End Modification Research Articles

Towing Tank Model Tests for Propulsive Performance Analysis of a Waterjet-Propelled Amphibious Vehicle

The present study concerns a series of model tests in a towing tank on waterjet propulsive performance. The test model was an armored vehicle consisting of a box-shaped hull, two waterjets, a bow flap, and a trim tab. As per the powering prediction procedure of high-speed vessels, resistance tests, waterjet system tests, and self-propulsion tests were performed. The Froude number based on the characteristic length and advance speed for the model tests ranged from .981 to 1.178. Bollard pull tests were also conducted to investigate the interaction between the hull and two installed waterjets and to validate the flow rate estimation. In the self-propulsion condition, the dry transom and nozzle end modification changed the interaction efficiency. The waterjet reduced the vehicle trim in the self-propulsion condition, owing to the nozzle exit flow onto the trim tab. Introduction Waterjet propulsion systems have been widely used in marine vessels, thanks to its advantages of low cavitation in high loading, safe operation in shallow water, and good maneuverability at low advance speed (Allison 1993). However, the propulsive performance of waterjets is a complicated problem and hard to analyze. The extrapolation method for the powering performance prediction of waterjet-propelled vessel is suggested by the International Towing Tank Conference (ITTC) (ITTC 2011), but it is less comprehensive than that of the conventional ship with screw propellers (ITTC 2017a), as test institutions for waterjet-propelled vessels are scarce and test methodology is not standardized (Altosole et al. 2012).

Synthetic Biodegradable Polymers with Chain End Modification: Polylactide, Poly(butylene succinate), and Poly(hydroxyalkanoate)

Abstract Of the various synthetic biodegradable polymers, polylactide, poly(butylene succinate), and poly(hydroxyalkanoate) have been widely studied and developed. This review focuses on studies of the chain end modification of these polymers. The selected research was categorized into initiators, chain end modification, including chain extending, and the degradation reaction. We cover the recent literature on this topic, and discuss the developing trends and challenges of biodegradable polymers.

Mitochondrial RNA quality control in trypanosomes.

Unicellular parasites Trypanosoma brucei spp. cause African human and animal trypanosomiasis, a spectrum of diseases that jeopardize public health and afflict the economy in sub-Saharan Africa. These hemoflagellates are distinguished by a single mitochondrion, which contains a kinetoplast nucleoid composed of DNA and histone-like proteins. Kinetoplast DNA (kDNA) represents a densely packed network of interlinked relaxed circular molecules: a few ~23-kb maxicircles encoding ribosomal RNAs (rRNAs) and proteins, and approximately 5,000 1-kb minicircles bearing guide RNA (gRNA) genes. The transcription start site defines the mRNA's 5' terminus while the primary RNA is remodeled into a monocistronic messenger by 3'-5' exonucleolytic trimming, 5' and 3' end modifications, and, in most cases, by internal U-insertion/deletion editing. Ribosomal and guide RNA precursors are also trimmed, and the processed molecules are uridylated. For 35 years, mRNA editing has attracted a major effort, but more recently the essential pre- and postediting processing and turnover events have been discovered and the key effectors have been identified. Among these, pentatricopeptide repeat (PPR) RNA binding proteins emerged as conduits coupling modifications of mRNA termini with internal sequence changes introduced by editing. Among 39 annotated PPRs, 20 belong to ribosomal subunits or assembly intermediates, four function as polyadenylation factors, a single factor directs 5' mRNA modification, and one protein is found in F1-ATPase. Nuclear and mitochondrial RNases P consist of a single PPR polypeptide, PRORP1 and PROP2, respectively. Here, we review PPR-mediated mitochondrial processes and discuss their potential roles in mRNA maturation, quality control, translational activation, and decay. This article is categorized under: RNA Processing > Capping and 5' End Modifications RNA Processing > 3' End Processing RNA Processing > RNA Editing and Modification.

Processing of coding and non-coding RNAs in plant development and environmental responses.

