liver cancer tissues and normal tissues. This exonucleation-based fluorescence enhancement strategy holds great promise for further applications in early miRNA-related disease diagnosis and prognosis.

CRISPR (clustered regularly interspaced short palindromic repeats) systems have been established as valuable genome‐editing tools. Controlling CRISPR systems has high biological significance and this field has garnered intense interest. There is a considerable need for simple approaches with no need for protein engineering. The CRISPR systems usually require a guide RNA (gRNA) moiety to recruit and direct the nuclease complexes. In this respect, the ninhydrin (1,2,3‐indantrione monohydrate) seems to have considerable potential, as yet unexploited, for modifying gRNA. In this study, ninhydrin chemistry is explored for reversible postsynthetic modification of gRNA molecules. It is further shown that ninhydrin chemistry is efficient in modulating two important CRISPR systems. Thus, ninhydrin chemistry exhibits potential applications in future chemical biology studies., In this study, ninhydrin chemistry is explored for reversible modification of guide RNA molecules. It is further shown that ninhydrin chemistry is useful in modulating two important clustered regularly interspaced short palindromic repeats systems. Thus, ninhydrin chemistry exhibits potential applications in future chemical biology studies.

As a left‐handed helical structure, Z‐DNA is biologically active and it may be correlated with transcription and genome stability. Until recently, it remained a significant challenge to control the B/Z‐DNA transition under physiological conditions. The current study represents the first to reversibly control B/Z‐DNA transition using cucurbit[7]uril‐based supramolecular approach. It is demonstrated that cucurbit[7]uril can encapsulate the central butanediamine moiety [HN(CH2)4NH] and reverses Z‐DNA caused by spermine back to B‐DNA. The subsequent treatment with 1‐adamantanamine disassembles the cucurbit[7]uril/spermine complex and readily induces reconversion of B‐ into Z‐DNA. The DNA conformational change is unequivocally demonstrated using different independent methods. Direct evidence for supramolecular interactions involved in DNA conformational changes is further provided. These findings can therefore open a new route to control DNA helical structure in a reversible way.

Methods based on fluorescent “turn-on” sensors have been developed for methylglyoxal (MGO) detection, but the two-photon one is hardly ever reported. In this study, a naphthalimide derivative PDN-1, which is a novel two-photon fluorescent “turn-on” probe for rapid and sensitive detection of methylglyoxal, is designed and synthesized. Under physiological conditions, the probe showed minimal background emission, whereas, after interacting with MGO, it exhibited significant fluorescence enhancement (33-fold) through the inhibition of the photoinduced electron transfer (PET) effect. The fluorescence enhancement showed a decent linear relationship with the MGO concentration ranging from 0 to 10 μM, with a detection limit of 77 nM. The mechanism of the PDN-1–MGO reaction was evaluated by 1H, 13C NMR spectroscopy and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. The specificity of PDN-1 for MGO to other aldehydes, ions, peroxide and nitric oxide is satisfactory. Imaging MGO in living cells by PDN-1 is also accomplished with high sensitivity and low cytotoxicity.

G-triplex has recently been identified as a new secondary structure in G-rich sequences. However, its functions and biological roles remain largely unknown. This study first developed two kinds of Amplex Red oxidases, which were based on relatively new G-triplex structure and a common G-quadruplex one. A collection of DNA binding assays including circular dichroism (CD) spectroscopy, a CD melting assay, and a UV titration study were used to determine the G-triplex structure of G3 oligomer. The low intrinsic oxidative activity of hemin was significantly enhanced using G-triplex or G-quadruplex. Only one key guanine deletion from the G3 oligomer or G4 one could result in a much decreased Amplex Red oxidation activity. To the best of our knowledge, this is the first case reporting direct use of air as the oxidant for fluorescence generation based on DNAzyme strategies. Further mechanism studies demonstrated an involvement of on-site H2O2 generation from O2 and water and a following oxidation of Amplex Red to resorufin, causing a fluorescence enhancement. Furthermore, the newly developed oxidases have been effectively used in microRNA detection, using only one biotin-labeled probe and one small-molecule substrate. The conjugation of a target DNA to the G-triplex- or G-quadruplex-forming sequence enabled one to produce G-triplex or G-quadruplex by endonuclease in the presence of a slight amount of miRNA and amplify the signal of fluorescence from the oxidation of Amplex Red. Our findings of novel Amplex Red oxidases could potentially be used in a wide range of applications.

We have first demonstrated the distinctive effects of three newly reported epigenetic modifications, including 5hmC, 5fC, and 5caC, on B-Z transition of CpG dinucleotide DNAs. We have performed detailed assays and compared their effects. We further studied the regulation of B-Z transition of CpG dinucleotide dodecamers by alternating oxidation and alternating reduction.

