Complementary Base Research Articles

Solid-State Nanopores Used for the Detection of DNA Molecules

Solid-state nanopore is crucial in dection of DNA molescules. DNA is made up of two antiparallel strands of polynucleotides. They are joined together by hydrogen bonds between complementary base pairs. The DNA structures are essential for the ability of genetic carrier to control gene expression, promote DNA recombination, and enhance mutagenesis. There are many ways to do DNA testing. Among these methods, nanopore have relatively small size which allows single-molecule detection. It is also less expensive. There are two kinds of nanopores, which are solid-state nanopore and biological nanopore. Solid state nanopore has better capacity to be incorporated into systems and arrays. The channel length and diameter of it can be controlled easily. In addition, its surface properties are also tunable. Therefore, this essay discussed concerning with the different types of nanopore technology: FEB, FIB and wet etching. The mechanism of nanopore was also explained. The existence of nanopores is conducive to a series of research on genes, pharmaceuticals, biology and so on.

Long-range RNA structures in the human transcriptome beyond evolutionarily conserved regions.

RNA structure has been increasingly recognized as a critical player in the biogenesis and turnover of many transcripts classes. In eukaryotes, the prediction of RNA structure by thermodynamic modeling meets fundamental limitations due to the large sizes and complex, discontinuous organization of eukaryotic genes. Signatures of functional RNA structures can be found by detecting compensatory substitutions in homologous sequences, but a comparative approach is applicable only within conserved sequence blocks. Here, we developed a computational pipeline called PHRIC, which is not limited to conserved regions and relies on RNA contacts derived from RNA in situ conformation sequencing (RIC-seq) experiments. It extracts pairs of short RNA fragments surrounded by nested clusters of RNA contacts and predicts long, nearly perfect complementary base pairings formed between these fragments. In application to a panel of RIC-seq experiments in seven human cell lines, PHRIC predicted ~12,000 stable long-range RNA structures with equilibrium free energy below -15 kcal/mol, the vast majority of which fall outside of regions annotated as conserved among vertebrates. These structures, nevertheless, show some level of sequence conservation and remarkable compensatory substitution patterns in other clades. Furthermore, we found that introns have a higher propensity to form stable long-range RNA structures between each other, and moreover that RNA structures tend to concentrate within the same intron rather than connect adjacent introns. These results for the first time extend the application of proximity ligation assays to RNA structure prediction beyond conserved regions.

A smartphone-assisted portable strategy based on maple leaf-like Au/Cu2S/MoS2 composite for photothermal and colorimetric sensing of cortisol

Herein, we describe a first-time synthesis of a maple leaf-like Au/Cu2S/MoS2 composite (denoted as ACM throughout this paper) with both photothermal and peroxidase (POD) activities. Based on the ACM, we developed a smartphone-assisted portable detection platform for the photothermal and colorimetric dual-mode sensing of cortisol in human saliva. Because of complementary base pairing, the “Y”-type signal-probe (formed by the coincubation of ACM-DNA1 and ACM-DNA2) is fixed on cortisol-specific aptamer-functionalized magnetic beads (MB–Aptcortisol). ​In the presence of target cortisol, MB-Aptcortisol is more likely to combine with cortisol, “Y”-type signal-probes are released, which can oxidize 3,3′,5,5′-tetramethylbenzidine (TMB) to blue oxTMB in the existence of H2O2. Notably, the oxTMB exhibits a distinct photothermal response which, in combination with the photothermal properties of the ACM, achieves transduction and signal amplification of cortisol through a cascade enzyme reaction. The photothermal and colorimetric signals increase with increasing target concentrations. This portable dual-signal sensing platform enables the detection of cortisol in the range of 5–10000 ng/mL, with detection limits of 0.11 and 0.25 ng/mL for photothermal and colorimetric signals, respectively (The reference concentration of cortisol in saliva of healthy people is 1–12 ng/mL in the morning and 0.1–3 ng/mL at night). It is inexpensive, user-friendly, and allows for rapid analysis, rendering it suitable for clinical applications.