Precursor RNAs undergo extensive processing to become mature RNAs. RNA transcripts are subjected to 5' capping, 3'-end processing, splicing, and modification; they also form dynamic secondary structures during co-transcriptional and post-transcriptional processing. Like coding RNAs, non-coding RNAs (ncRNAs) undergo extensive processing. For example, secondary small interfering RNA (siRNA) transcripts undergo RNA processing, followed by further cleavage to become mature siRNAs. Transcriptome studies have revealed roles for co-transcriptional and post-transcriptional RNA processing in the regulation of gene expression and the coordination of plant development and plant-environment interactions. In this review, we present the latest progress on RNA processing in gene expression and discuss phased siRNAs (phasiRNAs), a kind of germ cell-specific secondary small RNA (sRNA), focusing on their functions in plant development and environmental responses.

Ester modification at the 3′ end of anti-microRNA oligonucleotides increases potency of microRNA inhibition

MicroRNAs (miRNAs) are short noncoding RNAs that play a fundamental role in gene regulation. Deregulation of miRNA expression has a strong correlation with disease and antisense oligonucleotides that bind and inhibit miRNAs associated with disease have therapeutic potential. Current research on the chemical modification of anti-miRNA oligonucleotides (anti-miRs) is focused on alterations of the phosphodiester-ribose backbone to improve nuclease resistance and binding affinity to miRNA strands. Here we describe a structure-guided approach for modification of the 3′-end of anti-miRs by screening for modifications compatible with a nucleotide-binding pocket present on human Argonaute2 (hAgo2). We computationally screened a library of 190 triazole-modified nucleoside analogs for complementarity to the t1A-binding pocket of hAgo2. Seventeen top scoring triazoles were then incorporated into the 3′ end of anti-miR21 and potency was evaluated for each in a cell-based assay for anti-miR activity. Four triazole-modified anti-miRs showed higher potency than anti-miR21 bearing a 3′ adenosine. In particular, a triazole-modified nucleoside bearing an ester substituent imparted a nine-fold and five-fold increase in activity for both anti-miR21 and anti-miR122 at 300 and 5 nM, respectively. The ester group was shown to be critical as a similar carboxylic acid and amide were inactive. Furthermore, anti-miR 3′ end modification with triazole-modified nucleoside analogs improved resistance to snake venom phosphodiesterase, a 3′-exonuclease. Thus, the modifications described here are good candidates for improvement of anti-miR activity.

Extracellular microRNA 3’ end modification across diverse body fluids

ABSTRACT microRNAs (miRNAs) are small non-coding RNAs that play critical roles in gene regulation. The presence of miRNAs in extracellular biofluids is increasingly recognized. However, most previous characterization of extracellular miRNAs focused on their overall expression levels. Alternative sequence isoforms and modifications of miRNAs were rarely considered in the extracellular space. Here, we developed a highly accurate bioinformatic method, called miNTA, to identify 3’ non-templated additions (NTAs) of miRNAs using small RNA-sequencing data. Using miNTA, we conducted an in-depth analysis of miRNA 3’ NTA profiles in 1047 extracellular RNA-sequencing data sets of 4 types of biofluids. This analysis identified hundreds of miRNAs with 3’ uridylation or adenylation, with the former being more prevalent. Among these miRNAs, up to 53% (22%) had an average 3’ uridylation (adenylation) level of at least 10% in a specific biofluid. Strikingly, we found that 3’ uridylation levels enabled segregation of different types of biofluids, more effectively than overall miRNA expression levels. This observation suggests that 3’ NTA levels possess fluid-specific information relatively robust to batch effects. In addition, we observed that extracellular miRNAs with 3’ uridylations are enriched in processes related to angiogenesis, apoptosis, and inflammatory response, and this type of modification may stabilize base-pairing between miRNAs and their target genes. Together, our study provides a comprehensive landscape of miRNA NTAs in human biofluids, which paves way for further biomarker discoveries. The insights generated in our work built a foundation for future functional, mechanistic, and translational discoveries.

