Complementary Base Research Articles

Abstract 3787: miR 2355-5p regulates tumor growth and angiogenesis in VHL-inactivated clear cell renal cell carcinoma

Abstract Background: Clear Cell Renal Cell Carcinoma (ccRCC) constitutes more than 75% of kidney cancer diagnostics. Inactivation of the tumor suppressor gene termed von Hippel-Lindau (VHL) is considered the major truncal event and occurs in more than 85% of patients. The most notable role of VHL is its ability to negatively regulate the Hypoxia-Induced Factors (HIFα), which in turn, stimulate the transcription of multiple oncogenes, including microRNAs (miRNAs). MiRNAs are small non-coding RNAs that negatively regulate gene expression through complementary base pairing. Using ccRCC cell models, we observed an overexpression of the miR 2355-5p following the loss of VHL in a HIF2α dependent manner. Hypothesis: We hypothesize that the miR 2355-5p overexpression is involved in the tumorigenesis of VHL-inactivated ccRCC. Our specific aims are to i) quantify the expression of miR 2355-5p in ccRCC clinical samples, ii) characterize the functional impact of miR 2355-5p in ccRCC development, and iii) identify miR 2355-5p targeted genes in ccRCC tumors. Methods: Clinical samples (tissues and plasma) from consented patients with ccRCC were recruited through the Université de Sherbrooke. Normal adjacent tissue and plasma from healthy individuals were used as controls. miR 2355-5p expression was quantified through RT-qPCR with Taqman probes. Then, 786-0 and A498 VHL-deficient ccRCC cell lines were used. miR 2355-5p knockout models (KO) were generated using CRISPR/cas9 technology or stably overexpressed using miRNA precursor plasmid (786-0++2355). The impact on cell survival and proliferation was assessed with clonogenic assay and daily cell counts, respectively. Furthermore, cell models were injected into immunodeficient mice. Angiogenesis was evaluated by tube formation assay and angiogenesis proteome profiler kit. Finally, miRNA pulldown was performed to identify miR 2355-5p potential targets. Results: Our findings showed a significant increase in miR 2355-5p expression in tumor tissue compared to normal adjacent tissue as well as in plasma samples compared to healthy individuals. Inhibition of miR 2355-5p significantly reduced cell survival and cell proliferation in vitro and in vivo. Altered expression of the miRNA also disturbed the expression of multiple angiogenic factors and reduced the ability of cells to stimulate tube formation. MiRNA pulldown identified over 267 potential targets, where 161 were mRNA coding for functioning proteins. Close to 80% of identified proteins were direct targets of miR 2355-5p according to prediction software. Further analysis showed an inverse correlation between the tumor suppressor gene SPRY4 and miR 2355-5p, uncovering a potential link between the two. Discussion: Our results demonstrate an important role of miR 2355-5p on angiogenesis and ccRCC tumor growth. Further research on the interaction between miR-2355-5p, BTG2, SLIT2, and CMTM4 could unlock new potential avenues for targeted therapies. Citation Format: Patric Page, Sandra Turcotte, Mykella Martin, Patrick Richard, Tamiko Nishimura, Yasser Riazalhosseini. miR 2355-5p regulates tumor growth and angiogenesis in VHL-inactivated clear cell renal cell carcinoma. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3787.

Fakes within Context of Historical Knowledge Interacting with Language and Thought Structures: Interdisciplinary Model

The phenomenon of fake news is considered as a multifaceted scientific problem that cannot be solved without using an interdisciplinary approach. The relevance of the study is due to the high degree of influence of falsifications on the information perception of a person, and consequently, on the cognitive safety of society. A fake is analyzed as a complex construct that does not have clear signs, but has an intentional effect on a person. Particular attention is paid to the characteristics of the interaction of cognitive mechanisms and language forms in the practice of interaction with fakes. The concept of “post-truth” is considered as an instrument of influence of multiple subjects on the audience by proclaiming the multiplicity of truths. The practices of combating illegal information content, based on the experience of various states are described. It is noted that in Russia, history is considered a key factor in the state policy of cognitive security. The article substantiates the need to find complementary resources in linguistic and historical sciences for effective countermeasures against information manipulation and presentation of unreliable information. The authors concluded that the priority task of interdisciplinary research at the present stage is the creation of a complementary empirical scientific base taking into account the methods of cognitive linguistics and the testing of theoretical models on recipients.

