Universal labeling of 5'-triphosphate RNAs by artificial RNA ligase enzyme with broad substrate specificity

Nature-inspired engineering of an artificial ligase enzyme by domain fusion

The function of most proteins is accomplished through the interplay of two or more protein domains and fine-tuned by natural evolution. In contrast, artificial enzymes have often been engineered from a single domain scaffold and frequently have lower catalytic activity than natural enzymes. We previously generated an artificial enzyme that catalyzed an RNA ligation by >2 million-fold but was likely limited in its activity by low substrate affinity. Inspired by nature's concept of domain fusion, we fused the artificial enzyme to a series of protein domains known to bind nucleic acids with the goal of improving its catalytic activity. The effect of the fused domains on catalytic activity varied greatly, yielding severalfold increases but also reductions caused by domains that previously enhanced nucleic acid binding in other protein engineering projects. The combination of the two better performing binding domains improved the activity of the parental ligase by more than an order of magnitude. These results demonstrate for the first time that nature's successful evolutionary mechanism of domain fusion can also improve an unevolved primordial-like protein whose structure and function had just been created in the test tube. The generation of multi-domain proteins might therefore be an ancient evolutionary process.

Construction of robust bienzyme-mimicking nanocatalysts for dye degradation by self-assembly of hematin, metal ions, and nucleotides

The growing proportion of the textile industry has led to an increase in the concentration of colored dyes in aquatic systems.

De novo proteins from random sequences through in vitro evolution

Natural proteins are the result of billions of years of evolution. The earliest predecessors of today's proteins are believed to have emerged from random polypeptides. While we have no means to determine how this process exactly happened, there is great interest in understanding how it reasonably could have happened. We are reviewing how researchers have utilized in vitro selection and molecular evolution methods to investigate plausible scenarios for the emergence of early functional proteins. The studies range from analyzing general properties and structural features of unevolved random polypeptides to isolating de novo proteins with specific functions from synthetic randomized sequence libraries or generating novel proteins by combining evolution with rational design. While the results are exciting, more work is needed to fully unravel the mechanisms that seeded protein-dominated biology.

Extensive libraries of gene truncation variants generated by in vitro transposition

The detailed analysis of the impact of deletions on proteins or nucleic acids can reveal important functional regions and lead to variants with improved macromolecular properties. We present a method to generate large libraries of mutants with deletions of varying length that are randomly distributed throughout a given gene. This technique facilitates the identification of crucial sequence regions in nucleic acids or proteins. The approach utilizes in vitro transposition to generate 5΄ and 3΄ fragment sub-libraries of a given gene, which are then randomly recombined to yield a final library comprising both terminal and internal deletions. The method is easy to implement and can generate libraries in three to four days. We used this approach to produce a library of >9000 random deletion mutants of an artificial RNA ligase enzyme representing 32% of all possible deletions. The quality of the library was assessed by next-generation sequencing and detailed bioinformatics analysis. Finally, we subjected this library to in vitro selection and obtained fully functional variants with deletions of up to 18 amino acids of the parental enzyme that had been 95 amino acids in length.

A biomimetic enzyme modified electrode for H2O2 highly sensitive detection

An efficient catalyst based on artificial bionic peroxidase was synthesized for electrocatalysis. A poly(ethyleneimine)/Au nanoparticle composite (PEI-AuNP) was prepared and it was then linked to hemin via a coupling reaction between carboxyl groups in hemin and amino groups in PEI without the activation of a carboxyl group by carbodiimide. Fourier transform infrared (FTIR) spectroscopy verified the formation of amido bonds within the structure. The presence of AuNPs contributed greatly in establishing the amido bonds within the composite. Transmission electron microscopy (TEM) and UV-visible spectroscopy were also used to characterize the PEI-AuNP-hemin catalyst. PEI-AuNP-hemin exhibited intrinsic peroxidase-like catalytic activities. The PEI-AuNP-hemin deposited on a glass carbon electrode had strong sensing for H2O2 with a well-defined linear relationship between the amperometric response and H2O2 concentration in the range from 1 μM to 0.25 mM. The detection limit was 0.247 nM with a high sensitivity of 0.347 mA mM(-1) cm(-2). The peroxidase-like catalytic activity of PEI-AuNP-hemin is discussed in relation to its microstructure. The study suggests that PEI-AuNP-hemin may have promising application prospects in biocatalysis and bioelectronics.