Phosphine-Mediated Bioconjugation of the 3′-End of RNA

Staudinger ligation is an attractive bio-orthogonal reaction that has been widely used to tag proteins, carbohydrates, and nucleic acids. Here, we explore the traceless variant of the Staudinger ligation for 3'-end modification of oligoribonucleotides. An azido-containing dinucleotide was used to study the ligation. Nine phosphines containing reactive groups, affinity purification tags, or photoswitch probes have been successfully obtained. The corresponding modified dinucleotides were synthesized and characterized by LC/MS. Mechanistic interpretations of the reaction are proposed, in particular, the unprecedented formation of an oxazaphospholane nucleotide derivative, which was favored by the vicinal position of 2'-N3 and 3'-OH functional groups on the terminal ribose has been observed. The post-functionalization of a 24-nt RNA with a photoactivable tag is also reported.

Chemical Modification of Reducing End-Groups in Cellulose Nanocrystals.

Native plant cellulose has an intrinsic supramolecular structure. Consequently, it can be isolated as nanocellulose species, which can be utilized as building blocks for renewable nanomaterials. The structure of cellulose also permits its end‐wise modification, i.e., chemical reactions exclusively on one end of a cellulose chain or a nanocellulose particle. The premises for end‐wise modification have been known for decades. Nevertheless, different approaches for the reactions have emerged only recently, because of formidable synthetic and analytical challenges associated with the issue, including the adverse reactivity of the cellulose reducing end and the low abundance of newly introduced functionalities. This Review gives a full account of the scientific underpinnings and challenges related to end‐wise modification of cellulose nanocrystals. Furthermore, we present how the chemical modification of cellulose nanocrystal ends may be applied to directed assembly, resulting in numerous possibilities for the construction of new materials, such as responsive liquid crystal templates and composites with tailored interactions.

NMR Characterization of Conformational Interconversions of Lys48-Linked Ubiquitin Chains.

Ubiquitin (Ub) molecules can be enzymatically connected through a specific isopeptide linkage, thereby mediating various cellular processes by binding to Ub-interacting proteins through their hydrophobic surfaces. The Lys48-linked Ub chains, which serve as tags for proteasomal degradation, undergo conformational interconversions between open and closed states, in which the hydrophobic surfaces are exposed and shielded, respectively. Here, we provide a quantitative view of such dynamic processes of Lys48-linked triUb and tetraUb in solution. The native and cyclic forms of Ub chains are prepared with isotope labeling by in vitro enzymatic reactions. Our comparative NMR analyses using monomeric Ub and cyclic diUb as reference molecules enabled the quantification of populations of the open and closed states for each Ub unit of the native Ub chains. The data indicate that the most distal Ub unit in the Ub chains is the most apt to expose its hydrophobic surface, suggesting its preferential involvement in interactions with the Ub-recognizing proteins. We also demonstrate that a mutational modification of the distal end of the Ub chain can remotely affect the solvent exposure of the hydrophobic surfaces of the other Ub units, suggesting that Ub chains could be unique design frameworks for the creation of allosterically controllable multidomain proteins.

Design and Evaluation of AgoshRNAs with 3'-Terminal HDV Ribozymes to Enhance the Silencing Activity.

Since the first application of RNA interference (RNAi) in mammalian cells, the expression of short hairpin RNA (shRNA) molecules for targeted gene silencing has become a benchmark technology. Plasmid and viral vector systems can be used to express shRNA precursor transcripts that are processed by the cellular RNAi pathway to trigger sequence-specific gene knockdown. Intensive RNAi investigations documented that only a small percentage of computationally predicted target sequences can be used for efficient gene silencing, in part because not all shRNA designs are active. Many factors influence the shRNA activity and guidelines for optimal shRNA design have been proposed. We recently described an alternatively processed shRNA molecule termed AgoshRNA with a ~18base pairs (bp) stem and a 3-5 nucleotides(nt) loop. This molecule is alternatively processed by the Argonaute (Ago) protein into a single guide RNA strand that efficiently induces the RNAi mechanism. The design rules proposed for regular shRNAs do not apply to AgoshRNA molecules and therefore new rules had to be defined. We optimized the AgoshRNA design and managed to create a set of active AgoshRNAs targeted against the human immunodeficiency virus (HIV). In an attempt to enhance the silencing activity of the AgoshRNA molecules, we included the hepatitis delta virus (HDV) ribozyme at the 3' terminus, which generates a uniform 3' end instead of a 3' U-tail of variable length. We evaluated the impact of this 3'-end modification on AgoshRNA processing and its gene silencing activity and we demonstrate that this novel AgoshRNA-HDV design exhibits enhanced antiviral activity.

