Locating, tracing and sequencing multiple expanded genetic letters in complex DNA context via a bridge-base approach.

A panel of unnatural base pairs is developed to expand genetic alphabets. One or more unnatural base pairs (UBPs) can be inserted to enlarge the capacity, diversity, and functionality of canonical DNA, so monitoring the multiple-UBPs-containing DNA by simple and convenient approaches is essential. Herein, we report a bridge-base approach to repurpose the capability of determining TPT3-NaM UBPs. The success of this approach depends on the design of isoTAT that can simultaneously pair with NaM and G as a bridge base, as well as the discovering of the transformation of NaM to A in absence of its complementary base. TPT3-NaM can be transferred to C-G or A-T by simple PCR assays with high read-through ratios and low sequence-dependent properties, permitting for the first time to dually locate the multiple sites of TPT3-NaM pairs. Then we show the unprecedented capacity of this approach to trace accurate changes and retention ratios of multiple TPT3-NaM UPBs during in vivo replications. In addition, the method can also be applied to identify multiple-site DNA lesions, transferring TPT3-NaM makers to different natural bases. Taken together, our work presents the first general and convenient approach capable of locating, tracing, and sequencing site- and number-unlimited TPT3-NaM pairs.

Peripheral substitution effects on unnatural base pairs: A case of brominated TPT3 to enhance replication fidelity.

The high fidelity poses a central role in developing unnatural base pairs (UBPs), which means the high pairing capacity of unnatural bases with their partners, and low mispairing with all the natural bases. Different strategies have been used to develop higher-fidelity UBPs, including optimizing hydrophobic interaction forces between UBPs. Variant substituent groups are allowed to fine tune the hydrophobic forces of different UBPs' candidates. However, the modifications on the skeleton of TPT3 base are rare and the replication fidelity of TPT3-NaM remains hardly to improve so far. In this paper, we reasoned that modifying and/or expanding the aromatic surface by Bromo-substituents to slightly increase hydrophobicity of TPT3 might offer a way to increase the fidelity of this pair. Based on the hypothesis, we synthesized the bromine substituted TPT3, 2-bromo-TPT3 and 2, 4-dibromo-TPT3 as the new TPT3 analogs. While the enzyme reaction kinetic experiments showed that d2-bromo-TPT3-dNaM pair and d2, 4-dibromo-TPT3TP-dNaM pair had slightly less efficient incorporation and extension rates than that of dTPT3-dNaM pair, the assays did reveal that the mispairing of 2-bromo-TPT3 and 2, 4-dibromo-TPT3 with all the natural bases could dramatically decrease in contrast to TPT3. Their lower mispairing capacity promoted us to run polymerase chain amplification reactions, and a higher fidelity of d2-bromo-TPT3-dNaM pair could be obtained with 99.72 ± 0.01% of the in vitro replication fidelity than that of dTPT3-dNaM pair, 99.52 ± 0.09%. In addition, d2-bromo-TPT3-dNaM can also be effectively copied in E. coli cells, which showed the same replication fidelity as that of dTPT3-dNaM in the specific sequence, but a higher fidelity in the random sequence context.

Amplification, Enrichment, and Sequencing of Mutagenic Methylated DNA Adduct through Specifically Pairing with Unnatural Nucleobases.

3-Methylthymine (m3T) is a long-known chemically stable but strongly mutagenic DNA base adduct; however, the sequencing method to determine m3T is lacking so far. Two of the main obstacles include the capacity of m3T to stall DNA elongation and its low abundance. To address the challenges, we report an unnatural base pairing strategy in this paper. A new m3T-TPT3 base pair was developed with a Vmax/Km value 82-fold higher than that of the m3T-A pair. The TPT3 nucleobase can be specifically incorporated opposite the m3T base, and the resulting m3T-TPT3 base pair can be effectively extended to give full-length products in the presence of commercial DNA polymerases. Importantly, the feature of the m3T-TPT3 pair enables a replacement PCR amplification to transfer m3T lesions at the exact positions into unnatural base pairs, which permits Sanger sequencings as well as biotin-streptavidin-based enrichments of m3T lesions. Taken together, this work offers a simple, convenient, and practical method for amplification, enrichment, and sequencing of m3T for the first time.

Mechanistic Insight into the Photoinduced Damage of an Unnatural Base Pair.

