Chemical Etiology of Nucleic Acid Structure: The Pentulofuranosyl Oligonucleotide Systems: The (1′→3′)‐β‐L‐Ribulo, (4′→3′)‐α‐L‐Xylulo,and (1′→3′)‐α‐L‐Xylulo Nucleic Acids

Under potentially prebiotic scenarios, ribose (pentose), the component of RNA is formed in meager amounts, as opposed to ribulose and xylulose (pentuloses). Consequently, replacement of ribose in RNA, with pentulose sugars, gives rise to prospective oligonucleotide candidates that are potentially prebiotic structural variants of RNA that could be formed by the same type of chemical pathways that gave rise to RNA from ribose. The potentially natural alternative (1′→3′)‐ribulo oligonucleotides and (4′→3′)‐ and (1′→3′)‐xylulo oligonucleotides consisting of adenine and thymine were synthesized and found to exhibit no self‐pairing or cross‐pairing with RNA. This signifies that even though pentulose sugars may have been abundant in a prebiotic scenario, the pentulose nucleic acids (NAs), if and when formed, would not have been competitors of RNA, or interfered with the emergence of RNA as a functional informational system. The reason for the lack of base pairing in pentulose NA highlights the contrasting and central role played by the furanosyl ring in RNA and pentulose NA, enabling and optimizing the base pairing in RNA, while impeding it in pentulose NA.     

Functional Nanoparticles with a Reducible Tetrasulfide Motif to Upregulate mRNA Translation and Enhance Transfection in Hard‐to‐Transfect Cells

Effective messenger RNA (mRNA) transfection in hard‐to‐transfect cells delivered by vectors is a long‐standing challenge. Now it is hypothesized that the high intracellular glutathione level is associated with suppressed mRNA translation. This theory leads to a new design principle of next‐generation mRNA vectors: nanoparticles with glutathione depletion chemistry upregulate mRNA translation and enhance transfection, which is beneficial for mRNA delivery in hard‐to‐transfect cells in vitro and in vivo.     

Nitroanilines as Quenchers of Pyrene Fluorescence

The quenching of pyrene and 1‐methylpyrene fluorescence by nitroanilines (NAs), such as 2‐, 3‐, and 4‐nitroaniline (2‐NA, 3‐NA, and 4‐NA, respectively), 4‐methyl‐3‐nitroaniline (4‐M ‐3‐NA), 2‐methyl‐4‐nitroaniline (2‐M‐4‐NA), and 4‐methyl‐3,5‐dinitroaniline (4‐M‐3,5‐DNA), are studied in toluene and 1,4‐dioxane. Steady‐state fluorescence data show the higher efficiency of the 4‐NAs as quenchers and fit with a sphere‐of‐action model. This suggests a 4‐NA tendency of being in close proximity to the fluorophore, which could be connected with their high polarity/hyperpolarizability. In addition, emission and excitation spectra evidence the formation of emissive pyrene—NA ground‐state complexes in the case of the 4‐NAs and, in a minor degree, in the 2‐NA. Moreover, time‐resolved fluorescence experiments show that increasing amounts of NA decrease the pyrene fluorescence lifetime to a degree that depends on the NA nature and is larger in the less viscous solvent (toluene). Although the NA absorption and the pyrene (Py) emission overlap, we found no evidence of dipole–dipole energy transfer from the pyrene singlet excited state (¹Py) to the NAs; this could be due to the low NA concentration used in these experiments. Transient absorption spectra show that the formation of the pyrene triplet excited state (³Py) is barely affected by the presence of the NAs in spite of their efficiency in ¹Py quenching, suggesting the involvement of ¹Py—NA exciplexes which—after intersystem crossing—decay efficiently into ³Py.     

Molecular profiling of naphthenic acids in technical mixtures and oil sands process‐affected water using polar reversed‐phase liquid chromatography–mass spectrometry