Expression of nonmuscle myosin IIC is regulated by non-canonical binding activity of miRNAs

The expression of mechanoresponsive nonmuscle myosin II (NMII)C is found to be inducible during tumor progression, but its mechanism is yet to be explored. Here, we report a group of microRNAs (mmu-miR-200a-5p, mmu-miR-532-3p, mmu-miR-680, and mmu-miR-1901) can significantly repress the expression of nonmuscle myosin IIC (NMIIC). Interestingly, these microRNAs have both canonical and non-canonical binding sites at 3/UTR and coding sequence (CDS) of NMIIC's heavy chain (HC) mRNA. Each of the miRNA downregulates NMHC-IIC to a different degree as assessed by dual-luciferase and immunoblot analyses. When we abolish the complementary base pairing at canonical binding site, mmu-miR-532-3p can still bind at non-canonical binding site and form Argonaute2 (AGO2)-miRNA complex to downregulate the expression of NMIIC. Modulating the expression of NMIIC by miR-532-3p in mouse mammary tumor cells, 4T1, increases its tumorigenic potential both invitro and invivo. Together, these studies provide the functional role of miRNA's non-canonical binding mediated NMIIC regulation in tumor cells.

Bacterial cellulose loaded with silver nanoparticles as a flexible, stable and sensitive SERS-active substrate for detection of the shellfish toxin DTX-1.

Diarrheal shellfish toxins are considered one of the most lethal red tide algae toxins in the worldwide. In this work, we propose an Ag NPs-loaded bacterial cellulose membrane (BCM) surface-enhanced Raman scattering (SERS) sensor based on an aptamer (Apt) for the ultrasensitive detection of dinophysistoxin (DTX-1), a type of diarrheal shellfish toxin. During drying, Ag NPs can be further densified on "gel-like" BCM to form high-density SERS "hot spots". We developed the "Apt-SH@Ag NPs@BCM" SERS sensor and used the competition of DTX-1 and complementary base (Cob) in the process of base complementary pairing to achieve SERS detection of DTX-1, with a minimum detection limit of 9.5×10-10mol/L. Sample assays showed DTX-1 recovery rates ranging from 95.8% and 108.2% and the detection results were comparable to those obtained by LC-MS. Therefore, this work holds great potential for detecting of toxic substances in shellfish products, especially for the oyster (portuguese oyster) and mussel (blue mussel).

Small Non-Coding RNAs in Male Reproduction.

Male reproductive functions are strictly regulated in order to maintain sperm production and fertility. All processes are controlled by precise regulation of gene expression, which creates specific gene expression programs for different developmental stages and cell types, and forms the functional basis for the reproductive system. Small non-coding RNAs (sncRNAs) are involved in gene regulation by targeting mRNAs for translational repression and degradation through complementary base pairing to recognize their targets. This review article summarizes the current knowledge on the function of different classes of sncRNAs, in particular microRNAs (miRNAs) and PIWI-interacting RNAs (piRNAs), during male germ cell differentiation, with the focus on sncRNAs expressed in the germline. Although transcriptionally inactive, mature spermatozoa contain a complex population of sncRNAs, and we also discuss the recently identified role of sperm sncRNAs in the intergenerational transmission of epigenetic information on father's environmental and lifestyle exposures to offspring. Finally, we summarize the current information on the utility of sncRNAs as potential biomarkers of infertility that may aid in the diagnosis and prediction of outcomes of medically assisted reproduction.

SRIM Simulation of Ion Beam Irradiation Effects on Oxide Thin Films

In recent studies, multifunctional oxide thin films have been given attention because of their special properties, such as ferroelectricity, gas sensitivity, and magnetism. Ion beam irradiation arose as a well-developed technique for tuning such properties. This study investigates the ion beam irradiation effects of He, Ni, and Kr ions on BiFeO3, SnO2, and ZnO thin films, respectively. The study utilized the 2013 version of Stopping and Range of Ions in Matter (SRIM) software to identify ion trajectory distribution and oxygen target vacancy differences on the Transport of Ions in Matter (TRIM) calculation types at various ion energies. A greater distribution of ion trajectories and higher peaks of oxygen target vacancies in oxide thin films were generated from monolayer TRIM than full cascade TRIM for all ion–thin-film pairs. The monolayer TRIM is preferable for ion beam irradiation of oxide thin films with its greater oxygen target vacancies and ion trajectory distribution for better analysis of ferroelectric coercive fields, adsorbed oxygen ions interaction with gas molecules, and the emergence of green emission for photoluminescence. The use of SRIM allows an alternative yet more flexible way of analyzing beam irradiation effects on oxide films considered in this work without resorting to costly or sophisticated experimental setups, which are a usual approach considered in most of the work under this topic. As such, the results presented here provide an initial or complementary basis should irradiation effect experiments require analysis of ion trajectories and oxygen vacancies.

