DNA-based Research Articles

Prebiotic Chemistry and Sepiolite: A Density Functional Theory Approach

In this study, the molecular interactions of sepiolite, a biocompatibility clay mineral with known as biomaterial, and purine and pyrimidine molecules forming the bases of DNA and RNA molecules were modeled by Density Functional Theory. In addition to the geometry optimization, interaction energy, bond critical point, and electrostatic potential calculations revealed that essential molecules for our source of life interact with the basal surface of the clay. For example, the best interaction energies between bases / sepiolite were found to be -127.47, -121.35 kJ / mol for guanine and cytosine, respectively. Looking at the modeling results, one of the most important factors affecting the interaction energies is H-bond. In order to reveal this, bond critical points analyze were performed and it was computed that a large amount of intermolecular interaction energies came from H-bonds. For example, it has been calculated that close to 70% of the total energy in the guanine/TOT model is from H-bonds. Besides, this value of the cytosine/TOT model was found to be around 72%. The most effective indexes in these two models are 145 and 135, and the H-bond energies were recorded as -22.41 and 31.41 kJ/mol, respectively. Considering all the analyzes run, it can be concluded that the basal surfaces of the sepiolite are a suitable host for the nitrogenous bases, which are the main sources of life.

Clustered DNA Damage and its Complexity: Tracking the History.

The concept of radiation-induced clustered damage in DNA has grown over the past several decades to become a topic of considerable interest across the scientific disciplines involved in studies of the biological effects of ionizing radiation. This paper, prepared for the 70th anniversary issue of Radiation Research, traces historical development of the three main threads of physics, chemistry, and biochemical/cellular responses that led to the hypothesis and demonstration that a key component of the biological effectiveness of ionizing radiation is its characteristic of producing clustered DNA damage of varying complexities. The physics thread has roots that started as early as the 1920s, grew to identify critical nanometre-scale clusterings of ionizations relevant to biological effectiveness, and then, by the turn of the century, had produced an extensive array of quantitative predictions on the complexity of clustered DNA damage from different radiations. Monte Carlo track structure simulation techniques played a key role through these developments, and they are now incorporated into many recent and ongoing studies modelling the effects of radiation. The chemistry thread was seeded by water-radiolysis descriptions of events in water as radical-containing "spurs," demonstration of the important role of the hydroxyl radical in radiation-inactivation of cells and the difficulty of protection by radical scavengers. This led to the concept and description of locally multiply damaged sites (LMDS) for DNA double-strand breaks and other combinations of DNA base damage and strand breakage that could arise from a spur overlapping, or created in very close proximity to, the DNA. In these ways, both the physics and the chemistry threads, largely in parallel, put out the challenge to the experimental research community to verify these predictions of clustered DNA damage from ionizing radiations and to investigate their relevance to DNA repair and subsequent cellular effects. The third thread, biochemical and cell-based research, responded strongly to the challenge by demonstrating the existence and biological importance of clustered DNA damage. Investigations have included repair of a wide variety of defined constructs of clustered damage, evaluation of mutagenic consequences, identification of clustered base-damage within irradiated cells, and identification of co-localization of repair complexes indicative of complex clustered damage after high-LET irradiation, as well as extensive studies of the repair pathways involved in repair of simple double-strand breaks. There remains, however, a great deal more to be learned because of the diversity of clustered DNA damage and of the biological responses.

Exploring the electronic structure and interaction mechanism of nucleic acid bases on pristine graphene and beryllium-oxide-graphene layers

The interaction between nucleic acid bases and graphene, along with its derivatives, is crucial for various applications like biosensors, drug delivery, and bio-nanotechnology. The present study focuses on optimizing nucleic acid bases, and the graphene layer using the B3LYP/6-31G** method and the beryllium-oxide-graphene layer using the PBE/6-31G** method. The optimized coordinates are then used to investigate the interaction of nucleic acid bases with pristine graphene and beryllium-oxide-graphene in parallel stacking mode. Various functionals including hybrid B3LYP, PBEPBE, and range-separated ωB97XD along with 6-31G(d,p) basis sets, are employed for this analysis. Based on the obtained interaction energy values, it is concluded that the wB97XD/6-31G(d,p) method provides superior results for the interaction study. Additionally, it is noted that the interaction with pristine graphene primarily involves aromatic π-π interactions and hydrogen bonds, while beryllium oxide graphene seems to form coordination bonds with electron-rich sites. Also, the beryllium-oxide-graphene layer exhibited reduced rigidity compared to pristine carbon graphene layer.