In this work, a reversed‐phase ultra‐HPLC (UHPLC) ultrahigh resolution MS (UHRMS) method was evaluated for the comprehensive profiling of NAs containing two O atoms in each molecule (O2NAs; general formula C_nH_{2n + z}O₂, where n is the number of carbon atoms and z represents hydrogen deficiency). Using a polar cyanopropyl‐bonded phase column and negative‐ion electrospray ionization mass spectrometric detection at 120,000 FWHM (m/z 400), 187 and 226 O2NA species were found in two naphthenic acid technical mixtures, and 424 and 198 species with molecular formulas corresponding to O2NAs were found in two oil sands process‐affected water samples (one from a surface mining operation and the other from a steam‐assisted gravity drainage operation), respectively. To our knowledge, these are the highest numbers of molecular compositions of O2NAs that have been profiled thus far in environmental samples. Assignments were based on accurate mass measurements (≤3 ppm) combined with rational molecular formula generation, correlation of chromatographic behavior of O2NA homologues with their elemental compositions, and confirmation with carboxyl group‐specific chemical derivatization using 3‐nitrophenylhydrazine. Application of this UHPLC–UHRMS method to the quantitation of O2NAs in the surface mining operation‐derived water sample showed excellent linearity (R² = 0.9999) with external calibration, a linear range of 256‐fold in concentration, and quantitation accuracies of 64.9 and 69.4% at two “standard substance” spiking levels.     

Microfluidic Isolation of Nucleic Acids

The detection of nucleic acids (NAs) within micro total analysis systems (μTASs) for point‐of‐care use is a rapidly developing research area. The efficient isolation of NAs from a raw sample is crucial for these systems to be maximally effective. The use of microfluidics assists in reducing sample sizes and reagent consumption, increases speed, avoids contamination, and enables automation. Through miniaturization into microchips, new techniques have been realized that would be unfavorable and inconvenient to use on a macroscopic scale, but provide an excellent platform for the purification of NAs on a microscopic scale. This Review considers the complexities of NA isolation with miniaturized and microfluidic devices, as well as the considerations when choosing a technique for microfluidic NA isolation, along with their advantages, disadvantages, and potential applications. The techniques presented include using silica‐based surfaces, functionalized paramagnetic beads, oligonucleotide‐modified polymer surfaces, pH‐dependent charged surfaces, Al₂O₃ membranes, and liquid‐phase isolation. This Review provides a basis to develop the chemistry to improve NA isolation and move it toward achieving 100 % efficiencies.     

Nonisothermal crystallization behaviors of polypropylene with α/β nucleating agents

In this work, the nonisothermal crystallization and subsequent melting behaviors of polypropylene (PP) nucleated with different nucleating agents (NAs) have been studied. α‐phase NA 1,3:2,4‐bis (3,4‐dimethylbenzylidene) sorbitol (DMDBS, Millad 3988), β‐phase NA aryl amides compound (TMB‐5), and their compounds were introduced into PP matrix, respectively. The results show that the nonisothermal crystallization behaviors and crystalline structures of PP with compounded NAs are dependent on the composition of NAs. In the sample of PP with 0.1 wt % DMDBS and 0.1 wt % TMB‐5, the nucleation efficiency (NE) of TMB‐5 is much higher than that of DMDBS and PP crystallizes mainly nucleated by TMB‐5, and in this condition, β‐phase PP is the main crystallization structure. For the sample of PP with 0.2 wt % DMDBS and 0.2 wt % TMB‐5, 0.2 wt % DMDBS has higher NE than 0.2 wt % TMB5, and α‐phase is the main crystalline structure. The cooling rate is proved to be very important in controlling the nonisothermal crystallization behavior and the final crystalline structure of nucleated PP. © 2008 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 46: 1853–1867, 2008     

Inhibition of translation by small RNA-stabilized mRNA structures in human cells

RNA-mediated gene regulation and expression are critically dependent on both nucleic acid architecture and recognition. We present a novel mechanism for the regulation of gene expression through direct RNA-RNA interactions between small RNA and mRNA in human cells. Using mRNA reporters containing G-rich sequences in the 5'-untranslated region (5'-UTR), in the coding region, or both, we showed that G-rich small RNAs bind to the reporter mRNAs and form an intermolecular RNA G-quadruplex that can inhibit gene translation in living cells. Using a combination of circular dichroism (CD) and RNase footprinting in vitro, we found that the intermolecular G-quadruplexes show a parallel G-quadruplex structure. We next investigated whether the intermolecular G-quadruplex is present in living cells. Employing the fluorophore-labeled probes, we found that two G-rich RNA molecules form an intermolecular G-quadruplex structure in living cells. These results extend the concept of small RNA-mediated expression and suggest an important role for such RNA structures in the inhibition of mRNA translation.     