Programming Nucleation and Growth in Colloidal Crystals Using DNA.

Colloidal crystal engineering with DNA has advanced beyond controlling the lattice symmetry and parameters of ordered crystals to now tuning crystal habit and size. However, the predominately used slow-cooling procedure that enables faceted crystal habits also limits control over crystal size and uniformity because nucleation and growth cannot be separated. Here, we explore how DNA sequence design can be used to deliberately separate nucleation and growth in a given crystallization process. Specifically, two batches of complementary particles are created with one batch exhibiting perfectly complementary base pairs while the other has a strategically introduced mismatch. This design enables the weaker binding "growth" particles to participate in heterogeneous growth on the nucleates formed from the stronger binding "seed" particles, effectively eliminating secondary nucleation pathways. By eliminating secondary nucleation events, this approach improves crystal uniformity, as measured by polydispersity (from PDI = 0.201 to 0.091). By using this approach with two different particle cores (gold and silver), we show how core-shell colloidal crystals can be synthesized in a one-pot fashion. This work shows how tuning DNA interaction strength can profoundly impact crystal size, uniformity, and structure, parameters central to using such materials as device components.

Locating, tracingand sequencing multiple expanded genetic letters in complex DNA context via a bridge-base approach.

A panel of unnatural base pairs is developed to expand genetic alphabets. One or more unnatural base pairs (UBPs) can be inserted to enlarge the capacity, diversity, and functionality of canonical DNA, so monitoring the multiple-UBPs-containing DNA by simple and convenient approaches is essential. Herein, we report a bridge-base approach to repurpose the capability of determining TPT3-NaM UBPs. The success of this approach depends on the design of isoTAT that can simultaneously pair with NaM and G as a bridge base, as well as the discovering of the transformation of NaM to A in absence of its complementary base. TPT3-NaM can be transferred to C-G or A-T by simple PCR assays with high read-through ratios and low sequence-dependent properties, permitting for the first time to dually locate the multiple sites of TPT3-NaM pairs. Then we show the unprecedented capacity of this approach to trace accurate changes and retention ratios of multiple TPT3-NaM UPBs during in vivo replications. In addition, the method can also be applied to identify multiple-site DNA lesions, transferring TPT3-NaM makers to different natural bases. Taken together, our work presents the first general and convenient approach capable of locating, tracing, and sequencing site- and number-unlimited TPT3-NaM pairs.

Optimal scheduling model of hydro-photovoltaic complementary based on simulation optimization algorithm

The total amount of hydro-photovoltaic generation is limited by the grid channel after large-scale grid connection of photovoltaic in the hydro-photovoltaic complementary clean energy base, resulting in the reduction of power generation efficiency of the system, an optimization scheduling model of hydro-photovoltaic complementary with yearly, monthly and daily scheduling cycles is established. The model adopts the simulation optimization algorithm, introduces the photovoltaic absorption measurement method, aiming at maximizing the power generation benefit of the system, and finally determines the cascade hydropower dispatching method. Taking the Tibet section of the Mekong River as an example, five typical hydrological years are cited to conduct a case study on the optimal scheduling of the hydro-photovoltaic complementary clean energy base. The results show that, on the basis of guaranteeing the hydropower benefit, this dispatching method can effectively improve the photovoltaic absorption rate, and realize the improvement of the total power generation benefit of the hydro-photovoltaic complementary base.

Enhanced fluorescent detection of nucleic acid based on hairpin DNA-assisted toehold-mediated strand displacement reaction

A new hairpin DNA regulated strand displacement strategy for detection of nucleic acid is proposed via the conformational transformation of hairpin DNA. In this entropy-driven signal amplification strategy, we introduce a hairpin structure (single strand B) into a duplex strand which makes the entire strand displacement process easier and faster when the target DNA exists. The strand migration process of displacing the single strand B with the target is a process of constantly displacing bases. As the number of displaced bases increases, the stem ends of the B strand tend to be in a flexible state. When the number of bases is large enough, the two parts of the stem in B strand will undergo complementary base pairing. Therefore, in the subsequent displacement process, target DNA will displace strand B avoiding completely displacing all the bases at the end of the B strand. Regardless of thermodynamics or kinetics, the formation of this hairpin structure has a certain impetus for the displacement reaction. Since the entire reaction process is truly enzyme-free, simple to operate and low in cost, and thus is expected to provide a novel strategy for clinical analysis.