Hydrophilic interaction chromatographic evaluation of zwitterionic polymer grafted silica gel via multiple binding sites.

A novel zwitterionic polymer grafted silica stationary phase, Sil-PZIC, was prepared by bonding poly(ethylene maleic anhydride) molecules on the surface of silica via multiple binding sites, followed by ammonolysis of maleic anhydride through a nucleophilic substitution reaction with ethylenediamine. The stationary phase was characterized by solid-state 13C nuclear magnetic resonance, zeta potential, and elemental analysis and the results show the successful encapsulation of zwitterionic polymer on the surface of silica. The chromatographic performance of Sil-PZIC was investigated by using nucleosides and nucleic bases as test analytes The variation of retention and separation performance of these model compounds were investigated by varying the chromatographic conditions such as the components of mobile phase, salt concentration, and pH. The results show that the retention of the Sil-PZIC phase was dominated by a hydrophilic partitioning mechanism accompanied by secondary interactions such as electrostatic and hydrogen bonding. In addition, saccharides and Amadori compounds were also well separated on the Sil-PZIC, indicating that the Sil-PZIC column has potential application for separation of the polar compound.

Dulaglutide reduces oxidative DNA damage and hypermethylation in the somatic cells of mice fed a high-energy diet by restoring redox balance, inflammatory responses, and DNA repair gene expressions.

Obesity is an established risk factor for numerous malignancies, although it remains uncertain whether the disease itself or weight-loss drugs are responsible for a greater predisposition to cancer. The objective of the current study was to determine the impact of dulaglutide on genetic and epigenetic DNA damage caused by obesity, which is a crucial factor in the development of cancer. Mice were administered a low-fat or high-fat diet for 12 weeks, followed by a 5-week treatment with dulaglutide. Following that, modifications of the DNA bases were examined using the comet assay. To clarify the underlying molecular mechanisms, oxidized and methylated DNA bases, changes in the redox status, levels of inflammatory cytokines, and the expression levels of some DNA repair genes were evaluated. Animals fed a high-fat diet exhibited increased body weights, elevated DNA damage, oxidation of DNA bases, and DNA hypermethylation. In addition, obese mice showed altered inflammatory responses, redox imbalances, and repair gene expressions. The findings demonstrated that dulaglutide does not exhibit genotoxicity in the investigated conditions. Following dulaglutide administration, animals fed a high-fat diet demonstrated low DNA damage, less oxidation and methylation of DNA bases, restored redox balance, and improved inflammatory responses. In addition, dulaglutide treatment restored the upregulated DNMT1, Ogg1, and p53 gene expression. Overall, dulaglutide effectively maintains DNA integrity in obese animals. It reduces oxidative DNA damage and hypermethylation by restoring redox balance, modulating inflammatory responses, and recovering altered gene expressions. These findings demonstrate dulaglutide's expediency in treating obesity and its associated complications.

Topical nanoencapsulated cannabidiol cream as an innovative strategy combating UV-A–induced nuclear and mitochondrial DNA injury: A pilot randomized clinical study

BackgroundUltraviolet-A radiation (UVA) contributes to photoaging/photocarcinogenesis by generating inflammation and oxidative damage. Current photoprotective strategies are limited by availability/utilization of UVA filters, highlighting an unmet need. Cannabidiol (CBD), having anti-inflammatory/antioxidant properties via regulation of NFR-2, HMOX1, and PPAR-y, could potentially mitigate damage from UVA exposure. Objective/MethodsProspective, single-center, pilot clinical trial (NCT05279495). Nineteen participants applied nano-CBD (nCBD) or vehicle (VC) cream to randomized, blinded buttock sites twice-daily for 14-days, then treated sites were irradiated with ≤3x UVA minimal erythema dose. After 24-hours, punch biopsies were obtained for histology, immunohistochemistry, real-time PCR. ResultsAt 24-hours, 21% of participants had less observed erythema on CBD-treated skin than VC skin. Histologically, nCBD-treated skin had reduced UVA-induced epidermal hyperplasia than VC (p=0.01). Immunohistochemistry detected reduced cytoplasmic/nuclear 8-oxo-guanine glycosylase 1 staining in nCBD-treated skin compared to VC (p<0.01). Quantitative mtDNA PCR demonstrated UVA-induced deletion of ND4 (proxy:4977bp deletion; p=0.003) and ND1 (proxy:3895bp deletion; p=0.002) were significantly reduced by in vivo nCBD treatment compared to VC. LimitationsSample size. ConclusionTopically applied nCBD cream reduced UVA-induced formation of a frequent mutagenic nuclear DNA base lesion and protected against mtDNA mutations associated with UVA-induced skin aging. This trial is the first to identify UV-protective capacity of CBD-containing topicals in humans.