Proximal disruptor aided ligation (ProDAL) of kilobase-long RNAs

RNA with site-specific modification is a useful tool for RNA biology studies. However, generating kilobase (kb) -long RNA with internal modification at a site distant from RNA termini remains challenging. Here we report an enhanced splint ligation technique, proximal disruptor aided ligation (ProDAL), which allows adequate efficiency toward this purpose. The key to our approach is using multiple DNA oligonucleotides, 'proximal disruptors', to target the RNA substrate sequence next to the ligation site. The binding of disruptors helps to free the ligation site from intramolecular RNA basepairing, and consequently promotes more efficient formation of the pre-ligation complex and a higher overall ligation yield. We used naturally occurring 1.0 kb renilla and 1.9 kb firefly luciferase mRNA sequences to test the efficacy of our approach. ProDAL yielded 9-14% efficiency for the ligation between two RNA substrates, both of which were between 414 and 1313 nucleotides (nt) long. ProDAL also allowed similarly high efficiency for generating kb-long RNA with site-specific internal modification by a simple three-part ligation between two long RNA substrates and a modification-carrying RNA oligonucleotide. In comparison, classical splint ligation yielded a significantly lower efficiency of 0-2% in all cases. We expect that ProDAL will benefit studies involving kb-long RNAs, including translation, long non-coding RNAs, RNA splicing and modification, and large ribonucleoprotein complexes.

Efficient Automated Solid-Phase Synthesis of DNA and RNA 5'-Triphosphates

A fast, high-yielding and reliable method for the synthesis of DNA- and RNA 5'-triphosphates is reported. After synthesizing DNA or RNA oligonucleotides by automated oligonucleotide synthesis, 5-chloro-saligenyl-N,N-diisopropylphosphoramidite was coupled to the 5'-end. Oxidation of the formed 5'-phosphite using the same oxidizing reagent used in standard oligonucleotide synthesis led to 5'-cycloSal-oligonucleotides. Reaction of the support-bonded 5'-cycloSal-oligonucleotide with pyrophosphate yielded the corresponding 5'-triphosphates. The 5'-triphosphorylated DNA and RNA oligonucleotides were obtained after cleavage from the support in high purity and excellent yields. The whole reaction sequence was adapted to be used on a standard oligonucleotide synthesizer.

Thermostable artificial enzyme isolated by in vitro selection

Artificial enzymes hold the potential to catalyze valuable reactions not observed in nature. One approach to build artificial enzymes introduces mutations into an existing protein scaffold to enable a new catalytic activity. This process commonly results in a simultaneous reduction of protein stability as an undesired side effect. While protein stability can be increased through techniques like directed evolution, care needs to be taken that added stability, conversely, does not sacrifice the desired activity of the enzyme. Ideally, enzymatic activity and protein stability are engineered simultaneously to ensure that stable enzymes with the desired catalytic properties are isolated. Here, we present the use of the in vitro selection technique mRNA display to isolate enzymes with improved stability and activity in a single step. Starting with a library of artificial RNA ligase enzymes that were previously isolated at ambient temperature and were therefore mostly mesophilic, we selected for thermostable active enzyme variants by performing the selection step at 65°C. The most efficient enzyme, ligase 10C, was not only active at 65°C, but was also an order of magnitude more active at room temperature compared to related enzymes previously isolated at ambient temperature. Concurrently, the melting temperature of ligase 10C increased by 35 degrees compared to these related enzymes. While low stability and solubility of the previously selected enzymes prevented a structural characterization, the improved properties of the heat-stable ligase 10C finally allowed us to solve the three-dimensional structure by NMR. This artificial enzyme adopted an entirely novel fold that has not been seen in nature, which was published elsewhere. These results highlight the versatility of the in vitro selection technique mRNA display as a powerful method for the isolation of thermostable novel enzymes.

A facile one-pot method to synthesize a polypyrrole/hemin nanocomposite and its application in biosensor, dye removal, and photothermal therapy

In this work, we introduced a facile method for the construction of a polypyrrole/hemin (PPy/hemin) nanocomposite via one-pot chemical oxidative polymerization. In this process, a hemin molecule serving as a dopant was entrapped in the PPy nanocomposite during chemical oxidative polymerization. Scanning electron microscopy (SEM), transmission electron microscopy (TEM), Fourier transform infrared spectroscopy (FTIR), and UV-visible spectroscopy results demonstrated that the PPy/hemin nanocomposite was successfully synthesized. The as-prepared nanocomposite exhibited intrinsic peroxidase-like catalytic activities, strong adsorption properties, and an excellent near-infrared (NIR) light-induced thermal effect. We utilized the nanomaterials to catalyze the oxidation of a peroxidase substrate 3,3,5,5-tetramethylbenzidine by H2O2 to the oxidized colored product which provided a colorimetric detection of glucose. As low as 50 μM glucose could be detected with a linear range from 0.05 to 8 mM. Moreover, the obtained nanocomposite also showed excellent removal efficiency for methyl orange and rhodamine B and a photothermal effect, which implied a promising application as the pollutant adsorbent and photothermal agent. The unique nature of the PPy/hemin nanocomposite makes it very promising for the fabrication of inexpensive, high-performance bioelectronic devices in the future.