Perfect splitting of a two-photon pulse

We employ a cascaded system approach to numerically simulate the interaction of photon pulses with a two-level scatterer in a chiral waveguide QED setup and show that the scattering of a two-photon pulse may lead to the predominant population of only two output wave packet modes in an entangled state, $|2,0\ensuremath{\rangle}--|0,2\ensuremath{\rangle}$. In a complementary wave-packet basis, this is a product state of two orthogonal single-photon wave packets. Operating this process in reverse allows a perfect merging of distinguishable single-photon wave packets into a single-mode pulse carrying two identical photons.

Transcriptome-Wide Analysis of microRNA-mRNA Correlations in Tissue Identifies microRNA Targeting Determinants.

MicroRNAs are small RNAs that regulate gene expression through complementary base pairing with their target mRNAs. A substantial understanding of microRNA target recognition and repression mechanisms has been reached using diverse empirical and bioinformatic approaches, primarily in vitro biochemical or cell culture perturbation settings. We sought to determine if rules of microRNA target efficacy could be inferred from extensive gene expression data of human tissues. A transcriptome-wide assessment of all the microRNA-mRNA canonical interactions' efficacy was performed using a normalized Spearman correlation (Z-score) between the abundance of the transcripts in the PRAD-TCGA dataset tissues (RNA-seq mRNAs and small RNA-seq for microRNAs, 546 samples). Using the Z-score of correlation as a surrogate marker of microRNA target efficacy, we confirmed hallmarks of microRNAs, such as repression of their targets, the hierarchy of preference for gene regions (3'UTR > CDS > 5'UTR), and seed length (6 mer < 7 mer < 8 mer), as well as the contribution of the 3'-supplementary pairing at nucleotides 13-16 of the microRNA. Interactions mediated by 6 mer + supplementary showed similar inferred repression as 7 mer sites, suggesting that the 6 mer + supplementary sites may be relevant in vivo. However, aggregated 7 mer-A1 seeds appear more repressive than 7 mer-m8 seeds, while similar when pairing possibilities at the 3'-supplementary sites. We then examined the 3'-supplementary pairing using 39 microRNAs with Z-score-inferred repressive 3'-supplementary interactions. The approach was sensitive to the offset of the bridge between seed and 3'-supplementary pairing sites, and the pattern of offset-associated repression found supports previous findings. The 39 microRNAs with effective repressive 3'supplementary sites show low GC content at positions 13-16. Our study suggests that the transcriptome-wide analysis of microRNA-mRNA correlations may uncover hints of microRNA targeting determinants. Finally, we provide a bioinformatic tool to identify microRNA-mRNA candidate interactions based on the sequence complementarity of the seed and 3'-supplementary regions.

Stability and structural evolution of double-stranded DNA molecules under high pressures: A molecular dynamics study

Conformational changes and stability of interacting double-stranded DNA chains under high hydrostatic pressure in biological systems are striking topics of importance to study several biomolecular phenomena. For example, to unravel the physiological conditions at which life might occur and to ensure the right functionality of the biochemical processes into the cell under extreme thermodynamic conditions. Furthermore, such processes could shed light on the physicochemical properties of the DNA under high confinement and how, through different mechanisms, a virus releases its genome in order to infect a cell and, therefore, to promote the process of viral replication. To achieve a few steps toward this direction, we propose an all-atomistic molecular dynamics approach in the NPT isothermal-isobaric ensemble to account for how the interplay of DNA—DNA interaction, hydrogen bonding, and the hydrostatic pressure modifies both the DNA conformational degrees of freedom and the spatial organization of the DNA chains in the available volume. We consider two interacting double-stranded DNA chains immersed in an explicit aqueous solution, i.e., water and ions. Our preliminary results highlight the role of hydrogen bonding and electrostatic interactions between DNA strands to avoid denaturation and, therefore, to provide mechanical stability for the DNA molecules. However, the structural evolution, whose kinetics depends on the relaxation of the stresses induced by the pressure, indicates that almost in all pressure conditions, the equilibrium configuration corresponds to an alignment of the two double-stranded DNA molecules along their main axis of symmetry; the rearrangement between the two approaching DNA dodecamers does not always correspond to complementary base pairs and becomes a function of the thermodynamic conditions.