How to sensitize glioblastomas to temozolomide chemotherapy: a gap-centered view.

Temozolomide (TMZ) is a methylating agent used as the first-line drug in the chemotherapy of glioblastomas. However, cancer cells eventually acquire resistance, necessitating the development of TMZ-potentiating therapy agents. TMZ induces several DNA base adducts, including O 6 -meG, 3-meA, and 7-meG. TMZ cytotoxicity stems from the ability of these adducts to directly (3-meA) or indirectly (O 6 -meG) impair DNA replication. Although TMZ toxicity is generally attributed to O 6 -meG, other alkylated bases can be similarly important depending on the status of various DNA repair pathways of the treated cells. In this mini-review we emphasize the necessity to distinguish TMZ-sensitive glioblastomas, which do not express methylguanine-DNA methyltransferase (MGMT) and are killed by the futile cycle of mismatch repair (MMR) of the O 6 -meG/T pairs, vs. TMZ-resistant MGMT-positive or MMR-negative glioblastomas, which are selected in the course of the treatment and are killed only at higher TMZ doses by the replication-blocking 3-meA. These two types of cells can be TMZ-sensitized by inhibiting different DNA repair pathways. However, in both cases, the toxic intermediates appear to be ssDNA gaps, a vulnerability also seen in BRCA-deficient cancers. PARP inhibitors (PARPi), which were initially developed to treat BRCA1/2-deficient cancers by synthetic lethality, were re-purposed in clinical trials to potentiate the effects of TMZ. We discuss how the recent advances in our understanding of the genetic determinants of TMZ toxicity might lead to new approaches for the treatment of glioblastomas by inhibiting PARP1 and other enzymes involved in the repair of alkylation damage (e.g., APE1).

Molecular structure of DNA via Zagreb connection descriptors.

Topological indices quantify the connectivity and structural properties of chemical compounds. We use the topological indices for predicting and evaluating the numerous properties of molecules, such as boiling temperatures, toxicity, and biological activity. Zagreb connection indices are a useful tool for studying the structural characteristics of the DNA backbone network. These indices provide important information on the arrangement and connections between nucleotide bases inside the DNA molecule. These indices show compactness, complexity, and topological properties in order to predict DNA bending propensity, DNA-protein interaction, and DNA stability. DNA folding patterns and the impact of mutations on DNA networks are areas of further research for these topological indices. In this study, we calculate Zagreb connection indices and modified Zagreb connection indices for backbone DNA network and subdivided backbone DNA network. Furthermore, we compute the hyper-Zagreb connection index, the inverse sum connection index, and the harmonic connection index.

Theoretical Study for Spin Transport properties of FM-(G/C)10- FM

In the present study, we propose a physical model to study spin transport through DNA system and provide apparent physical mechanism for spin dependent phenomenon. The system considered in our work is DNA bases guanine-cytosine coupled to two ferromagnetic leads (FM-(G/C)10-FM) in parallel and anti-parallel configuration case, throughout magnetic quantum contacts. Our treatment is based on the tight binding model to derive obvious formula for the transmission spectrum which is employed to investigate the spin dependent current-bias voltage characteristics and the temperature - Conductance dependence. Our calculations of for strong, weak and without backbone regimes. Various factors are involved in our -study. These are the electrical contacts between DNA molecules and electrodes, the structure of DNA molecule and the environment around DNA molecule. The system spin dependent factors, that are investigated extensively in our study include the spin dependent coupling between subsystems, the quantum contacts between active region and electrodes, majority and minority electrons spin in the ferromagnetic leads as well as externally applied bias voltage. Variation of these factors can enhanced or suppressed spin transport through (G/C)10 molecule. The transmission spectrum calculations conform that the spin transport throughout (G/C)10 originates by a coherent tunneling process between neighboring bases through the overlapping of the LUMO orbitals of the bases. Our results showed that the spin-polarized transport that can be effectively regulated by the type of regime as well as the spin configuration in the leads which can exhibit efficient spin filtering and spin switching by employing the spin blockade phenomenon

Epigenetic regulation of TERRA transcription and metacyclogenesis by base J in Leishmania major.