Chemical- and photostability of unnatural base pairs (UBPs) are important to maintain the genetic code integrity, and critical for developing healthy semisynthetic organisms. As reported, dTPT3 was less stable upon irradiation, and thus might act as a pervasive photosensitizer to induce oxidative damage within DNA, causing harm to living semi-synthetic organisms when exposed to UVA radiation. However, there was no knowledge about molecular-level understanding of this damage process. In this paper, we not only identified four photoproducts of dTPT3, including desulfur-dTPT3 (dTPT3H ), TPT3 sulphinate (TPT3SO2 ), TPT3 sulphonate (TPT3SO3 ) and TPT3-thioTPT3 (TPT3S TPT3), but also established a Type II photosensitized oxidation mechanism. In addition, the antioxidant (sodium ascorbate) was able to effectively inhibit the photoproducts formation of dTPT3 and dTPT3 in DNA, suggesting that a reductive environment might protect DNA bearing dTPT3 against UVA oxidation and ameliorate its adverse biological effects. The comprehensive understanding of TPT3' photochemical stability will give researchers helpful guidance to design more photostable UBPs and construct healthier semisynthetic organisms.

Light-Responsive, Reversible Emulsification and Demulsification of Oil-in-Water Pickering Emulsions for Catalysis.

Pickering emulsions are an excellent platform for interfacial catalysis. However, developing simple and efficient strategies to achieve product separation and catalyst and emulsifier recovery is still a challenge. Herein, we report the reversible transition between emulsification and demulsification of a light-responsive Pickering emulsion, triggered by alternating between UV and visible light irradiation. The Pickering emulsion is fabricated from Pd-supported silica nanoparticles, azobenzene ionic liquid surfactant, n-octane, and water. This phase behavior is attributed to the adsorption of azobenzene ionic liquid surfactant on the surface of the nanoparticles and the light-responsive activity of ionic liquid surfactant. The Pickering emulsion can be used as a microreactor that enables catalytic reaction, product separation as well as emulsifier and catalyst recycling. Catalytic hydrogenation of unsaturated hydrocarbons at room temperature and atmospheric pressure has been performed in this system to demonstrate product separation and emulsifier and catalyst re-use.

Medium Rings Bearing Bitriazolyls: Easily Accessible Structures with Superior Performance as Cu Catalyst Ligands.

Benefiting from their unique properties, the development of structurally novel and easily accessible medium rings is of significant interest in the pharmaceutical industry and academic research. However, synthetic access to medium-ring scaffolds is very difficult due to their rigid skeleton and large-angle strains. In this paper, a new class of medium rings bearing bitriazolyls (MRBTs) was designed, synthesized, identified as a promising new skeleton ligand for the Cu(I)-catalyzed click reaction, and used in site-special modification of protein. One of the MRBTs, 3aa, exhibited a turnover number (TON) as high as 55 000 and dramatic accelerating effects ( kobs = 1.95 M-1 s-1) and ranked among the most efficient ligands for copper-catalyzed alkyne and azide cycloaddition. Unlike the difficult access to other known medium rings, these 7-12-membered MRBTs can be prepared in straightforward, one-step manner from structurally diverse linear terminal diynes and azides. The unique accessibility and intriguing properties therefore imply their broad application perspectives.

Multicomponent Aqueous Synthesis of Iodo-1,2,3-triazoles: Single-Step Models for Dual Modification of Free Peptide and Radioactive Iodo Labeling.

Iodo-1,2,3-triazoles are of considerable interest for chemical and biomedical applications. However, current synthetic methods for preparing iodo-1,2,3-triazoles cannot easily be applied to the direct modification of bioactive molecules in water. Through the combination of water-compatible oxidative iodination and the copper-catalyzed alkyne-azide cycloaddition reaction, a novel copper-catalyzed aqueous multicomponent synthetic method for the preparation of 5-iodo-1,2,3-triazoles has been developed. The method is highly effective and selective for substrates including biologically relevant compounds with nucleoside, sugar, and amino acid moieties. Based on this aqueous tandem reaction, a direct single-step multicomponent dual modification of peptide is developed from readily available starting materials. Furthermore, the method could also be applied to concise and fast multicomponent radioactive 125 I labeling from an aqueous solution of commercially available sodium 125 iodide as a starting material.

Tuning the Hydrophilicity and Hydrophobicity of the Respective Cation and Anion: Reversible Phase Transfer of Ionic Liquids.

The separation and recycling of catalyst and cocatalyst from the products and solvents are of critical importance. In this work, a class of functionalized ionic liquids (ILs) were designed and synthesized, and by tuning the hydrophilicity and hydrophobicity of cation and anion, respectively, these ILs could reversibly transfer between water and organics triggered upon undergoing a temperature change. From a combination of multiple spectroscopic techniques, it was shown that the driving force behind the transfer was originated from a change in conformation of the PEG chain of the IL upon temperature variation. By utilizing the novel property of this class of ILs, a highly efficient and controllable CuI-catalyzed cycloaddition reaction was achieved wherein the IL was used to entrain, activate, and recycle the catalyst, as well as to control the reaction.