Naphthyridine‐Benzoazaquinolone: Evaluation of a Tricyclic System for the Binding to (CAG)n Repeat DNA and RNA

The expansion of CAG repeats in the human genome causes the neurological disorder Huntington's disease. The small‐molecule naphthyridine‐azaquinolone NA we reported earlier bound to the CAG/CAG motif in the hairpin structure of the CAG repeat DNA. In order to investigate and improve NA ‐binding to the CAG repeat DNA and RNA, we conducted systematic structure‐binding studies of NA to CAG repeats. Among the five new NA derivatives we synthesized, surface plasmon resonance (SPR) assay showed that all of the derivatives modified from amide linkages in NA to a carbamate linkage failed to bind to CAG repeat DNA and RNA. One derivative, NBzA , modified by incorporating an additional ring to the azaquinolone was found to bind to both d(CAG)₉ and r(CAG)₉. NBzA binding to d(CAG)₉ was similar to NA binding in terms of large changes in the SPR assay and circular dichroism (CD) as well as pairwise binding, as assessed by electron spray ionization time‐of‐flight (ESI‐TOF) mass spectrometry. For the binding to r(CAG)₉, both NA and NBzA showed stepwise binding in ESI‐TOF MS, and NBzA ‐binding to r(CAG)₉ induced more extensive conformational change than NA ‐binding. The tricyclic system in NBzA did not show significant effects on the binding, selectivity, and translation, but provides a large chemical space for further modification to gain higher affinity and selectivity. These studies revealed that the linker structure in NA and NBzA was suitable for the binding to CAG DNA and RNA, and that the tricyclic benzoazaquinolone did not interfere with the binding.     

Nucleation characteristics of the α/β compounded nucleating agents and their influences on crystallization behavior and mechanical properties of isotactic polypropylene

Nucleation characteristics of isotactic polypropylene (iPP) nucleated by the α/β compounded nucleating agents (NAs) were investigated by wide‐angle X‐ray scattering, differential scanning calorimetry and mechanical testing. The results showed that the nucleation effect of the α/β compounded NAs depends on not only nucleation efficiency (NE) of individual β and α NAs and their ratios but also the processing conditions, especially the cooling rates. The nucleating characteristics of the α/β compounded NAs can be illustrated by competitive nucleation. The NA with high NE played a leading role during iPP crystallization even at a low weight ratio and at different cooling rates. The stiffness and toughness of iPP can be simultaneously improved by using suitable compositions at the appropriate ratios. Finally, the nonisothermal crystallization kinetics of iPP nucleated with the α/β compounded NAs was described by Caze method and the crystallization activation energy of nucleated iPP was calculated by Kissinger equation. The result indicated that the crystal growth pattern of nucleated iPP was heterogeneous nucleation followed by three‐dimension spherical growth. © 2010 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 48: 653–665, 2010     

Atomic detail investigation of the structure and dynamics of DNA.RNA hybrids: a molecular dynamics study

DNA.RNA hybrid duplexes are biologically important molecules and are shown to have potential therapeutic properties. To investigate the relationship between structures, energetics, solvation and RNase H activity of hybrid duplexes in comparison with pure DNA and RNA duplexes, a molecular dynamics study using the CHARMM27 force field was undertaken. The structural properties of all four nucleic acids considered are in very good agreement with the experimental data. The backbone dihedral angles and the puckering of the (deoxy)ribose indicate that the purine rich strands retain their A-/B-like properties but the pyrimidine rich DNA strand undergoes A-B conformational transitions. The minor groove widths of the hybrid structures are narrower than those in the RNA duplex, a requirement for RNase H binding. In addition, sampling of noncanonical phosphodiester backbone dihedrals by the DNA strands, differential solvation properties and helical properties, most notably rise, are suggested to contribute to hybrids being RNase H substrates. Differential RNase H activity toward hybrids containing purine versus pyrimidine rich RNA strands is suggested to be due to sampling of values of the phosphodiester backbone dihedrals in the DNA strands. Notably, the present results indicate that hybrids have decreased flexibility as compared to RNA, in contrast to previous reports.     

One‐Step Nucleic Acid Purification and Noise‐Resistant Polymerase Chain Reaction by Electrokinetic Concentration for Ultralow‐Abundance Nucleic Acid Detection

Nucleic acid amplification tests (NAATs)integrated on a chip hold great promise for point‐of‐care diagnostics. Currently, nucleic acid (NA) purification remains time‐consuming and labor‐intensive, and it takes extensive efforts to optimize the amplification chemistry. Using selective electrokinetic concentration, we report one‐step, liquid‐phase NA purification that is simpler and faster than conventional solid‐phase extraction. By further re‐concentrating NAs and performing polymerase chain reaction (PCR) in a microfluidic chamber, our platform suppresses non‐specific amplification caused by non‐optimal PCR designs. We achieved the detection of 5 copies of M. tuberculosis genomic DNA (equaling 0.3 cell) in real biofluids using both optimized and non‐optimal PCR designs, which is 10‐ and 1000‐fold fewer than those of the standard bench‐top method, respectively. By simplifying the workflow and shortening the development cycle of NAATs, our platform may find use in point‐of‐care diagnosis.     