The hyper-modified DNA base J helps control termination of Pol II transcription at polycistronic transcription units (PTUs) in T. brucei and L. major , allowing epigenetic control of gene expression. The Telomere Repeat-containing RNA (TERRA) is synthesized in T. brucei by Pol I readthrough transcription of a telomeric PTU. While little is understood regarding TERRA synthesis and function, the hyper-modified DNA base J is highly enriched at telomeres in L. major promastigotes. We now show that TERRA is synthesized by Pol II in L. major and loss of base J leads to increased TERRA. For at least one site, the increased TERRA is by Pol II readthrough transcription from an adjacent PTU. Furthermore, Pol II readthrough defects and increased TERRA correlate with increased differentiation of promastigotes to the infectious metacyclic life stage and decreased cell viability. These results help explain the essential nature of base J in Leishmania and provide insight regarding epigenetic control of coding and non-coding RNA expression and parasite development during the life cycle of L. major .

Tracking DOT1L methyltransferase activity by stable isotope labelling using a selective synthetic co-factor

Epigenetic processes influence health and disease through mechanisms which alter gene expression. In contrast to genetic changes which affect DNA sequences, epigenetic marks include DNA base modifications or post-translational modification (PTM) of proteins. Histone methylation is a prominent and versatile example of an epigenetic marker: gene expression or silencing is dependent on the location and extent of the methylation. Protein methyltransferases exhibit functional redundancy and broad preferences for multiple histone residues, which presents a challenge for the study of their individual activities. We developed an isotopically labelled analogue of co-factor S-adenosyl-L-methionine (13CD3-BrSAM), with selectivity for the histone lysine methyltransferase DOT1L, permitting tracking of methylation activity by mass spectrometry (MS). This concept could be applied to other methyltransferases, linking PTM discovery to enzymatic mediators.

Characterization of Cichorium intybus L. Extract in Preventing Oxidative DNA Base Damage Using Gas Chromatography–Tandem Mass Spectrometry (GC–MS/MS)

Free radicals are unstable and are known for electron deficiency. This state renders DNA, proteins, and various biomolecules susceptible to detrimental interactions, leading to damage. However, this process can be regulated by antioxidants produced naturally on-site or externally through food or herbal supplements. In recent years, interest in characterizing alternative, natural and safe antioxidants obtained from plant sources has been increasing. Within this context, Cichorium intybus L. has garnered attention for its notable antioxidant content. In our previous study, we determined optimum conditions for ultrasound-assisted extraction of antioxidants from Cichorium intybus L. using central composite design-response surface methodology. In this study, the quantitative determination of phenolics in the extract prepared under optimal conditions was undertaken employing high-performance liquid chromatography with diode array detection (HPLC-DAD). The study’s primary goal is to investigate the impact of the extract derived from Cichorium intybus on the formation of products resulting from oxidative damage to DNA bases by gas chromatography–tandem mass spectrometry (GC–MS/MS). For this purpose, different volumes of extract were added to the DNA + Fenton medium. When 25 µL of extract were added, 239.98 ± 5.81 ng of damaged product/mg DNA was present. 233.12 ± 5.63 ng of damaged product/mg DNA were obtained for 50 µL of extract and 165.76 ± 4.58 ng of damaged product/mg DNA for 100 µL. This study shows that Cichorium intybus has potential therapeutic effects on supporting antioxidant defenses and reducing oxidative DNA damage.

DNA Repair Protein XRCC1 Stimulates Activity of DNA Polymerase λ under Conditions of Microphase Separation.

Non-membrane compartments or biomolecular condensates play an important role in the regulation of cellular processes including DNA repair. Here, an ability of XRCC1, a scaffold protein involved in DNA base excision repair (BER) and single-strand break repair, to form protein-rich microphases in the presence of DNA duplexes was discovered. We also showed that the gap-filling activity of BER-related DNA polymerase λ (Pol λ) is significantly increased by the presence of XRCC1. The stimulation of the Pol λ activity was observed only at micromolar XRCC1 concentrations, which were well above the nanomolar dissociation constant determined for the XRCC1-Pol λ complex and pointed to the presence of an auxiliary stimulatory factor in addition to protein-protein interactions. Indeed, according to dynamic light scattering measurements, the stimulation of the Pol λ activity by XRCC1 was coupled with microphase separation in a protein-DNA mixture. Fluorescence microscopy revealed colocalization of Pol λ, XRCC1, and gapped DNA within the microphases. Thus, stimulation of Pol λ activity is caused both by its interaction with XRCC1 and by specific conditions of microphase separation; this phenomenon is shown for the first time.