Climate change increases the instability of the water supply for hydropower stations on the Tibetan Plateau

In recent decades, global warming has had a significant impact on the streamflow across the Tibetan Plateau. As the largest tributary in the upper reaches of the Yangtze River, the Yalong river is known for its abundant hydropower resources, and the world’s largest multi-energy complementary base has been built in the Yalong River Basin. However, prudent water resource planning is limited by the lack of long-term, detailed and reliable streamflow records over the Yalong river basin. Here, we develop an October–June streamflow reconstruction for the Yalong River, based on composite tree-ring chronology of Picea likiangensis from seven sampling sites. The reconstruction goes back to 1480 CE, and accounts for 46.5% of the instrumental streamflow variance during 1962–2012. This record indicates that the Interdecadal Pacific Oscillation and the Atlantic Multi-decadal Oscillation were the major contributing factors to streamflow variations. A significant and stable correlation with temperature was found over the past few centuries on the interannual scale. Projections suggest that future climate change may lead to more frequent flood disasters in the Yalong River Basin.

Leveraging QM/MM and Molecular Dynamics Simulations to Decipher the Reaction Mechanism of the Cas9 HNH Domain to Investigate Off-Target Effects.

The clustered regularly interspaced short palindromic repeats (CRISPR) technology is an RNA-guided targeted genome-editing tool using Cas family proteins. Two magnesium-dependent nuclease domains of the Cas9 enzyme, termed HNH and RuvC, are responsible for cleaving the target DNA (t-DNA) and nontarget DNA strands, respectively. The HNH domain is believed to determine the DNA cleavage activity of both endonuclease domains and is sensitive to complementary RNA-DNA base pairing. However, the underlying molecular mechanisms of CRISPR-Cas9, by which it rebukes or accepts mismatches, are poorly understood. Thus, investigation of the structure and dynamics of the catalytic state of Cas9 with either matched or mismatched t-DNA can provide insights into improving its specificity by reducing off-target cleavages. Here, we focus on a recently discovered catalytic-active form of the Streptococcus pyogenes Cas9 (SpCas9) and employ classical molecular dynamics and coupled quantum mechanics/molecular mechanics simulations to study two possible mechanisms of t-DNA cleavage reaction catalyzed by the HNH domain. Moreover, by designing a mismatched t-DNA structure called MM5 (C to G at the fifth position from the protospacer adjacent motif region), the impact of single-guide RNA (sgRNA) and t-DNA complementarity on the catalysis process was investigated. Based on these simulations, our calculated binding affinities, minimum energy paths, and analysis of catalytically important residues provide atomic-level details of the differences between matched and mismatched cleavage reactions. In addition, several residues exhibit significant differences in their catalytic roles for the two studied systems, including K253, K263, R820, K896, and K913.

Exonuclease III‑assisted and target-induced conformational change of DNA hairpins for electrochemical detection of mercury (II)

Here, we report a DNA hairpin strategy for electrochemical determination of Hg2+ based on T-Hg2+-T pairs and exonuclease III (Exo III) assistance. The innovation of this work lies in the designed DNA structure and detection principles. Unlike the previously reported DNA hairpin structure, the ring portion of the hairpin DNA we designed consisting of T bases serves as a recognition probe, forming a T-Hg-T complex with Hg2+. The stem is composed of 5 pairs of complementary bases, which is conducive to the stability of the hairpin structure. After the formation of T-Hg-T in the ring, with the help of Exo III, Exo III can digest more DNA than the T bases designed in the stem. In this event, the shorter the length of the remaining DNA strand on the electrode, the weaker the repulsive force against [Fe(CN)6]3−/4−, and the stronger the differential pulse voltammetry (DPV) current signal, achieving “signal-on” transitions. Under the optimal conditions, the DPV current response increases with increasing Hg2+ concentration and is linear with the logarithm of Hg2+ concentration (1 nM–10 μM). The limit ofdetection is 0.16 nM. The electrochemical sensor was successfully applied to the determination of Hg2+ in river water.