Exogenous interference and autofluorescence-free ratiometric aptasensor for detection of OTA based on dual-colored persistent luminescence nanoparticles

Accurate and sensitive detection of ochratoxin A (OTA) is highly necessary due to its high carcinogenicity, teratogenicity and mutagenicity. Herein, we reported an exogenous interference and autofluorescence-free ratiometric aptasensor based on dual-colored persistent luminescent nanoparticles for precise detection of OTA. Green-emitting ZnGeO:Mn bonded with OTA aptamer and BHQ1-modified complementary base was acted as detection and specific recognition probe (ZGM@BHQ1). Quaternary ammonium modified ZnGaGeO:Cr with red emission was employed as reference probe and further bonded to ZGM@BHQ1 through electrostatic interaction to construct the ratiometric aptasensor. The developed ratiometric aptasensor was free from real-time excitation, external interference and autofluorescence and gave low detection limit of 3.4 pg mL−1, wide linearity in the range of 0.01–50 ng mL−1 and high precision of 3.1 % (11 replicate determinations, at 1 ng mL−1 level). The applicability of the aptasensor was successfully demonstrated by analyzing OTA in in grain samples with recoveries of 97.6 %-105.2 %.

The Complete Mitochondrial Genome of Torix tukubana (Annelida: Hirudinea: Glossiphoniidae).

Torix tukubana is a poorly understood proboscidate leech species, generally an ectoparasite on amphibian species. In this study, the complete mitochondrial genome (mitogenome) of T. tukubana was sequenced using next-generation sequencing (NGS), and the essential characteristics, gene arrangement, and phylogenetic relationship were analyzed. The results showed that the T. tukubana mitogenome was 14,814 bp in length, consisting of 13 protein-coding genes (PCGs), 22 tRNAs, 2 rRNAs, and 1 control region (CR). The mitogenome composition presented a strong A + T bias (73.6%). All tRNAs had the typical clover structure except the trnS1 (TCT), whose dihydrouridine (DHU) arm was short, having only one complementary base pair. Additionally, 8 gene order patterns were identified among 25 known Hirudinea species, and T. tukubana was identical to the Hirudinea ground pattern. A phylogenetic analysis based on 13 PCGs indicated that all the studied species clustered into three main clades. The relationships among Hirudinea species were basically consistent with their gene arrangement results, but different from their morphological taxonomy. T. tukubana was in the monophyletic group of Glossiphoniidae, a finding consistent with previous research. Our results provided the essential characteristics of the T. tukubana mitogenome. As the first complete mitogenome of Torix, it could offer valuable information for a systematic understanding of the Hirudinea species.

The Multi-Causal Basis of Developmental Potential Construction

In this article we analyse the issue of what accounts for developmental potential, i.e., the possible phenotypes a developing organism can manifest during ontogeny. We shall argue in favour of two theses. First, although the developing organism is the unit of development, the complete causal basis for its potential to develop does neither lie entirely in itself as a whole nor in any specific part of itself (such as its genome). Thus, the extra-organismal environment must be counted as one of the three necessary, partial and complementary causal bases for development potential. Secondly, we shall defend a constructivist view of the developmental process. If the genome, the developing organism and the extra-organismal environment are to be counted as proper elements of the causal basis for an organism’s developmental potential, the latter is not a given. Rather, it is the result of an interaction-based construction, a process sometimes generating genuine developmental novelty. We will thus argue for an interactionist multi-causal basis view of developmental potential construction. We contend that our view provides a biologically tenable and metaphysically coherent account of developmental dynamics.