Identification of DNA Barcodes from rbcL Chloroplast DNA in Katokkon Chili (Capsicum annuum var. chinense) Origin of Tana Toraja, South Sulawesi

Katokkon chili (Capsicum annuum var. chinense) is a type of chili which are commonly found in Tana Toraja. It has a distinctive aroma, high spiciness, and a potential economic value but has not been widely identified and explored, thus, it is necessary to carry out molecular identification using DNA barcodes from chloroplast DNA. The aim of this study was to determine genetic variation and the results of constructing a phylogenetic tree from DNA sequences katokkon chili (C. annuum var. chinense) using the rbcL marker. This study used 6 samples of katokkon chilies (C. annuum var. chinense) and 3 outgroup samples (C. frutescens, C. chinense and C. baccatum). The stages of the research included total DNA isolation, qualitative and quantitative tests, PCR amplification using rbcL primers, and sequencing. Data analysis used is sequence alignment, phylogenetic, genetic distance matrix, haplotypes and phylogeography. The results showed genetic variation with 7 polymorphisms consisting of 4 singleton sites at the nucleotide base sequences of 6th, 525, 715 and 737, and 3 parsimony informative sites at the nucleotide base sequences 370, 616 and 902 and the haplotype distribution is divided into 4 haplotypes namely Hap_1 (A1, A2, A3, B1, B2 and B3), Hap_2 (C1), Hap_3 (C2), and Hap_3 (C3). The phylogenetic tree construction formed two clades, namely clade I consist of six samples of katokkon chilies (C. annuum var. chinense) and clade II consisting of three outgroup samples. Mark the highest bootstrap is 96 and the lowest bootstrap value is 29. Genetic distance matrix values are in the range of 0.000–0.005.

Role of Shape Deformation of DNA-Binding Sites in Regulating the Efficiency and Specificity in Their Recognition by DNA-Binding Proteins.

Accurate transcription of genetic information is crucial, involving precise recognition of the binding motifs by DNA-binding proteins. While some proteins rely on short-range hydrophobic and hydrogen bonding interactions at binding sites, others employ a DNA shape readout mechanism for specific recognition. In this mechanism, variations in DNA shape at the binding motif resulted from either inherent flexibility or binding of proteins at adjacent sites are sensed and capitalized by the searching proteins to locate them specifically. Through extensive computer simulations, we investigate both scenarios to uncover the underlying mechanism and origin of specificity in the DNA shape readout mechanism. Our findings reveal that deformation in shape at the binding motif creates an entropy funnel, allowing information about altered shapes to manifest as fluctuations in minor groove widths. This signal enhances the efficiency of nonspecific search of nearby proteins by directing their movement toward the binding site, primarily driven by a gain in entropy. We propose this as a generic mechanism for DNA shape readout, where specificity arises from the alignment between the molecular frustration of the searching protein and the ruggedness of the entropic funnel governed by molecular features of the protein and arrangement of the DNA bases at the binding site, respectively.

Nanopores map the acid-base properties of a single site in a single DNA molecule.

Nanopores are increasingly powerful tools for single molecule sensing, in particular, for sequencing DNA, RNA and peptides. This success has spurred efforts to sequence non-canonical nucleic acid bases and amino acids. While canonical DNA and RNA bases have pKas far from neutral, certain non-canonical bases, natural RNA modifications, and amino acids are known to have pKas near neutral pHs at which nanopore sequencing is typically performed. Previous reports have suggested that the nanopore signal may be sensitive to the protonation state of an individual moiety. We sequenced ion currents with the MspA nanopore using a single stranded DNA containing a single non-canonical DNA base (Z) at various pH conditions. The Z-base has a near-neutral pKa ∼ 7.8. We find that the measured ion current is remarkably sensitive to the protonation state of the Z-base. We demonstrate how nanopores can be used to localize and determine the pKa of individual moieties along a polymer. More broadly, these experiments provide a path to mapping different protonation sites along polymers and give insight in how to optimize sequencing of polymers that contain moieties with near-neutral pKas.