To surmount the challenges of the locus determination and accurate quantification of 5-methyl-2'-deoxycytidine ((5Me)dC) in DNA fragments that contain multiple (5Me)dC residues, we designed and synthesized two N-halogeno-N-sodiobenzenesulfonamide reagents that provide a new chemical method for probing (5Me)dC in DNA sequences. When the strategy we provided was combined with β-glucosyltransferase, (5Me)dC could be distinguished from 5-hydroxymethyl-2'-deoxycytidine ((5hm)dC) and deoxycytidine (dC) through the introduction of a glucose moiety to the hydroxyl group of (5hm)dC.

This paper reviews the latest research progress of the nucleic acid probes based on small molecules. The related nucleic acid structures include quadruplex nucleic acids (including G-quadruplex and i-motif), triple-stranded nucleic acid structures, left-handed DNA helix structures, as well as irregular nucleic acid structures (bulge structures and loop structures). The related small molecules includ transition metal complexes, the macrocyclic conjugated compounds, cyclic peptides, and oligosaccharide antibiotics.

The fine control of enzyme activity is essential for the regulation of many important cellular and organismal functions. The light-regulation of proteins serves as an important method for the spatiotemporal control over the production and degradation of an enzyme product. This area is of intense interest for researchers. To the best of our knowledge, the use of small molecules as light-triggered molecular switches to reversibly control enzyme activity at the protein level has not yet been studied. In the present study, we demonstrate the light-controlled reversible regulation of the enzyme using a small-molecule-triggered switch, which is based on molecular recognition between an azobenzene derivative and telomere DNA. This molecule interconverts between the trans and cis states under alternate 365 nm UV and visible light irradiation, which consequently triggers the compaction and extension of telomere DNA. We further provide direct evidence for this structural switch using a circular dichroism study. Furthermore, our strategy has been successfully used to effectively control blood clotting in human plasma.

A series of tetrapyrrolic macrocycles such as porphyrins, phthalocyanines and corroles were found to have inhibitory abilities toward acetylcholinesterase (AChE). Their structure-activity relationship was studied. Several compounds were found to have good inhibitory abilities, which could be developed as potential candidates of acetylcholinesterase (AchE) inhibitors.

A series of cationic porphyrins, and analogues such as cationic corroles and phthalocyanines were found to have biological activities towards topoisomerases I and II in vitro. Cationic porphyrins and phthalocyanines do not induce Topo I-DNA covalent complexes but inhibit topoisomerase I by direct binding to DNA, which limits topoisomerase I access to the DNA substrate. The lowest concentration where an inhibition effect is clearly visible of some derivatives is between 0.1 and 0.6 microM. Furthermore, some complexes were found to inhibit the activity of the topoisomerase II.

Beta-octabromo- meso-tetra(4-carboxyl)phenyl porphyrin 6 and beta-octaphenyl- meso-tetra(4-carboxyl)phenyl porphyrin 8 were synthesized and fully characterized by (1)H NMR, UV, and HRMS. Their cytotoxicities to tumor cells were tested using MTT assays. One kind of tumor cell apoptosis induced by these anionic porphyrins under irradiation was examined by flow cytometric analysis. The inhibition of Topo I (Topoisomerase I) indicates that Topo I preferentially binds to the synthesized compounds, thus blocking the interaction between Topo I and DNA. The results implied that compounds 4, 6, and 8 are potential inhibitors to Topo I, which might be one of the important factors inducing apoptosis of tumor cells.

A label-free and biocompatible pH sensor system based on the aggregation-caused quenching (ACQ) probe has been reported herein. The DNA i-motif, a kind of pH-triggered structure, affects the aggregation of PTCDI derivatives by structural switch that would provide significant fluorescence signals responding to the different pH values. Our method not only shows sensitive and reversible response to pH changes, but also could expand the detection range by allosteric control of the DNA i-motif.

Here, we have provided novel insights into the effects of 8-oxodG substitutions on B–Z transitions of CpG dinucleotide DNAs. A combination of different techniques including a CD study, a PAGE analysis, DFT calculations and molecular modeling has been collectively used.