Formation and Effects of Upstream DNA-RNA Base Pairing in Telomerase.

Telomere elongation by telomerase consists of two types of translocation: duplex translocation during each repeat synthesis and template translocation at the end of repeat synthesis. Our replica exchange molecular dynamics simulations show that in addition to the Watson-Crick interactions in the active site, templating RNA can also form base pairs with the upstream regions of DNA, mostly with the second upstream DNA repeat with respect to the 3'-end. At the end of the repeat synthesis, dG10-P442 and dG11-N446 hydrogen bonds form. Then, active-site base pairs dissociate one by one, and the RNA bases reanneal with the complementary base on the upstream DNA repeat. For each dissociating base pair a new one forms, thus conserving the number of base pairs during template translocation.

FADH2-mediated radical polymerization amplification for microRNA-21 detection

For early diagnosis of disease, ultrasensitive mircoRNA-21 detection has considerable potential. In this paper, an ultra-sensitive fluorescence detection method for microRNA was developed by atom transfer radical polymerization (ATRP). This ATRP reaction was first initiated by using flavin mononucleotide (FADH2). The DNA probe 1 modified with amino group was fixed on the magnetic nanoparticle Fe3O4, and microRNA-21 was added to form the probe 1-microRNA-21. Another carboxy-modified DNA 2 forms a sandwich structure with the bound microRNA-21. Two terminally modified DNA types are used as microRNA probes, using complementary base pairing to form a stable super-sandwich structure between the DNA probe and the microRNA. Under optimal conditions, microRNA was detected in PBS buffer with a detection limit of 0.19 fM. And even in 10% of human serum, microRNA-21 can be detected with a detection limit of 47.8 fM. Results show that this method has high selectivity, efficiency and stability, which broad application prospect in microRNA ultra-sensitive detection.

Synchronous detection of Burkholderia pseudomallei and its ceftazidime resistance mutation based on RNase-HII hydrolysis combined with lateral flow strip assay.

Melioidosis is a severe and often fatal infectious disease caused by Burkholderia pseudomallei, which poses significant challenges due to its high mortality rate and frequent misdiagnosis. To effectively treat infected patients, especially in epidemic regions like Hainan with a high resistance rate to ceftazidime (CAZ), early diagnosis and resistance testing are critical. Here, we designed a strategy that combines RNase-HII-dependent PCR with lateral flow strip assay (LFSA) for simultaneous detection of B. pseudomallei and its CAZ resistance mutation. In this strategy, we utilized rhPCR technology to design specific primers with a C3-spacer modification. These primers target a 115-base pair region within the ORF2 of the B. pseudomallei type III secretion system gene cluster, as well as the P174L mutation in the penA gene, which is a major mutation associated with CAZ resistance in Hainan. The primers contain complementary RNA bases that can be hydrolyzed only in the presence of thermostable RNase-HII enzymes, facilitating subsequent PCR reactions. Additionally, we introduced two pairs of universal probes carrying fluorescein isothiocyanate (FITC) and biotin, as well as digoxin and biotin. The sequences of these universal probes align with specific regions of the primers, resulting in target products labeled with different tags. The resulting amplification products are then subjected to LFSA, where the presence of specific markers is visually interpreted based on color development. These markers flow to test line 1 (T1) and are captured by a fixed anti-FITC antibody, generating a red line that indicates the presence of B. pseudomallei. Similarly, the occurrence of a red line on test line 2 (T2), which is fixed with anti-digoxin antibodies, indicates the presence of the P174L mutation in B. pseudomallei. This protocol serves as an excellent tool for the rapid diagnosis of melioidosis and provides a basis for selecting appropriate antibiotic medication. It has the potential to revolutionize the diagnosis of melioidosis, particularly in resource-limited settings. Furthermore, this technique holds promise as a versatile tool for disease diagnosis in general. IMPORTANCE This study focused on the development of a reaction system using rhPCR to amplify a specific gene, ORF2, of B. pseudomallei and to identify the P174L mutation associated with increased drug resistance to ceftazidime (CAZ). The system incorporated universal primer probes and a simple temperature cycle reaction. The amplified products were then analyzed using lateral flow strip assay (LFSA) for strain identification and mutation interpretation. The developed system provides a reliable basis for diagnosing melioidosis and selecting appropriate drugs. Its potential impact is particularly significant in resource-limited settings where access to advanced diagnostic techniques is limited. This platform stands out for its simplicity, convenience, sensitivity, specificity, and portability. It shows promise as a point-of-care testing method for detecting single nucleotide polymorphism in genes associated with other diseases. By leveraging the advantages of this platform, researchers and healthcare professionals can potentially expand its use beyond melioidosis and apply it to the rapid detection of genetic variations in other disease-related genes.