Systematic Characterization of Hydrophilized Polydimethylsiloxane

Flexible microfluidics have found extensive utility in the biological and biomedical fields. A leading substrate material for compliant devices is polydimethylsiloxane (PDMS). Despite its many advantages, PDMS is inherently hydrophobic and consequently its use in passive (pumpless) microfluidics becomes problematic. To this end, many physical and chemical modifications have been introduced to render PDMS hydrophilic, ranging from amphiphilic molecule additions to surface plasma treatments. However, when transitioning from lab benchtop to realized medical devices, these modifications must exhibit long-term stability. Unfortunately, these modifications are often presented but their mechanisms and long-term stability are not studied in detail. We have investigated an array of PDMS modifications, utilizing contact angle goniometry to study surface energy over a 30-day evolution study. Samples were stored in air and water, and Fourier Transform Infrared-Attenuated Total Reflectance (FTIR-ATR) analysis was used to confirm surface functional group uniformity. We have identified preferred modification techniques for long-lasting PDMS devices and characterized often overlooked material stability.

NUDT21 suppresses the growth of small cell lung cancer by modulating GLS1 splicing

The mRNA precursor 3′-end modification factor NUDT21 is a major regulator of 3′UTR shortening and an important component of pre-mRNA cleavage and polyadenylation. However, its role in pathologic progress of small cell lung cancer (SCLC) remains unclear. In this study, we observed that NUDT21 expression is downregulated in SCLC tissues. Hypoxia-induced down-regulation of NUDT21 through HIF-1α. NUDT21 shRNA transduction promotes proliferation and inhibits apoptosis of A549 cells. NUDT21 inhibition also promotes tumor growth in a mouse xenograft model. Furthermore, we clarified that HIF-1α mediated NUDT21 downregulation which altered the expression patterns of two isoforms of GLS1, GAC and KGA. These results link the hypoxic tumor environments to aberrant glutamine metabolism which is important for cellular energy in SCLC cells. Therefore, NUDT21 could be considered as a potential target for the treatment of SCLC.

User-Friendly Reverse Genetics System for Modification of the Right End of Fowl Adenovirus 4 Genome.

A novel fowl adenovirus 4 (FAdV-4) has caused significant economic losses to the poultry industry in China since 2015. We established an easy-to-use reverse genetics system for modification of the whole right and partial left ends of the novel FAdV-4 genome, which worked through cell-free reactions of restriction digestion and Gibson assembly. Three recombinant viruses were constructed to test the assumption that species-specific viral genes of ORF4 and ORF19A might be responsible for the enhanced virulence: viral genes of ORF1, ORF1b and ORF2 were replaced with GFP to generate FAdV4-GFP, ORF4 was replaced with mCherry in FAdV4-GFP to generate FAdV4-GX4C, and ORF19A was deleted in FAdV4-GFP to generate FAdV4-CX19A. Deletion of ORF4 made FAdV4-GX4C form smaller plaques while ORF19A deletion made FAdV4-CX19A form larger ones on chicken LMH cells. Coding sequence (CDS) replacement with reporter mCherry demonstrated that ORF4 had a weak promoter. Survival analysis showed that FAdV4-CX19A-infected chicken embryos survived one more day than FAdV4-GFP- or FAdV4-GX4C-infected ones. The results illustrated that ORF4 and ORF19A were non-essential genes for FAdV-4 replication although deletion of either gene influenced virus growth. This work would help function study of genes on the right end of FAdV-4 genome and facilitate development of attenuated vaccines.

Reducing end modification on cellulose nanocrystals: strategy, characterization, applications and challenges.