Existence of G-quadruplex DNA in vivo always attract widespread interest in the field of biology and biological chemistry. We reported our findings for the existence of G-quadruplex structures in promoter region of oncogenes confirmed by G-quadruplex DNA cross-linking strategy. Probes for selective G-quadruplex cross-linking was designed and synthesized that show high selectivity for G-quadruplex cross-linking. Further biological studies demonstrated its good inhibition activity against murine melanoma cells. To further investigate if G-quadruplex DNA was formed in vivo and as the target, a derivative was synthesized and pull-down process toward chromosome DNAs combined with circular dichroism and high throughput deep sequencing were performed. Several simulated intracellular conditions, including X. laevis oocytes, Ficoll 70 and PEG, was used to investigate the compound's pure cross-linking ability upon preformed G-quadruplex. Thus, as a potent G-quadruplex cross-linking agent, our strategy provided both valuable evidence of G-quadruplex structures in vivo and intense potential in anti-cancer therapy.

Multidrug-resistant Mycobacterium tuberculosis is resistant to two first-line antituberculosis drugs, isoniazid and rifampin, resulting in the relapse of tuberculosis. M. tuberculosis grows very slowly, and thus traditional examination methods take time to test its drug resistance and cannot meet clinical needs. The use of a DNA probe makes it possible to test rifampin resistance. We developed an asymmetrical split-assembly DNA peroxidase assay to detect drug-resistant mutation of rifampin-resistant M. tuberculosis in the rpoB gene rapidly and visibly. A new strategy was also designed to eliminate the adverse effects caused by the complicated secondary structure of the target DNA and to improve the efficiency of the probes. This detection system consists of five group detections, covers rifampin-resistant determination region of the rpoB gene, and tests 40 kinds of mutations, including the most common mutations at codons 531 and 526. Every group detection or individual mutant allele detection can distinguish corresponding mutant DNA sequences from the wild-type DNA sequences.

The analysis of DNA methylation and MTase (methyltransferase) activity is important in epigenetic study. We have developed a novel strategy for sensitive analysis of MTase activity based on a hairpin shaped DNAzyme; 8–17 DNAzyme amplicon has been adopted and found to be very effective in such analysis.

On target: We have developed two cascade amplification strategies that combine duplex specific nuclease (DSN) amplicon with either G-quadruplex-based DNA peroxidase or 8-17 DNAzyme amplicon for miRNA detection. In this way, sensitive and convenient detection of miRNAs was achieved. In the DNA peroxidase-based system, a visual color change could be observed in the presence of target miRNAs (see scheme).

In an attempt to combine the HIV-inhibitory capacity of different 2',3'-dideoxynucleoside (ddN) analogs, we have designed and synthesized several dimers of [AZT]-[AZT] and [AZT]-[d4T]. In addition, we also synthesized the dimers of 1-(1H-benzimidazol-1-yl)-1-deoxy-beta-D-ribofuranose. The in vitro anti-HIV activity of these compounds on a pseudotype virus, pNL4-3.Luc.R-E-, in the 293T cells has been determined. Among these compounds, 2,2'-(propane-1,3-diyl)bis[1-(beta-D-ribofuranosyl)-1H-benzimidazole] showed the highest anti-HIV activity with similar effect as AZT.

Three water soluble anthraquinone derivatives were designed and synthesized employing click chemistry to prepare novel and potent antitumor drugs. An MTT assay indicated that all compounds had significant inhibitory activity against BGC gastric cancer cells in vitro. Apoptosis induced by these compounds was observed by flow cytometry and laser confocal microscopy. Mechanistic analysis showed that these compounds induced the generation of several reactive oxygen species, the loss of mitochondrial membrane potential (Δψm), the transition of mitochondrial permeability, and the release of cytochrome C from the mitochondrion to cytoplasm. These results suggest that the anthraquinones might be potential lead compounds for the cancer chemotherapy.

Three water soluble anthraquinone derivatives were designed and synthesized employing click chemistry to prepare novel and potent antitumor drugs. An MTT assay indicated that all compounds had significant inhibitory activity against BGC gastric cancer cells in vitro. Apoptosis induced by these compounds was observed by flow cytometry and laser confocal microscopy. Mechanistic analysis showed that these compounds induced the generation of several reactive oxygen species, the loss of mitochondrial membrane potential (Delta psi m), the transition of mitochondrial permeability, and the release of cytochrome C from the mitochondrion to cytoplasm. These results suggest that the anthraquinones might be potential lead compounds for the cancer chemotherapy.

This study is the first to investigate the interactions of hemin with a G-triplex DNA of T1 using different DNA binding assays. The low intrinsic peroxidatic activity of hemin could be significantly enhanced using T1. Furthermore, much decreased oxidation enhancement by T2 or T3 with one key guanine mutation was observed, and the observed peroxidatic activity of T1 should be directly due to the G-triplex complexed with hemin.

Two new bis(benzimidazole)aryl derivatives have been prepared and one of them has been shown to induce and stabilize formation of a G-quadruplex.