Origin of iodine preferential attack at sulfur in phosphorothioate and subsequent P-O or P-S bond dissociation

2',4'-LNA-Functionalized 5'-S-Phosphorothioester CDNs as STING Agonists

Cyclic dinucleotides (CDNs) have garnered popularity over the last decade as immunotherapeutic agents, which activate the cyclic GMP-AMP synthase-stimulator of interferon genes (cGAS-STING) pathway to trigger an immune response. Many analogs of 2'3'-cGAMP, c-di-GMP, and c-di-AMP have been developed and shown as effective cancer vaccines and immunomodulators for the induction of both the adaptive and innate immune systems. Unfortunately, the effectiveness of these CDNs is limited by their chemical and enzymatic instability. We recently introduced 5'-endo-phosphorothoiate 2'3'-cGAMP analogs as potent STING agonist with improved resistance to cleavage by clinically relevant phosphodiesterases. We herein report the synthesis of locked nucleic acid-functionalized (LNA) endo-S-CDNs and evaluate their ability to activate STING in THP1 monocytes. Interestingly, some of our synthesized LNA 3'3'-endo-S-CDNs can moderately activate hSTING REF haplotype (R232H), which exhibit diminished response to both 2'3'-cGAMP and ADU-S100. Also, we show that one of our most potent endo-S-CDNs has remarkable chemical (oxidants I2 and H2O2) and phosphodiesterase stability.

PT-seq: A method for metagenomic analysis of phosphorothioate epigenetics in complex microbial communities

Among dozens of known epigenetic marks, naturally occurring phosphorothioate (PT) DNA modifications are unique in replacing a non-bridging phosphate oxygen with redox-active sulfur and function in prokaryotic restriction-modification and transcriptional regulation. Interest in PTs has grown due to the widespread distribution of the dnd, ssp, and brx genes among bacteria and archaea, as well as the discovery of PTs in 5-10% of gut microbes. Efforts to map PTs in complex microbiomes using existing next-generation and direct sequencing technologies have failed due to poor sensitivity. Here we developed PT-seq as a high-sensitivity method to quantitatively map PTs across genomes and metagenomically identify PT-containing microbes in complex genomic mixtures. Like other methods for mapping PTs in individual genomes, PT-seq exploits targeted DNA strand cleavage at PTs by iodine, followed by sequencing library construction using ligation or template switching approaches. However, PT-specific sequencing reads are dramatically increased by adding steps to heat denature the DNA, block pre-existing 3'-ends, fragment DNA after T-tailing, and enrich iodine-induced breaks using biotin-labeling and streptavidin beads capture. Iterative optimization of the sensitivity and specificity of PT-seq is demonstrated with individual bacteria and human fecal DNA.

Development of PCR primers enabling the design of flexible sticky ends for efficient concatenation of long DNA fragments

We developed chemically modified PCR primers that allow the design of flexible sticky ends by introducing a photo-cleavable group at the phosphate moiety. Nucleic acid derivatives containing o-nitrobenzyl photo-cleavable groups with a tert-butyl group at the benzyl position were stable during strong base treatment for oligonucleotide synthesis and thermal cycling in PCR reactions. PCR using primers incorporating these nucleic acid derivatives confirmed that chain extension reactions completely stopped at position 1 before and after the site of the photo-cleavable group was introduced. DNA fragments of 2 and 3 kbp, with sticky ends of 50 bases, were successfully concatenated with a high yield of 77%. A plasmid was constructed using this method. Finally, we applied this approach to construct a 48.5 kbp lambda phage DNA, which is difficult to achieve using restriction enzyme-based methods. After 7 days, we were able to confirm the generation of DNA of the desired length. Although the efficiency is yet to be improved, the chemically modified PCR primer offers potential to complement enzymatic methods and serve as a DNA concatenation technique.