Different from traditional chemical surface modification, localized modification of the reducing end groups of cellulose nanocrystals (CNCs), i.e. the active aldehyde groups, provides new opportunities for diverse functional applications of this renewable nanomaterial without altering its surface chemistry and properties. Numerous reviews have deeply discussed the surface modification of the hydroxyl groups of CNCs, but no critical comment has been reported on the reducing end modification approach. This review is a comprehensive summary on the modification of the CNC reducing end, presenting the reaction mechanisms and conditions, discussing the different chemical modification strategies and characterization techniques, potential applications and future challenges in this field. In addition, the comparison between surface and end modification strategies of CNCs will highlight the potential of reducing end-functionalized CNCs to be used in various applications as an alternative to traditional surface-modified CNCs, or as additional functional nanoparticles for the design of advanced functional materials.

An efficient gene knock-in strategy using 5'-modified double-stranded DNA donors with short homology arms.

Here, we report a rapid CRISPR-Cas9-mediated gene knock-in strategy that uses Cas9 ribonucleoprotein and 5'-modified double-stranded DNA donors with 50-base-pair homology arms and achieved unprecedented 65/40% knock-in rates for 0.7/2.5 kilobase inserts, respectively, in human embryonic kidney 293T cells. The identified 5'-end modification led to up to a fivefold increase in gene knock-in rates at various genomic loci in human cancer and stem cells.

Design of customizable long linear DNA substrates with controlled end modifications for single-molecule studies

Many strategies have been developed to manipulate DNA molecules and investigate protein–DNA interactions with single-molecule resolution. Often, these require long DNA molecules with a length of several 10s of kb that are chemically modified at specific regions. This need has traditionally been met by commercially available DNA from bacteriophage λ. However, λ DNA does not allow for the generation of highly customizable substrates in a straightforward manner, an important factor when developing assays to study complex biochemical reactions. Here we present a generalizable method for the design and production of very long chemically modified DNA substrates derived from a single plasmid. We show the versatility of this design by demonstrating its application in studying DNA replication in vitro. We anticipate this strategy will be broadly useful in producing a range of long chemically modified DNA molecules required for a diverse range of single-molecule approaches.

Structural basis for the evolution of cyclic phosphodiesterase activity in the U6 snRNA exoribonuclease Usb1.

U6 snRNA undergoes post-transcriptional 3′ end modification prior to incorporation into the active site of spliceosomes. The responsible exoribonuclease is Usb1, which removes nucleotides from the 3′ end of U6 and, in humans, leaves a 2′,3′ cyclic phosphate that is recognized by the Lsm2–8 complex. Saccharomycescerevisiae Usb1 has additional 2′,3′ cyclic phosphodiesterase (CPDase) activity, which converts the cyclic phosphate into a 3′ phosphate group. Here we investigate the molecular basis for the evolution of Usb1 CPDase activity. We examine the structure and function of Usb1 from Kluyveromyces marxianus, which shares 25 and 19% sequence identity to the S. cerevisiae and Homo sapiens orthologs of Usb1, respectively. We show that K. marxianus Usb1 enzyme has CPDase activity and determined its structure, free and bound to the substrate analog uridine 5′-monophosphate. We find that the origin of CPDase activity is related to a loop structure that is conserved in yeast and forms a distinct penultimate (n – 1) nucleotide binding site. These data provide structural and mechanistic insight into the evolutionary divergence of Usb1 catalysis.

RAFT polymerization of styrene mediated by naphthyl-functionalized trithiocarbonate RAFT agents

