DNA-based nanostructures for RNA delivery.

RNA-based therapeutics have emerged as a promising approach for the treatment of various diseases, including cancer, genetic disorders, and infectious diseases. However, the delivery of RNA molecules into target cells has been a major challenge due to their susceptibility to degradation and inefficient cellular uptake. To overcome these hurdles, DNA-based nano technology offers an unprecedented opportunity as a potential delivery platform for RNA therapeutics. Due to its excellent characteristics such as programmability and biocompatibility, these DNA-based nanostructures, composed of DNA molecules assembled into precise and programmable structures, have garnered significant attention as ideal building materials for protecting and delivering RNA payloads to the desired cellular destinations. In this review, we highlight the current progress in the design and application of three DNA-based nanostructures: DNA origami, lipid-nanoparticle (LNP) technology related to frame guided assembly (FGA), and DNA hydrogel for the delivery of RNA molecules. Their biomedical applications are briefly discussed and the challenges and future perspectives in this field are also highlighted.

Genome-wide profiling of 5-hydroxymethylcytosines in circulating cell-free DNA reveals population-specific pathways in the development of multiple myeloma.

Multiple myeloma (MM) and its precursors monoclonal gammopathy of undetermined significance (MGUS) and smoldering myeloma (SMM) are 2-3 times more common in African Americans (AA) than European Americans (EA). Although epigenetic changes are well recognized in the context of myeloma cell biology, the contribution of 5-hydroxymethylcytosines (5hmC) to racial disparities in MM is unknown. Using the 5hmC-Seal and next-generation sequencing, we profiled genome-wide 5hmC in circulating cell-free DNA (cfDNA) from 342 newly diagnosed patients with MM (n = 294), SMM (n = 18), and MGUS (n = 30). We compared differential 5hmC modifications between MM and its precursors among 227 EA and 115 AA patients. The captured 5hmC modifications in cfDNA were found to be enriched in B-cell and T-cell-derived histone modifications marking enhancers. Of the top 500 gene bodies with differential 5hmC levels between MM and SMM/MGUS, the majority (94.8%) were distinct between EA and AA and enriched with population-specific pathways, including amino acid metabolism in AA and mainly cancer-related signaling pathways in EA. These findings improved our understanding of the epigenetic contribution to racial disparities in MM and suggest epigenetic pathways that could be exploited as novel preventive strategies in high-risk populations.

m6A RNA modifications are measured at single-base resolution across the mammalian transcriptome.

Functional studies of the RNA N6-methyladenosine (m6A) modification have been limited by an inability to map individual m6A-modified sites in whole transcriptomes. To enable such studies, here, we introduce m6A-selective allyl chemical labeling and sequencing (m6A-SAC-seq), a method for quantitative, whole-transcriptome mapping of m6A at single-nucleotide resolution. The method requires only ~30 ng of poly(A) or rRNA-depleted RNA. We mapped m6A modification stoichiometries in RNA from cell lines and during in vitro monocytopoiesis from human hematopoietic stem and progenitor cells (HSPCs). We identified numerous cell-state-specific m6A sites whose methylation status was highly dynamic during cell differentiation. We observed changes of m6A stoichiometry as well as expression levels of transcripts encoding or regulated by key transcriptional factors (TFs) critical for HSPC differentiation. m6A-SAC-seq is a quantitative method to dissect the dynamics and functional roles of m6A sites in diverse biological processes using limited input RNA.

Discovery of Potent and Novel Quinazolinone Sulfide Inhibitors with Anti-ToCV Activity.

A series of novel quinazolinone sulfide derivatives containing a dithioacetal moiety were designed and synthesized using Tomato chlorosis virus coat protein (ToCVCP) as a potential drug target, and the inhibitory effect of ToCV was systematically evaluated in vitro and in vivo. The experimental results showed that most of the compounds presented a strong affinity. Notably, the binding abilities of compounds D8 and D16 to ToCVCP both reached a micromolar level, which were 0.19 and 0.83 µM, respectively. The relative expression level of ToCVCP gene was detected using real-time quantitative polymerase chain reaction in Nicotiana benthamiana. Compounds D8 and D16 significantly reduced the relative expression level of ToCVCP gene by 93.34 and 83.47%, respectively, which were better than those of conventional antiviral agents. This study lays a good foundation for the structural design and modification of quinazolinone sulfide derivatives as anti-ToCV drugs.

N6-methyldeoxyadenosine directs nucleosome positioning in Tetrahymena DNA.

