FTO demethylates internal N6-methyladenosine (m6A) and N6,2′-O-dimethyladenosine (m6Am; at the cap +1 position) in mRNA, m6A and m6Am in snRNA, and N1-methyladenosine (m1A) in tRNA in vivo, and in vitro evidence supports that it can also demethylate N6-methyldeoxyadenosine (6mA), 3-methylthymine (3mT), and 3-methyluracil (m3U). However, it remains unclear how FTO variously recognizes and catalyzes these diverse substrates. Here we demonstrate—in vitro and in vivo—that FTO has extensive demethylation enzymatic activity on both internal m6A and cap m6Am. Considering that 6mA, m6A, and m6Am all share the same nucleobase, we present a crystal structure of human FTO bound to 6mA-modified ssDNA, revealing the molecular basis of the catalytic demethylation of FTO toward multiple RNA substrates. We discovered that (i) N6-methyladenine is the most favorable nucleobase substrate of FTO, (ii) FTO displays the same demethylation activity toward internal m6A and m6Am in the same RNA sequence, suggesting that the substrate specificity of FTO primarily results from the interaction of residues in the catalytic pocket with the nucleobase (rather than the ribose ring), and (iii) the sequence and the tertiary structure of RNA can affect the catalytic activity of FTO. Our findings provide a structural basis for understanding the catalytic mechanism through which FTO demethylates its multiple substrates and pave the way forward for the structure-guided design of selective chemicals for functional studies and potential therapeutic applications.

A coumarin-based fluorescence chemoprobe was developed and evaluated for the selective and sensitive detection of hydrogen sulfide in degassed PBS buffers and fetal bovine serum. Fluorescence detection of hydrogen sulfide in living cells was also successfully achieved using two-photon confocal fluorescence imaging. Further in situ visualization of endogenous H(2)S was realized in cardiac tissues of normal rats and atherosclerosis (AS) rats.

We report the synthesis, characterization, and in vivo application of light-activated, negatively charged peptide nucleic acids (caged ncPNAs) for down-regulating gene expression during zebrafish embryonic development. The 18-mer ncPNAs were attached to a short complementary 2‘-OMe RNA sense strand (sRNA) via a heterobifunctional photocleavable linker (PL). Caged ncPNAs were designed to target chordin and bozozok mRNA. Modest UV irradiation cleaved the photoactive linker, which yielded the less stable ncPNA/sRNA duplex (ΔT m ∼ −20 °C for chordin and −41 °C for bozozok). These caged ncPNAs were microinjected into zebrafish (Danio rerio) embryos at the one- or two-cell stage. The conjugate was nontoxic, and most embryos showed no phenotypic response at 24 h post fertilization (24 hpf), which indicated low background activity. Embryos that were photoactivated at 2 or 3 hpf developed phenotypic abnormalities typical of embryos with loss of function of the chordin or bozozok gene. Phenotypic results were further confirmed by in situ hybridization experiments using molecular markers. Caged ncPNAs provide a promising “on → off” switch for down-regulating gene expression with high spatiotemporal control in biological systems.

Gene-based therapy is one of essential therapeutic strategies for precision medicine through targeting specific genes in specific cells of target tissues. However, there still exist many problems that need to be solved, such as safety, stability, selectivity, delivery, as well as immunity. Currently, the key challenges of gene-based therapy for clinical potential applications are the safe and effective nucleic acid drugs as well as their safe and efficient gene delivery systems. In this review, we first focus on current nucleic acid drugs and their formulation in clinical trials and on the market, including antisense oligonucleotide, siRNA, aptamer, and plasmid nucleic acid drugs. Subsequently, we summarize different chemical modifications of nucleic acid drugs as well as their delivery systems for gene-based therapeutics in vivo based on nucleic acid chemistry and nanotechnology methods.

Nitrogen-rich quantum dots (N-dots) were serendipitously synthesized in methanol or aqueous solution at a reaction temperature as low as 50 °C. These N-dots have a small size (less than 10 nm) and contain a high percentage of the element nitrogen, and are thus a new member of quantum-dot family. These N-dots show unique and distinct photoluminescence properties with an increasing percentage of nitrogen compared to the neighboring carbon dots. The photoluminescence behavior was adjusted from blue to green simply through variation of the reaction temperature. Furthermore, the detailed mechanism of N-dot formation was also proposed with the trapped intermediate. These N-dots have also shown promising applications as fluorescent ink and biocompatible staining in C. elegans.