New oxazolyl benzhydryl and oxazolyl benzyl-functionalized trithiocarbonate RAFT agents, 1-(butylsulfanylthiocarbonylsulfanyl)-1-[4-(4,5-dihydro-4,4-dimethyl-2-oxazolyl)phenyl]-1-phenylmethane and 2-[4-((butylsulfanylthiocarbonylsulfanyl)methyl)phenyl]-4,5-dihydro-4,4-dimethyloxazole, were prepared and employed as chain transfer agents in RAFT polymerization reactions. The RAFT polymerization of styrene, mediated by the appropriate oxazolyl-functionalized trithiocarbonate RAFT agent with AIBN as initiator at 70 °C, proceeded via controlled/living polymerization processes to produce the corresponding α-oxazolyl-functionalized polystyrene derivative, with the oxazolyl group introduced at the α-terminus of the polymer chain and the absence of any unfunctionalized polystyrene. Post-RAFT polymerization chain end modification of α-oxazolyl-functionalized polystyrene by acid-catalyzed hydrolysis reactions with dilute hydrochloric acid afforded the corresponding α-carboxyl-functionalized polystyrene derivative, with the retention of the butylsulfanylthiocarbonylsulfanyl moiety at the ω-terminus of the polymer chain. Polymer kinetic measurements show that each RAFT polymerization reaction follows first-order rate kinetics with respect to the percentage monomer consumption. The oxazolyl-functionalized benzhydryl fragmentation radical provides better control of the re-initiation of the polymerization of styrene than the oxazolyl-functionalized benzyl fragmentation radical. After consumption of the RAFT agent, the number average molecular weights of the functionalized polymers increases linearly with the percentage monomer conversion to produce α-oxazolyl-functionalized polystyrene derivatives with narrow molecular weight distributions. New oxazolyl benzhydryl and oxazolyl benzyl-functionalized trithiocarbonate RAFT agents, 1-(butylsulfanylthiocarbonylsulfanyl)-1-[4-(4,5-dihydro-4,4-dimethyl-2-oxazolyl)phenyl]-1-phenylmethane and 2-[4-((butylsulfanylthiocarbonylsulfanyl)methyl)phenyl]-4,5-dihydro-4,4-dimethyloxazole, were prepared and employed as chain transfer agents in RAFT polymerization reactions. The RAFT polymerization of styrene, mediated by 1-(butylsulfanylthiocarbonylsulfanyl)-1-[4-(4,5-dihydro-4,4-dimethyl-2-oxazolyl)phenyl]-1-phenylmethane or 2-[4-((butylsulfanylthiocarbonylsulfanyl)methyl)phenyl]-4,5-dihydro-4,4-dimethyloxazole as chain transfer agents with AIBN as the initiator at 70 °C, proceeds via a controlled/living polymerization process to produce the corresponding α-oxazolyl-functionalized polystyrene derivative, with the oxazolyl group introduced at the α-terminus of the polymer chain.

Efficient Generation of Hydrazides in Proteins by RadA Split Intein.

Protein C-terminal hydrazides are useful for bioconjugation and construction of proteins from multiple fragments through native chemical ligation. To generate C-terminal hydrazides in proteins, an efficient intein-based preparation method has been developed by using thiols and hydrazine to accelerate the formation of the transient thioester intermediate and subsequent hydrazinolysis. This approach not only increases the yield, but also improves biocompatibility. The scope of the method has been expanded by employing Pyrococcus horikoshii RadA split intein, which can accommodate a broad range of extein residues before the site of cleavage. The use of split RadA minimizes premature intein N cleavage in vivo and offers control over the initiation of the intein N cleavage reaction. It is expected that this versatile preparation method will expand the utilization of protein C-terminal hydrazides in protein preparation and modification.

Nanoporous poly(ether sulfone) from polylactide-b-poly(ether sulfone)-b-polylactide precursor

We report a route to synthesize polylactide-b-poly(ether sulfone)-b-polylactide (PLA-b-PES-b-PLA) containing PES and PLA, which provide a mechanically robust framework and a sacrificial template for pore formation, respectively. High-molar mass PES terminated with fluorine groups was synthesized by the step-growth nucleophilic aromatic substitution (SNAr) reaction, and the chain ends were transformed into benzylic hydroxyl groups by chain end modification. Growth of the PLA using the hydroxyl groups as initiating sites via chain-growth ring opening transesterification polymerization (ROTEP) produced the target triblock copolymer. Although the step-growth polymerization produced a PES middle block with high dispersity, small angle X-ray scattering (SAXS) and transmission electron microscopy (TEM) analyses indicated the formation of an ordered lamellar morphology. We further demonstrated that a nanoporous PES with slit-like pores could be obtained by selective removal of the PLA.