BACKGROUND: N6-methyldeoxyadenosine (6mA or m6dA) was shown more than 40 years ago in simple eukaryotes. Recent studies revealed the presence of 6mA in more prevalent eukaryotes, even in vertebrates. However, functional characterizations have been limited. RESULTS: We use Tetrahymena thermophila as a model organism to examine the effects of 6mA on nucleosome positioning. Independent methods reveal the enrichment of 6mA near and after transcription start sites with a periodic pattern and anti-correlation relationship with the positions of nucleosomes. The distribution pattern can be recapitulated by in vitro nucleosome assembly on native Tetrahymena genomic DNA but not on DNA without 6mA. Model DNA containing artificially installed 6mA resists nucleosome assembling compared to unmodified DNA in vitro. Computational simulation indicates that 6mA increases dsDNA rigidity, which disfavors nucleosome wrapping. Knockout of a potential 6mA methyltransferase leads to a transcriptome-wide change of gene expression. CONCLUSIONS: These findings uncover a mechanism by which DNA 6mA assists to shape the nucleosome positioning and potentially affects gene expression.

Synthesis and investigation of the antibacterial activity and action mechanism of 1,3,4-oxadiazole thioether derivatives.

Various 1,3,4-oxadiazole thioether derivatives containing 2-chloro-5-methylene pyridine, 2-chloro-5-methylene thiazole, 3,4-dimethoxy-2-methylene pyridine, and N,N-dimethyl-2-ethylamino moieties were designed, synthesized, and assessed for their antibacterial activities against Xanthomonas oryzae pv. oryzae (Xoo) via the turbidimeter test in vitro. Preliminary bioassay results confirmed good antibacterial activities for most of these compounds. Among these substances, compound 6r showed the best inhibitory effect against Xoo, and its half-maximal effective concentration (EC50) value is 4.78µg/mL, which is superior to that of commercial agent bismerthiazol (87.55µg/mL). We then performed a label-free quantitative proteomic analysis of the response of Xoo to 6r. A total of 1363 proteins were identified in the control and treatment groups. Upon treatment with the minimum inhibitory concentration, 349 proteins were found to be differentially expressed (fold changes>1.5, p<0.05), enriched, and may be involved in purine metabolism.

Binding constants of Southern rice black-streaked dwarf virus Coat Protein with ferulic acid derivatives.

The data present binding constants between ferulic acid derivatives and the Coat Protein (P10) by fluorescence titration in this article, which is hosted in the research article entitled "Interaction Research on an Antiviral Molecule that Targets the Coat Protein of Southern rice black-streaked dwarf virus'' (Ran et al., 2017) [1]. The data include fluorescence quenching spectrum, Stern-Volmer quenching constants, and binding parameters. In this article, a more comprehensive data interpretation and analysis is explained.

Interaction research on an antiviral molecule that targets the coat protein of southern rice black-streaked dwarf virus.

Southern rice black-streaked dwarf virus (SRBSDV) coat protein (P10) is the key protein required for viral transmission and host plant infection and is thus a promising target for anti-SRBSDV agent screening. In this study, P10 was obtained from Escherichia coli through cloning, expression, and purification. The antiviral agent Ningnanmycin was selected as control, and a series of antiviral compounds based on the structural scaffold of ferulic acid were analyzed. Size-exclusion chromatography analysis results showed that compound F27 can alter the aggregation of P10 proteins. Furthermore, fluorescence titration and microscale thermophoresis assay results indicated that F27 binds to P10 with KA of 5.75×105M-1 and KD of 7.81µM. The ligand- and receptor-based three-dimensional quantitative structure-activity analyses were performed to determine the requirements for the interaction between the carboxyl structures and P10s. On the basis of the obtained models and information, we provided insights regarding the design and optimization of novel molecules as anti-SRBSDV agents.

Binding interactions between enantiomeric α-aminophosphonate derivatives and tobacco mosaic virus coat protein.

Tobacco mosaic virus (TMV) is an important plant virus that can cause considerable crop loss. Our group synthesized a series of enantiomeric α-aminophosphonate derivatives with high anti-TMV activities. The activity of (R)-diphenyl-1-(4-methylbenzothiazole-2-amino)-1-(thiphene-2-yl)-methylphosphonate (Q-R) was found to be superior to that of (S)-diphenyl-1-(4-methyl benzothiazole-2-amino)-1-(thiphene-2-yl)-methylphosphonate (Q-S). However, the mechanism for inhibition of the R-isomer (Q-R) of infection activity is not clear. Thus, we studied the interactions between Q-R and Q-S and TMV by using TMV coat proteins (CP) as a potential target for fluorescence spectroscopy, isothermal titration calorimetry, microscale thermophoresis, and molecular docking. Arg90 was found to play a major role in the interaction of Q-R with TMV CP, as demonstrated by the interaction experiments and the results of molecular modeling. The substitution of arginine with glycine resulted in a mutant that was significantly less sensitive to Q-R. These results indicate that Q-R undermines the structural stability of the TMV R90G virus particle by binding with Arg90, eventually leading to the loss of the virus' ability for infection.