Macroalgae Diversity from San-Pedro Port Area

The work, one of the objectives which was to constitute a complementary reference base for the assessment biodiversity and esential habitats, was carried out within the framework the complementary studies biodiversity and sediments; Autonomous Port from San-Pédro. The methodology applied consisted in sampling macroalgae from June 10 to 14, 2021 in 5 sites located from San-Pedro Port Container Terminal, which are the turning site, the site of the channel from San-Pedro Autonomous Port, the site close to the breakwater and the area to be filled in, the marine site and the site close to the mouth and the area intended to house the marine base. The results obtained highlighted the absence of macroalgae in all the sampled sites with the exception of the site near the mouth and the area intended to accommodate the marine base in which the harvest of the red macroalgae Gelidium latifolium (Greville ) Bornet &amp; Thuret, 1876 was realized. This macroalgae of socio-economic importance, little exploited, but used for the agar extraction is under unspecified protection by order no. 1118-83 of 93/12/1, a protective measure which could constitute a beneficial asset for the ecosystems conservation in a dynamic sustainable development and would also promote the algae cultivation with a view to their industrial exploitation.

Supramolecular interactions in salts/cocrystals involving pyrimidine derivatives of sulfonate/carboxylic acid.

The crystal structures of three compounds involving aminopyrimidine derivatives are reported, namely, 5-fluorocytosinium sulfanilate-5-fluorocytosine-4-azaniumylbenzene-1-sulfonate (1/1/1), C4H5FN3O+·C6H6NO3S-·C4H4FN3O·C6H7NO3S, I, 5-fluorocytosine-indole-3-propionic acid (1/1), C4H4FN3O·C11H11NO2, II, and 2,4,6-triaminopyrimidinium 3-nitrobenzoate, C4H8N5+·C7H4NO4-, III, which have been synthesized and characterized by single-crystal X-ray diffraction. In I, there are two 5-fluorocytosine (5FC) molecules (5FC-A and 5FC-B) in the asymmetric unit, with one of the protons disordered between them. 5FC-A and 5FC-B are linked by triple hydrogen bonds, generating two fused rings [two R22(8) ring motifs]. The 5FC-A molecules form a self-complementary base pair [R22(8) ring motif] via a pair of N-H...O hydrogen bonds and the 5FC-B molecules form a similar complementary base pair [R22(8) ring motif]. The combination of these two types of pairing generates a supramolecular ribbon. The 5FC molecules are further hydrogen bonded to the sulfanilate anions and sulfanilic acid molecules via N-H...O hydrogen bonds, generating R44(22) and R66(36) ring motifs. In cocrystal II, two types of base pairs (homosynthons) are observed via a pair of N-H...O/N-H...N hydrogen bonds, generating R22(8) ring motifs. The first type of base pair is formed by the interaction of an N-H group and the carbonyl O atom of 5FC molecules through a couple of N-H...O hydrogen bonds. Another type of base pair is formed via the amino group and a pyrimidine ring N atom of the 5FC molecules through a pair of N-H...N hydrogen bonds. The base pairs (via N-H...N hydrogen bonds) are further bridged by the carboxyl OH group of indole-3-propionic acid and the O atom of 5FC through O-H...O hydrogen bonds on either side of the R22(8) motif. This leads to a DDAA array. In salt III, one of the N atoms of the pyrimidine ring is protonated and interacts with the carboxylate group of the anion through N-H...O hydrogen bonds, leading to the primary ring motif R22(8). Furthermore, the 2,4,6-triaminopyrimidinium (TAP) cations form base pairs [R22(8) homosynthon] via N-H...N hydrogen bonds. A carboxylate O atom of the 3-nitrobenzoate anion bridges two of the amino groups on either side of the paired TAP cations to form another ring [R32(8)]. This leads to the generation of a quadruple DADA array. The crystal structures are further stabilized by π-π stacking (I and III), C-H...π (I and II), C-F...π (I) and C-O...π (II) interactions.