Exploration of new ways for CRISPR/Cas12a activation: DNA hairpins without PAM and toehold and single strands containing DNA and RNA bases

The CRISPR/Cas12a system is emerging as a promising candidate for next-generation diagnostic biosensing platforms, with the discovery of new activation modes greatly expanding its applications. Here, we have identified two novel CRISPR/Cas12a system activation modes: PAM- and toehold-free DNA hairpins, and DNA-RNA hybrid strands. Utilizing a well-established real-time fluorescence method, we have demonstrated a strong correlation between DNA hairpin structures and Cas12a activation. Compared with previously reported activation modes involving single-stranded DNA and PAM-contained double-stranded DNA, the DNA hairpin activation way exhibits similar specificity and generality. Moreover, our findings indicate that increasing the number of RNA bases in DNA-RNA hybrid strands can decelerate the kinetics of Cas12a-triggered trans-cleavage of reporter probes. These newly discovered CRISPR/Cas12a activation ways hold significant potential for the development of high-performance biosensing strategies.

Pierisin, Cytotoxic and Apoptosis-Inducing DNA ADP-Ribosylating Protein in Cabbage Butterfly.

Pierisin-1 was serendipitously discovered as a strong cytotoxic and apoptosis-inducing protein from pupae of the cabbage butterfly Pieris rapae against cancer cell lines. This 98-kDa protein consists of the N-terminal region (27 kDa) and C-terminal region (71 kDa), and analysis of their biological function revealed that pierisin-1 binds to cell surface glycosphingolipids on the C-terminal side, is taken up into the cell, and is cleaved to N- and C-terminal portions, where the N-terminal portion mono-ADP-ribosylates the guanine base of DNA in the presence of NAD to induce cellular genetic mutation and apoptosis. Unlike other ADP-ribosyltransferases, pieisin-1 was first found to exhibit DNA mono-ADP-ribosylating activity and show anti-cancer activity in vitro and in vivo against various cancer cell lines. Pierisin-1 was most abundantly produced during the transition from the final larval stage to the pupal stage of the cabbage butterfly, and this production was regulated by ecdysteroid hormones. This suggests that pierisn-1 might play a pivotal role in the process of metamorphosis. Moreover, pierisin-1 could contribute as a defense factor against parasitization and microbial infections in the cabbage butterfly. Pierisin-like proteins in butterflies were shown to be present not only among the subtribe Pierina but also among the subtribes Aporiina and Appiadina, and pierisin-2, -3, and -4 were identified in these butterflies. Furthermore, DNA ADP-ribosylating activities were found in six different edible clams. Understanding of the biological nature of pierisin-1 with DNA mono-ADP-ribosylating activity could open up exciting avenues for research and potential therapeutic applications, making it a subject of great interest in the field of molecular biology and biotechnology.

Epigenetic regulation of megakaryopoiesis and platelet formation.

Platelets, produced by megakaryocytes, play unique roles in physiological processes, such as hemostasis, coagulation, and immune regulation, while also contributing to various clinical diseases. During megakaryocyte differentiation, the morphology and function of cells undergo significant changes due to the programmed expression of a series of genes. Epigenetic changes modify gene expression without altering the DNA base sequence, effectively affecting the inner workings of the cell at different stages of growth, proliferation, differentiation, and apoptosis. These modifications also play important roles in megakaryocyte development and platelet biogenesis. However, the specific mechanisms underlying epigenetic processes and the vast epigenetic regulatory network formed by their interactions remain unclear. In this review, we systematically summarize the key roles played by epigenetics in megakaryocyte development and platelet formation, including DNA methylation, histone modification, and non-coding RNA regulation. We expect our review to provide a deeper understanding of the biological processes underlying megakaryocyte development and platelet formation and to inform the development of new clinical interventions aimed at addressing platelet-related diseases and improving patients' prognoses.

Small nuclear RNAs enhance protein-free RNA-programmable base conversion on mammalian coding transcripts.

Endogenous U small nuclear RNAs (U snRNAs) form RNA-protein complexes responsible for eukaryotic processing of pre-mRNA into mature mRNA. Previous studies have demonstrated the utility of guide-programmable U snRNAs in targeted exon inclusion and exclusion. We investigated whether snRNAs can also enhance conversion of RNA bases over state-of-the-art RNA targeting technologies in human cells. When compared to adenosine deaminase acting on RNA (ADAR)-recruiting circular RNAs, we find that guided A>I snRNAs consistently increase adenosine-to-inosine editing efficiency for genes with higher exon counts, perturb substantially fewer genes in the transcriptome, and localize more persistently to the nucleus where ADAR is expressed. A>I snRNAs can also edit pre-mRNA 3' splice sites to promote splicing changes. Finally, snRNA fusions to H/ACA box snoRNAs (U>Ψ snRNAs) increase targeted RNA pseudouridylation efficiency. Altogether, our results advance the protein-free RNA base conversion toolbox and enhance minimally invasive RNA targeting technologies to treat genetic diseases.