Comparison of high- and low-resolution electrospray ionization mass spectrometry for the analysis of naphthenic acid mixtures in oil sands process water

The oil sands regions of Northern Alberta, Canada, contain an estimated 1.7 trillion barrels of oil in the form of bitumen, representing the second largest deposit of crude oil in the world. A rapidly expanding industry extracts surface-mined bitumen using alkaline hot water, resulting in large volumes of oil sands process water (OSPW) that must be contained on site due to toxicity. The toxicity has largely been attributed to naphthenic acids (NAs), a complex mixture of naturally occurring aliphatic and (poly-)alicyclic carboxylic acids. Research has increasingly focused on the environmental fate and remediation of OSPW NAs, but an understanding of these processes necessitates an analytical method that can accurately characterize and quantify NA mixtures. Here we report results of an interlaboratory comparison for the analysis of pure commercial NAs and environmental OSPW NAs using direct injection electrospray ionization mass spectrometry (ESI-MS) and high-pressure liquid chromatography/high-resolution mass spectrometry (HPLC/HRMS). Both methods provided very similar characterization of pure commercial NA mixture; however, the m/z selectivity of HPLC/HRMS was essential to prevent substantial false-positive detections and misclassifications in OSPW NA mixtures. For a range of concentrations encompassing those found in OSPW (10-100 mg/L), both methods produced linear response, although concentrations of commercial NAs above 50 mg/L resulted in slight non-linearity by HPLC/HRMS. A three-fold lower response factor for total OSPW NAs by HPLC/HRMS was largely attributable to other organic compounds in the OSPW, including hydroxylated NAs, which may explain the substantial misclassification by ESI-MS. For the quantitative analysis of unknown OSPW samples, both methods yielded total NA concentrations that correlated with results from Fourier transform infrared (FTIR), but the coefficients of determination were not high. Quantification by either MS method should therefore be considered semi-quantitative at best, albeit either method has substantial value in environmental fate experiments where relative concentration changes are the desired endpoints rather than absolute concentrations.     

Effects of nucleating agents on microstructure and fracture toughness of poly(propylene)/ethylene‐propylene‐diene terpolymer blends

The effects of nucleating agents (NAs) on fracture toughness of injection‐molded isotactic poly(propylene)/ethylene‐propylene‐diene terpolymer (PP/EPDM) were studied in this work. Compared with PP/EPDM blends without any NA, PP/EPDM/NA blends show very small and homogeneous PP spherulites. As we expected, PP/EPDM blends nucleated with β‐phase NA aryl amides compound (TMB‐5) present not only a significant enhancement in toughness but also a promotion of brittle‐ductile transition. However, the addition of α‐phase NA 1,3:2,4‐bis(3,4‐dimethylbenzylidene) sorbitol (DMDBS) has no apparent effect on the toughness of the blends. The impact‐fractured surface morphologies of such samples were analyzed via scanning electronic microscope (SEM). More detail work about the toughening mechanisms of elastomer and NA based on elastomer particles size and matrix crystal structures were carried out. Our results suggest that, besides the crystal structures of matrix, the elastomer particles size and size distribution plays an important role in controlling the toughening effect of nucleated PP/elastomer blends. The smaller the elastomer particles size and lower the polydispersity, the more apparent the synergistic toughening effect of NA and elastomer is. This investigation provides a fresh insight into the understanding of toughening mechanism of elastomers in PP blends and facilitates to the design of super toughened PP materials. © 2008 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 47: 46–59, 2009     

Structure and mechanical properties controlling of elastomer modified polypropylene by compounded β/α nucleating agents