Applications of Gene Therapy in Dentistry: A Review Article

AbstractGene therapy promises to possess a good prospect in bridging the gap between dental applications and medicine. The dynamic therapeutic modalities of gene therapy have been advancing rapidly. Conventional approaches are being revamped to be more comprehensive and pre-emptive, which could do away with the need for surgery and medicine altogether. The complementary base sequences known as genes convey the instructions required to manufacture proteins. The oral cavity is one of the most accessible locations for the therapeutic intervention of gene therapy for several oral tissues. In 1990, the first significant trial of gene therapy was overseen to alleviate adenosine deaminase deficiency. The notion of genetic engineering has become increasingly appealing as a reflection of its benefits over conventional treatment modalities. An example of how this technology may alter dentistry is the implementation of gene therapy for dental and oral ailments. The objective of this article is to examine the effects of gene therapy on the field of dentistry, periodontology and implantology. Furthermore, the therapeutic factors of disease therapy, minimal invasion, and appropriate outcome have indeed been taken into consideration.

Non-canonical base pairing

Non-canonical base pairs are planar hydrogen-bonded pairs of nucleobases, having hydrogen bonding patterns which differ from the patterns observed in Watson-Crick base pairs, as in the classic double-helical DNA. The structures of polynucleotide strands of both DNA and RNA molecules can be understood in terms of sugar-phosphate backbones consisting of phosphodiester-linked D 2’ deoxyribofuranose (D ribofuranose in RNA) sugar moieties, with purine or pyrimidine nucleobases covalently linked to them. Here, the N9 atoms of the purines, guanine and adenine, and the N1 atoms of the pyrimidines, cytosine and thymine (uracil in RNA), respectively, form glycosidic linkages with the C1’ atom of the sugars. These nucleobases can be schematically represented as triangles with one of their vertices linked to the sugar, and the three sides accounting for three edges through which they can form hydrogen bonds with other moieties, including with other nucleobases. As also explained in greater detail later in this article, the side opposite to the sugar-linked vertex is traditionally called the Watson-Crick edge, since they are involved in forming the Watson-Crick base pairs which constitute building blocks of double-helical DNA. The two sides adjacent to the sugar-linked vertex are referred to, respectively, as the Sugar and Hoogsteen (C-H for pyrimidines) edges. Each of the four different nucleobases is characterized by distinct edge-specific distribution patterns of their respective hydrogen bond donor and acceptor atoms, complementarity with which, in turn, define the hydrogen bonding patterns involved in base pairing. The double helical structures of DNA or RNA are generally known to have base pairs between complementary bases, Adenine: Thymine (Adenine: Uracil in RNA) or Guanine: Cytosine. They involve specific hydrogen bonding patterns corresponding to their respective Watson-Crick edges and are considered Canonical Base Pairs. At the same time, the helically twisted backbones in the double helical duplex DNA form two grooves, major and minor, through which the hydrogen bond donor and acceptor atoms corresponding respectively to the Hoogsteen and sugar edges are accessible for additional potential molecular recognition events. Experimental evidence reveals that the nucleotide bases are also capable of forming a wide variety of pairing between bases in various geometries, having hydrogen bonding patterns different from those observed in Canonical Base Pairs [Figure 1]. These base pairs, which are generally referred to as Non-Canonical Base Pairs, are held together by multiple hydrogen bonds and are mostly planar and stable. Most of these play very important roles in shaping the structure and function of different functional RNA molecules. In addition to their occurrences in several double-stranded stem regions, most of the loops and bulges that appear in single-stranded RNA secondary structures form recurrent 3D motifs, where non-canonical base pairs play a central role. Non-canonical base pairs also play crucial roles in mediating the tertiary contacts in RNA 3D structures.

An all-graphdiyne electrochemiluminescence biosensor for the ultrasensitive detection of microRNA-21 based on target recycling with DNA cascade reaction for signal amplification.

Graphdiyne oxide quantum dots (GDYO QDs), as derivatives of graphdiyne (GDY), have excellent electroconductibility and luminous properties and can be applied as a new ECL emitter. Herein, an electrochemiluminescence (ECL) biosensor for miRNA-21 ultrasensitive determination is constructed based on AuNPs/GDY, GDYO QD and oligonucleotide signal amplification strategy that integrates DNA walker and hybridization chain reaction (HCR) amplification. As electrode substrate material, AuNPs/GDY can not only bond with the aptamer CP but can also enhance the conductivity of the interface. When miRNA-21 exists, the DNA walker process is initiated, and the signaling probes are introduced on the electrode surface, producing abundant double-stranded H1/H2; then, H3/H4 undergoes complementary base pairing with H1/H2 through HCR. With the increase in miRNA-21, the 3D DNA nanomachine is actively manipulated, resulting in a gradual increase in ECL signal. This ECL biosensor demonstrates outstanding performance in the determination of miRNA-21 in the linear range from 0.1 fM to 1 nM. This study offers a new sensitive idea for the clinical analysis of cancer biomarkers.