Solvent-Driven Room-Temperature Curtius Rearrangements to Access Nucleotides Bearing Substituted Fused Pyridones.

The intramolecular Curtius rearrangement suffers from a high reaction temperature, low yields, tedious product isolation, and difficult scale up. This study presents a room-temperature Curtius rearrangement that can be novelly driven by the HFIP solvent, followed by light-illuminated intramolecular cyclization. Such a mild reaction allows for the preparation of various fused pyridone derivatives with diverse substituent groups that have rarely been incorporated by previous methods. The roles of HFIP and light are investigated by a set of control experiments through a combination of IR and NMR titration. Furthermore, using the substituted fused pyridones as unnatural bases, we can obtain a panel of new nucleotides.

Recognition and Sequencing of Mutagenic DNA Adduct at Single-Base Resolution Through Unnatural Base Pair.

DNA lesions are linked to cancer, aging, and various diseases. The recognition and sequencing of special DNA lesions are of great interest but highly challenging. In this paper, an unnatural-base-pair-promoting method for sequencing highly mutagenic ethenodeoxycytidine (εC) DNA lesions that occurred frequently is developed. First, a promising unnatural base pair of dεC-dNaM to recognize εC lesions is identified, and then a conversion PCR is developed to site-precise transfer dεC-dNaM to dTPT3-dNaM for convenient Sanger sequencing. The low sequence dependence of this method and its capacity for the enrichment of dεC in the abundance of as low as 1.6 × 10-6 nucleotides is also validated. Importantly, the current method can be smoothly applied for recognition, amplification, enrichment, and sequencing of the real biological samples in which εC lesions are generated in vitro or in vivo, thus offering the first sequencing methodology of εC lesions at single-base resolution. Owing to its simple operations and no destruction of inherent structures of DNA, the unnatural-base-pair strategy may provide a new platform to produce general tools for the sequencing of DNA lesions that are hardly sequenced by traditional strategies.

A copper(I)-catalyzed three-component domino process: assembly of complex 1,2,3-triazolyl-5-phosphonates from azides, alkynes, and H-phosphates.

Three is better than one! A new copper-catalyzed tricomponent reaction of a terminal alkyne, organic azide, and H-phosphate (CuAA[P]C) leads to a structurally diverse polysubstituted 1,2,3-triazolyl-5-phosphonate, which provides an efficient tool for the direct introduction of phosphonic acid groups by a "click reaction".

Designing a Light-Induced Glycosylation Reaction for Poststage Synthesis of ADP-2″-Deoxyribosyl Derivatives.

Modifications on the hydroxyl groups of ADP-ribosyl units can provide valuable tools for investigating ADP-ribosylation-related molecular interactions, but the chemical syntheses of these compounds are usually difficult due to their inherent complex structures. In this study, we report a poststage synthetic protocol for accessing novel ADP-2″-deoxyribosyl derivatives through designing a light-induced biomimetic reaction, and SPR assays revealed effective binding of ADP-2″-deoxyribosyl peptides to MacroH2A1.1 with a high affinity (KD = 3.75 × 10-6 M).

Access to Photostability-Enhanced Unnatural Base Pairs via Local Structural Modifications.

Completing the storage and retrieval of increased genetic information in vivo and producing therapeutic proteins have been achieved by the unnatural base pair dNaM-dTPT3. Up to now, some biological and chemical approaches are implemented to improve the semi-synthetic organism (SSO). However, the photosensitivity of this pair, suggested as a potential threat to the healthy growth of cells, is still a problem to solve. Hence, we designed and synthesized a panel of TPT3 analogues with the basic structural skeletons of TPT3 but modified thiophene rings at variant sites to improve the photostability of unnatural base pairs. A comprehensive screening strategy, including photosensitivity tests, kinetic experiments, and replication in vitro by PCR and in vivo by amplification, was implemented. A new pair, dNaM-dTAT1, which had almost equally high efficiency and fidelity with the dNaM-dTPT3 pair itself both in vivo and in vitro, was proven to be more photostable and thermostable and less toxic to E. coli cells. The discovery of dNaM-dTAT1 represents our first progress for the optimization of this type of bases toward more photostable properties; our data also suggest that less photosensitive unnatural base pairs will be beneficial to build a healthier cellular replication system.

Site-specific unnatural base excision via visible light.

Base excision (BE) is an important yet hard-to-control biological event. Unnatural base pairs are powerful tools to revolutionize biological studies in various areas. In this paper, we report a visible-light-induced method to construct site-specific unnatural BE and show the influence of its regulation on transcription and translation levels.