Previous work showed that there was a synergistic effect of nucleating agent (NA) and elastomer in improving the fracture resistance of isotactic polypropylene (PP), relating to the formation of large amounts of β‐PP (β‐NA nucleated system) or the decrease of the spherulites diameters of α‐PP (α‐NA nucleated system). To find the direct relation between the synergistic efficiency of NA/elastomer and the microstructures of the materials, in this work, the ethylene‐propylene‐diene terpolymer (EPDM) modified PP blends with compounded NAs (β/α) were adopted and the changes of the microstructure and mechanical properties were investigated comparatively. The results showed that, with the adjustment of the mass fraction of compounded NAs, the microstructures of PP matrix including supermolecular structure and the relative fraction of β‐PP (K_β) change accordingly. Specifically, the K_β of β‐PP was successfully adjusted in the wide range of 0–78.9%. Consequently, the stiffness and the fracture resistance of the PP/EPDM blends were easily controlled in different degrees. It is believed that this work could provide a guide map for the design and preparation of certain polymer blends satisfying certain requirement. © 2011 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys, 2011     

Bidirectional Regulation of mRNA Translation in Mammalian Cells by Using PUF Domains

The regulation of gene expression is crucial in diverse areas of biological science, engineering, and medicine. A genetically encoded system based on the RNA binding domain of the Pumilio and FBF (PUF) proteins was developed for the bidirectional regulation (i.e., either upregulation or downregulation) of the translation of a target mRNA. PUF domains serve as designable scaffolds for the recognition of specific RNA elements and the specificity can be easily altered to target any 8‐nucleotide RNA sequence. The expression of a reporter could be varied by over 17‐fold when using PUF‐based activators and repressors. The specificity of the method was established by using wild‐type and mutant PUF domains. Furthermore, this method could be used to activate the translation of target mRNA downstream of PUF binding sites in a light‐dependent manner. Such specific bidirectional control of mRNA translation could be particularly useful in the fields of synthetic biology, developmental biology, and metabolic engineering.     

Determination of dissolved naphthenic acids in natural waters by using negative-ion electrospray mass spectrometry

Naphthenic acids (NAs) have been implicated as some of the most toxic substances in oil sands leachates and identified as priority substances impacting on aquatic environments. As a group of compounds, NAs are not well characterized and comprise a large group of saturated aliphatic and alicyclic carboxylic acids found in hydrocarbon deposits (petroleum, oil sands bitumen, and crude oils). Described is an analytical method using negative-ion electrospray ionization mass spectrometry (ES/MS) of extracts. Preconcentration was achieved by using a solid-phase extraction procedure utilizing a crosslinked polystyrene-based polymer with acetonitrile elution. Recovery of the Fluka Chemicals NA mixture was highly pH-dependent, with 100% recovery at pH 3.0, but only 66 and 51% recoveries at pHs 7 and 9, respectively. The dissolved phase of the NA was very dependent on sample pH. It is thus critical to measure the pH and determine the appropriate mass profiles to identify NAs in natural waters. The ES/MS analytical procedure proved to be a fast and sensitive method for the recovery and detection of NAs in natural waters, with a detection limit of 0.01 mg/L.     

Functional Nanoparticles with a Reducible Tetrasulfide Motif to Upregulate mRNA Translation and Enhance Transfection in Hard-to-Transfect Cells

Effective messenger RNA (mRNA) transfection in hard-to-transfect cells delivered by vectors is a long-standing challenge. Now it is hypothesized that the high intracellular glutathione level is associated with suppressed mRNA translation. This theory leads to a new design principle of next-generation mRNA vectors: nanoparticles with glutathione depletion chemistry upregulate mRNA translation and enhance transfection, which is beneficial for mRNA delivery in hard-to-transfect cells in vitro and in vivo.     

Nucleobase‐Modified PNA Suppresses Translation by Forming a Triple Helix with a Hairpin Structure in mRNA In Vitro and in Cells

Compounds that bind specifically to double‐stranded regions of RNA have potential as regulators of structure‐based RNA function; however, sequence‐selective recognition of double‐stranded RNA is challenging. The modification of peptide nucleic acid (PNA) with unnatural nucleobases enables the formation of PNA–RNA triplexes. Herein, we demonstrate that a 9‐mer PNA forms a sequence‐specific PNA–RNA triplex with a dissociation constant of less than 1 nm at physiological pH. The triplex formed within the 5′ untranslated region of an mRNA reduces the protein expression levels both in vitro and in cells. A single triplet mismatch destabilizes the complex, and in this case, no translation suppression is observed. The triplex‐forming PNAs are unique and potent compounds that hold promise as inhibitors of cellular functions that are controlled by double‐stranded RNAs, such as RNA interference, RNA editing, and RNA localization mediated by protein–RNA interactions.