Engineering Nucleotidoproteins for Base‐Pairing‐Assisted Cytosolic Delivery and Genome Editing

AbstractProtein therapeutics targeting intracellular machineries hold profound potential for disease treatment, and hence robust cytosolic protein delivery technologies are imperatively demanded. Inspired by the super‐negatively charged, nucleotide‐enriched structure of nucleic acids, adenylated pro‐proteins (A‐proteins) with dramatically enhanced negative surface charges have been engineered for the first time via facile green synthesis. Then, thymidine‐modified polyethyleneimine is developed, which exhibits strong electrostatic attraction, complementary base pairing, and hydrophobic interaction with A‐proteins to form salt‐resistant nanocomplexes with robust cytosolic delivery efficiencies. The acidic endolysosomal environment enables traceless restoration of the A‐proteins and consequently promotes the intracellular release of the native proteins. This strategy shows high efficiency and universality for a variety of proteins with different molecular weights and isoelectric points in mammalian cells. Moreover, it enables highly efficient delivery of CRISPR‐Cas9 ribonucleoproteins targeting fusion oncogene EWSR1‐FLI1, leading to pronounced anti‐tumor efficacy against Ewing sarcoma. This study provides a potent and versatile platform for cytosolic protein delivery and gene editing, and may benefit the development of protein pharmaceuticals.

Engineering Nucleotidoproteins for Base-Pairing-Assisted Cytosolic Delivery and Genome Editing.

Protein therapeutics targeting intracellular machineries hold profound potential for disease treatment, and hence robust cytosolic protein delivery technologies are imperatively demanded. Inspired by the super-negatively charged, nucleotide-enriched structure of nucleic acids, adenylated pro-proteins (A-proteins) with dramatically enhanced negative surface charges have been engineered for the first time via facile green synthesis. Then, thymidine-modified polyethyleneimine is developed, which exhibits strong electrostatic attraction, complementary base pairing, and hydrophobic interaction with A-proteins to form salt-resistant nanocomplexes with robust cytosolic delivery efficiencies. The acidic endolysosomal environment enables traceless restoration of the A-proteins and consequently promotes the intracellular release of the native proteins. This strategy shows high efficiency and universality for a variety of proteins with different molecular weights and isoelectric points in mammalian cells. Moreover, it enables highly efficient delivery of CRISPR-Cas9 ribonucleoproteins targeting fusion oncogene EWSR1-FLI1, leading to pronounced anti-tumor efficacy against Ewing sarcoma. This study provides a potent and versatile platform for cytosolic protein delivery and gene editing, and may benefit the development of protein pharmaceuticals.