Copper-catalyzed in situ oxidative-coupling for one-pot synthesis of 5-aryl-1,4-disubstituted 1,2,3-triazoles under mild conditions.

A new reaction system with CuCl as catalyst, TEA as base and O2/chloramine-T as oxidant was developed for one-pot in situ oxidative-coupling to synthesize 5-aryl-1,4-disubstituted 1,2,3-triazoles in this paper. A variety of 5-arylated-1,2,3-triazole compounds could be efficiently prepared directly from the readily accessible organic azides, terminal alkynes and arylboronic acids. Advantages of the method include use of low-cost catalyst, clean oxidant, less-toxic additive, and low reaction temperature. Importantly, due to avoiding harsh strong basic reagents and high temperatures, the presented method can offer mild conditions for multi-component synthesis of 5-aryl-1,2,3-triazoles from the designed structurally complicated alkynyl or azide donors bearing natural product motifs and sensitive functional groups.

Biocompatible ionic liquid [Betaine][H2PO4] as a reusable catalyst for the substitution of xanthen-9-ol under solvent-free conditions.

An ionic liquid, namely [Betaine][H2PO4], was found to be an efficient catalyst for the direct substitution reaction of xanthen-9-ol with different nucleophiles under solvent-free conditions. This catalytic system is easy to be operated and the following work-up procedure is simple, with the ionic liquid catalyst reusable for at least five cycles at a high catalytic activity level. In addition, the ionic liquid is easy to prepare and its raw materials are inexpensive and have good biocompatibility. Therefore, our study presents an intriguing and sustainable protocol for the direct substitution of alcohol.

An efficient and easily-accessible ligand for Cu(I)-catalyzed azide-alkyne cycloaddition bioconjugation.

A novel ligand (6) for copper-catalyzed azide-alkyne cycloaddition (CuAAC) in bioconjugation has been developed. Both in vitro and in vivo experiments indicate that 6 is more efficient and less cytotoxic than the canonical CuAAC ligands. Besides, 6 is easily accessible and can be prepared at gram scale. Our study reveals that 6 might be an ideal CuAAC ligand for bioconjugations.

Biomimetic α-selective ribosylation enables two-step modular synthesis of biologically important ADP-ribosylated peptides.

The α-type ADP-ribosylated peptides represent a class of important molecular tools in the field of protein ADP-ribosylation, however, they are difficult to access because of their inherent complicated structures and the lack of effective synthetic tools. In this paper, we present a biomimetic α-selective ribosylation reaction to synthesize a key intermediate, α-ADP-ribosyl azide, directly from native ß-nicotinamide adenine dinucleotide in a clean ionic liquid system. This reaction in tandem with click chemistry then offers a two-step modular synthesis of α-ADP-ribosylated peptides. These syntheses can be performed open air in eppendorf tubes, without the need for specialized instruments or training. Importantly, we demonstrate that the synthesized α-ADP-ribosylated peptides show high binding affinity and desirable stability for enriching protein partners, and reactivity in post-stage poly ADP-ribosylations. Owing to their simple chemistry and multidimensional bio-applications, the presented methods may provide a powerful platform to produce general molecular tools for the study of protein ADP-ribosylation.

Effect of pressure on the selectivity for the esterification of ethylene glycol with propionic acid in supercritical CO2.

The esterification of ethylene glycol with propionic acid was investigated in supercritical CO2 at 50.0 degrees C. The effect of pressure on equilibrium conversion and selectivity of ethylene glycol monopropionate (monoester) and ethylene glycol dipropinonate (diester) was studied systematically. It was shown that the equilibrium conversion and selectivity was nearly independent of pressure as pressure was lower than 9 MPa. At higher pressure, however, the yield and selectivity of the diester increased considerably, while those of the monoester decreased with increasing pressure. The main reason was that reactants and products distributed between the vapor phase and liquid phase at higher pressures. The solvent power of CO2 for the diester is stronger than that for the monoester. More diester molecules in the liquid phase were extracted into the vapor at higher pressures, which shifted equilibrium of the consecutive reversible reactions.

A convenient preparation of 5-iodo-1,4-disubstituted-1,2,3-triazole: multicomponent one-pot reaction of azide and alkyne mediated by CuI-NBS.

The system of CuI and NBS was found to provide both I (+) and Cu (+) for the first time. An efficient method for preparation of 5-iodo-1,4-disubstituted-1,2,3-triazole was achieved by multicomponent one-pot reaction of azides with alkynes in the presence of the novel CuI and NBS catalytic system. The high tolerance of various sensitive groups revealed the potential applications of this method in organic synthesis and drug discovery.