Nonaqueous Oxidation in DNA Microarray Synthesis Improves the Oligonucleotide Quality and Preserves Surface Integrity on Gold and Indium Tin Oxide Substrates

Nucleic acids attached to electrically conductive surfaces are very frequently used platforms for sensing and analyte detection as well as for imaging. Synthesizing DNA on these uncommon substrates and preserving the conductive layer is challenging as this coating tends to be damaged by the repeated use of iodine and water, which is the standard oxidizing medium following phosphoramidite coupling. Here, we thoroughly investigate the use of camphorsulfonyl oxaziridine (CSO), a nonaqueous alternative to I2/H2O, for the synthesis of DNA microarrays in situ. We find that CSO performs equally well in producing high hybridization signals on glass microscope slides, and CSO also protects the conductive layer on gold and indium tin oxide (ITO)-coated slides. DNA synthesis on conductive substrates with CSO oxidation yields microarrays of quality approaching that of conventional glass with intact physicochemical properties.

Structural analysis of PLD3 reveals insights into the mechanism of lysosomal 5' exonuclease-mediated nucleic acid degradation

The phospholipase D (PLD) family is comprised of enzymes bearing phospholipase activity towards lipids or endo- and exonuclease activity towards nucleic acids. PLD3 is synthesized as a type II transmembrane protein and proteolytically cleaved in lysosomes, yielding a soluble active form. The deficiency of PLD3 leads to the slowed degradation of nucleic acids in lysosomes and chronic activation of nucleic acid-specific intracellular toll-like receptors. While the mechanism of PLD phospholipase activity has been extensively characterized, not much is known about how PLDs bind and hydrolyze nucleic acids. Here, we determined the high-resolution crystal structure of the luminal N-glycosylated domain of human PLD3 in its apo- and single-stranded DNA-bound forms. PLD3 has a typical phospholipase fold and forms homodimers with two independent catalytic centers via a newly identified dimerization interface. The structure of PLD3 in complex with an ssDNA-derived thymidine product in the catalytic center provides insights into the substrate binding mode of nucleic acids in the PLD family. Our structural data suggest a mechanism for substrate binding and nuclease activity in the PLD family and provide the structural basis to design immunomodulatory drugs targeting PLD3.

High-Molecular-Weight and Light-Colored Disulfide-Bond-Embedded Polyesters: Accelerated Hydrolysis Triggered by Redox Responsiveness

Disulfide bonds have attracted considerable attention due to their reduction responsiveness, but it is crucial and challenging to prepare disulfide-bond-based polyesters by melt polycondensation. Herein, the inherently poor thermal stability of the S-S bond in melting polycondensation was overcome. Moreover, poly(butylene succinate-co-dithiodipropionate) (PBSDi) with a light color and high molecular weights (Mn values up to 84.7 kg/mol) was obtained. These polyesters can be applied via melt processing with Td,5% > 318 °C. PBSDi10-PBSDi40 shows good crystallizability (crystallinity 56-38%) and compact lamellar thickness (2.9-3.2 nm). Compared with commercial poly(butylene adipate-co-terephthalate) (PBAT), the elevated mechanical and barrier performances of PBSDi make them better packaging materials. For the degradation behavior, the disulfide monomer obviously accelerates the enzyme degradation but has a weaker effect on hydrolysis. In 0.1 mol/L or higher concentrations of H2O2 solutions, the oxidation of disulfide bonds to sulfoxide and sulfone groups can be realized. This process results in a stronger nucleophilic attack, as confirmed by the Fukui function and DFT calculations. Additionally, the greater polarity and hydrophilicity of oxidation products, proved by noncovalent interaction analysis, accelerate the hydrolysis of polyesters. Moreover, glutathione-responsive breakage, from polymers to oligomers, is confirmed by an accelerated decline in molecular weight. Our research offers fresh perspectives on the effective synthesis of the disulfide polyester and lays a solid basis for the creation of high-performance biodegradable polyesters that degrade on demand.