The ZX-calculus as a language for topological quantum computation

Unitary fusion categories formalise the algebraic theory of topological quantum computation. These categories come naturally enriched in a subcategory of the category of Hilbert spaces, and by looking at this subcategory, one can identify a collection of generators for implementing quantum computation. We represent such generators for the Fibonacci and Ising models, namely the encoding of qubits and the associated braid group representations, with the ZX-calculus and show that in both cases, the Yang–Baxter equation is directly connected to an important rule in the complete ZX-calculus known as the P-rule, which enables one to interchange the phase gates defined with respect to complementary bases. In the Ising case, this reduces to a familiar rule relating two distinct Euler decompositions of the Hadamard gate as Z- and X-phase gates, whereas in the Fibonacci case, we give a previously unconsidered exact solution of the P-rule involving the Golden ratio. We demonstrate the utility of these representations by giving graphical derivations of the single-qubit braid equations for Fibonacci anyons and the single- and two-qubit braid equations for Ising anyons. We furthermore present a fully graphical procedure for simulating and simplifying braids with the ZX-representation of Fibonacci anyons.

Endogenous Enzyme-Activatable Spherical Nucleic Acids for Spatiotemporally Controlled Signal Amplification Molecular Imaging and Combinational Tumor Therapy.

Due to the adjustable hybridization activity, antinuclease digestion stability, and superior endocytosis, spherical nucleic acids (SNAs) have been actively developed as probes for molecular imaging and the development of noninvasive diagnosis and image-guided surgery. However, since highly expressed biomarkers in tumors are not negligible in normal tissues, an inevitable background signal and the inability to precisely release probes at the chosen region remain a challenge for SNAs. Herein, we proposed a rationally designed, endogenous enzyme-activatable functional SNA (Ep-SNA) for spatiotemporally controlled signal amplification molecular imaging and combinational tumor therapy. The self-assembled amphiphilic polymer micelles (SM-ASO), which were obtained by a simple and rapid copper-free strain-promoted azide-alkyne cycloaddition click reaction between dibenzocyclooctyne-modified antisense oligonucleotide and azide-containing aliphatic polymer polylactic acid, were introduced as the core elements of Ep-SNA. This Ep-SNA was then constructed by connecting two apurinic/apyrimidinic (AP) site-containing trailing DNA hairpins, which could occur via a hybridization chain reaction in the presence of low-abundance survivin mRNA to SM-ASO through complementary base pairing. Notably, the AP site-containing trailing DNA hairpins also empowered the SNA with the feasibility of drug delivery. Once this constructed intelligent Ep-SNA nanoprobe was specifically cleaved by the highly expressed cytoplasmic human apurinic/apyrimidinic endonuclease 1 in tumor cells, three key elements (trailing DNA hairpins, antisense oligonucleotide, and doxorubicin) could be released to enable subsequent high-sensitivity survivin mRNA imaging and combinational cancer therapy (gene silencing and chemotherapy). This strategy shows great application prospects of SNAs as a precise platform for the integration of disease diagnosis and treatment and can contribute to basic biomedical research.

Purine DNA Constructs Designed to Expand the Genetic Code: Functionalization, Impact of Ionic Forms, and Molecular Recognition of 7-Deazaxanthine-7-Deazapurine-2,6-diamine Base Pairs and Their Purine Counterparts.

Purine DNA represents an alternative pairing system formed by two purines in the base pair with the recognition elements of Watson-Crick DNA. Base functionalization of 7-deaza-2'-deoxyxanthosine with ethynyl and octadiynyl residues led to clickable side chain derivatives with short and long linker arms. As complementary bases, purine-2,6-diamine or 7-deazapurine-2,6-diamine 2'-deoxyribonucleosides were used. 7-Deaza-7-iodo-2'-deoxyxanthosine served as a starting material for Sonogashira cross-coupling and the p-nitrophenylethyl group for base protection. Phosphoramidite building blocks for DNA synthesis were prepared. Oligonucleotides containing single modifications or runs of three purine base pairs embedded in 12-mer Watson-Crick DNA were synthesized and hybridized with complementary strands with purine- or 7-deazapurine-2,6-diamine located opposite to the xanthine derivatives. The stability of base pairs was evaluated in a comparative study on the basis of DNA melting experiments and Tm values. As 7-deazaxanthine and xanthine nucleosides form anionic forms at neutral pH, duplex stability became pK-dependent, and the system with 7-deazapurine displayed a significant higher stability as that containing xanthine. Alkynyl side chains are well accommodated in the purine-purine helix. Click adducts with pyrene showed that short linker arms destabilize duplexes, whereas long linkers increase duplex stability. CD and fluorescence measurements provide further insights into purine-purine base pairing.