Long and Covalently Conjugated Branched DNA Structures for in Situ Gelation in Vivo

Long and Covalently Conjugated Branched DNA Structures for in Situ Gelation in Vivo

Norm-Conserving 4f-in-Core Pseudopotentials and Basis Sets Optimized for Trivalent Lanthanides (Ln = Ce–Lu)

We present here a set of scalar-relativistic norm-conserving 4f-in-core pseudopotentials, together with complementary valence-shell Gaussian basis sets, for the lanthanide (Ln) series (Ce-Lu). The Goedecker, Teter, and Hutter (GTH) formalism is adopted with the generalized gradient approximation (GGA) for the exchange-correlation Perdew-Burke-Ernzerhof (PBE) functional. The 4f-in-core pseudopotentials are built through attributing 4f-subconfiguration 4fn (n = 1-14) for Ln (Ln = Ce-Lu) into the atomic core region, making it possible to circumvent the difficulty of the description of the open 4fn valence shell. A wide variety of computational benchmarks and tests have been carried out on lanthanide systems including Ln3+-containing molecular complexes, aqueous solutions, and bulk solids to validate the accuracy, reliability, and efficiency of the optimized 4f-in-core GTH pseudopotentials and basis sets. The 4f-in-core GTH pseudopotentials successfully replicate the main features of lanthanide structural chemistry and reaction energetics, particularly for nonredox reactions. The chemical bonding features and solvation shells, hydrolysis energetics, acidity constants, and solid-state properties of selected lanthanide systems are also discussed in detail by utilizing these new 4f-in-core GTH pseudopotentials. This work bridges the idea of keeping highly localized 4f electrons in the atomic core and efficient pseudopotential formalism of GTH, thus providing a highly efficient approach for studying lanthanide chemistry in multi-scale modeling of constituent-wise and structurally complicated systems, including electronic structures of the condensed phase and first-principles molecular dynamics simulations.

Differential Surface Interactions and Surface Templating of Nucleotides (dGMP, dCMP, dAMP, and dTMP) on Oxide Particle Surfaces.

The fate of biomolecules in the environment depends in part on understanding the surface chemistry occurring at the biological-geochemical (bio-geo) interface. Little is known about how environmental DNA (eDNA) or smaller components, like nucleotides and oligonucleotides, persist in aquatic environments and the role of surface interactions. This study aims to probe surface interactions and adsorption behavior of nucleotides on oxide surfaces. We have investigated the interactions of individual nucleotides (dGMP, dCMP, dAMP, and dTMP) on TiO2 particle surfaces as a function of pH and in the presence of complementary and noncomplementary base pairs. Using attenuated total reflectance-Fourier transform infrared spectroscopy, there is an increased number of adsorbed nucleotides at lower pH with a preferential interaction of the phosphate group with the oxide surface. Additionally, differential adsorption behavior is seen where purine nucleotides are preferentially adsorbed, with higher surface saturation coverage, over their pyrimidine derivatives. These differences may be a result of intermolecular interactions between coadsorbed nucleotides. When the TiO2 surface was exposed to two-component solutions of nucleotides, there was preferential adsorption of dGMP compared to dCMP and dTMP, and dAMP compared to dTMP and dCMP. Complementary nucleotide base pairs showed hydrogen-bond interactions between a strongly adsorbed purine nucleotide layer and a weaker interacting hydrogen-bonded pyrimidine second layer. Noncomplementary base pairs did not form a second layer. These results highlight several important findings: (i) there is differential adsorption of nucleotides; (ii) complementary coadsorbed nucleotides show base pairing with a second layer, and the stability depends on the strength of the hydrogen bonding interactions and; (iii) the first layer coverage strongly depends on pH. Overall, the importance of surface interactions in the adsorption of nucleotides and the templating of specific interactions between nucleotides are discussed.