Biobased Biodegradable Copolyesters from 2,5-Thiophenedicarboxylic Acid: Effect of Aliphatic Diols on Barrier Properties and Degradation

The demand for sustainable development has led to increasing attention in biobased polyesters due to their adjustable thermal and mechanical properties and biodegradability. In this study, we used a novel bioderived aromatic diacid, 2,5-thiophenedicarboxylic acid (TDCA) to synthesize a list of novel aromatic-aliphatic poly(alkylene adipate-co-thiophenedicarboxylate) (PAATh) copolyesters through a facile melt polycondensation method. PAAThs are random copolyesters with weight-average molecular weights of 58400 to 84200 g·mol-1 and intrinsic viscosities of 0.80 to 1.27 dL·g-1. All PAAThs exhibit sufficiently high thermal stability as well as the highest tensile strength of 6.2 MPa and the best gas barrier performances against CO2 and O2, 4.3- and 3.3-fold better than those of poly(butylene adipate-co-terephthalate) (PBAT). The biodegradability of PAAThs was fully evaluated through a degradation experiment and various experimental parameters, including residue weights, surface morphology, and molecular compositions. The state-of-the-art molecular dynamics (MD) simulations were applied to elucidate the different enzymatic degradation behaviors of PAAThs due to the effect of diols with different chain structures. The sterically hindered carbonyl carbon of the PHATh-enzyme complex was more susceptible to nucleophilic attack and exhibited a higher tendency to enter a prereaction state. This study has introduced a group of novel biobased copolyesters with their structure-property relationships investigated thoroughly, and the effect of diol components on the enzymatic degradation was revealed by computational analysis. These findings may lay the foundation for the development of promising substitutes for commercial biodegradable polyesters and shed light on their complicated degradation mechanisms.

Understanding base and backbone contributions of phosphorothioate DNA for molecular recognition with SBD proteins

Bacterial DNA phosphorothioate (PT) modification provides a specific anchoring site for sulfur-binding proteins (SBDs). Besides, their recognition patterns include phosphate links and bases neighboring the PT-modified site, thereby bringing about genome sequence-dependent properties in PT-related epigenetics. Here, we analyze the contributions of the DNA backbone (phosphates and deoxyribose) and bases bound with two SBD proteins in Streptomyces pristinaespiralis and coelicolor (SBDSco and SBDSpr). The chalcogen-hydrophobic interactions remained constantly at the anchoring site while the adjacent bases formed conditional and distinctive non-covalent interactions. More importantly, SBD/PT-DNA interactions were not limited within the traditional "4-bp core" range from 5'-I to 3'-III but extended to upstream 5'-II and 5'-III bases and even 5''-I to 5''-III at the non-PT-modified complementary strand. From the epigenetic viewpoint, bases 3'-II, 5''-I, and 5''-III of SBDSpr and 3'-II, 5''-II, and 5''-III of SBDSco present remarkable differentiations in the molecular recognitions. From the protein viewpoint, H102 in SBDSpr and R191 in SBDSco contribute significantly while proline residues at the PT-bound site are strictly conserved for the PT-chalcogen bond. The mutual and make-up mutations are proposed to alter the SBD/PT-DNA recognition pattern, besides additional chiral phosphorothioate modifications on phosphates 5'-II, 5'-II, 3'-I, and 3'-II.

Dual-Target Electrochemical Sensor Based on 3D MoS2-rGO and Aptamer Functionalized Probes for Simultaneous Detection of Mycotoxins

A dual-target aptamer functionalized probes (DTAFP) was applied for the detection of aflatoxin B1 (AFB1) and zearalenone (ZEN) simultaneously, which has not been reported. Meanwhile, two functional materials for signal amplification of the DTAFP were synthesized: 1) a three-dimensional molybdenum disulfide-reduced graphene oxide (MoS₂-rGO) as a favorable loading interface; 2) a double-probes gold nanoparticles (AuNPs) modified by Thionin (Thi) and 6-(Ferrocenyl) hexanethiol (FC6S) as distinguishable and non-interfering signals. Mycotoxins on the electrode surface release into solution under the function of the DTAFP, leading a reduction of the differential peak impulse in signal response. Under the optimum conditions, the aptasensor exhibited a detection range of 1.0 pg mL⁻¹–100 ng mL⁻¹ for AFB1 and ZEN, with no observable cross reactivity. In addition, the aptasensor performed excellent stability, reproducibility, specificity, and favorable recovery in the detection of edible oil. This work demonstrated a novel method for the construction of a simple, rapid, and sensitive aptasensor in the detection of multiple mycotoxins simultaneously.