Evolution of High-Affinity ssDNA Sequence to Carbon Nanotube

Colloidal ssDNA-wrapped single walled carbon nanotube (ssDNA-SWCNT) has been used as the second near-infrared (NIR-II, 1000 -1700 nm) fluorescent nanoprobes with outstanding biocompatibility, and acts as various optical nano sensors for biological analytes such as a dopamine and serotonin. The stability and affinity of ssDNA on the SWCNT surface significantly depends on the sequence of ssDNA, however the large-scale quantitative analysis between ssDNA sequence library, which has high affinity to the SWCNT surface, was repeatedly selected from a random ssDNA(N30) library (~1018) and the resulting sequence data was analyzed. The binding affinity of ssDNA to SWCNT was quantitatively characterized. To quantitatively analyze the kinetics of the process which occurs solvatochromic shift by sodium cholate, assumed the dynamics follow a first-order kinetic model and fit the experimental data using exponential regression, from which decay time constants were determined. As a result, the highest binding affinity of ssDNA to SWCNT was quantitatively characterized by time constant (1.5 X106 sec) which increased by 100 times compared to the N30 random library. Through analysis of the ssDNA sequences with high affinity for the SWCNT surface, we found that the sequences contain high contents of cytosine and adenine nucleotides and complementary base pairs appeared at distance of 5 to 8 bases. This novel sequence library can be applied for the preparation of the ultra-stable ssDNA-SWCNT dispersion and used for anchoring surface ligands for SWCNT as biosensor. Figure 1

Characterization of circulating microRNA profiles of postpartum dairy cows with persistent subclinical endometritis

Subclinical endometritis (SCE) is an unresolved inflammation of the endometrium of postpartum dairy cows, seriously affecting fertility. Current diagnosis, which relies on uterine cytology or even more invasive biopsy sampling, would benefit from the identification of blood-based diagnostic biomarkers. Due to the known role of microRNAs (miRNAs) in other diseases, this case-control study evaluated the cell-free circulating miRNA profiles of SCE cows, and the network of transcripts predicted to interact with those miRNAs, previously identified as differentially expressed genes (DEG) in the endometrium of the same cows. Healthy (H, n = 6) and persistent SCE (n = 11) cows characterized by endometrial cytology and biopsy were blood sampled at 21 and 44 d postpartum (DPP). Following extraction of cell-free plasma miRNAs and RNA-seq analysis, differential abundance analysis of miRNAs was performed with the DESeq2 R package (adjusted p-value of 0.05), and in silico prediction of miRNA-interacting genes on a sequence complementary basis was conducted using the miRWalk database. The principal component analysis showed a clear clustering between groups of uterine health phenotypes (H vs. SCE), although the clustering between groups was less pronounced at 44 DPP than at 21 DPP. No effect of the stage (21 vs. 44 DPP) was observed. A total of 799 known circulating miRNAs were identified, from which 34 demonstrated differential abundance between H and SCE cows (12 less abundant and 22 more abundant in SCE than in H cows). These 34 miRNAs are predicted to interact with 10,104 transcripts, among which 43, 81, and 147 were previously identified as differentially expressed in, respectively, endometrial luminal epithelial, glandular epithelial, and stromal cells of the same cows. This accounts for approximately half of the DEG identified between those H and SCE cows, including genes involved in endometrial cell proliferation, angiogenesis and immune response, whose dysregulation in SCE cows may impair pregnancy establishment. From 219 miRNAs with mean normalized read counts above 100, the presence and abundance of miR-425-3p and miR-2285z had the highest discriminatory level to differentiate SCE from H cows. In conclusion, despite apparent confinement to the endometrium, SCE is associated with a distinct circulating miRNA profile, which may represent a link between the systemic changes associated with disease and the endometrial immune response. The validation of a miRNA panel consisting of circulating cell-free miR-425-3p and miR-2285z may prove a relevant advancement for the noninvasive diagnosis of persistent SCE.