Base Pair Sites Research Articles

Constructing Ru-Co2P Lewis Acid-Base Pairs to Prompt Hydrogen Evolution Reaction in Alkaline Seawater Electrolyte.

Seawater electrolysis is an ideal approach to generating green hydrogen. Nevertheless, the sluggish kinetics of water dissociation and the detrimental chlorine chemistry environment are serious obstructions for industrial applications. Herein, constructing unique (Co) Lewis acid and (Ru-P) base pair sites in Ru-Co2P decorated on nitrogen and phosphorus co-doped carbon (Ru-Co2P/NPC) significantly optimizes the energy barrier of water dissociation and enhances the anti-corrosive ability for alkaline seawater splitting. As expected, the optimal Ru-Co2P/NPC-2 exhibits exceptional hydrogen evolution reaction (HER) performances with overpotentials as low as 22.0 and 26.0mV to derive 10 mAcm-2 and operate steadily (@ 50 mAcm-2) over 30 h in alkaline and alkaline seawater electrolytes. The experimental and theoretical results elucidate that Co acting as Lewis acid sites prompts the water adsorption and breakage of the H─O bond, whereas Ru-P as Lewis base sites facilitates the hydrogen desorption in alkaline media. Furthermore, modulated chemical microenvironments can be beneficial to hinder chloride corrosion on the active sites of catalysts. This work sheds light on the rational construction of a highly efficient electrocatalyst for alkaline HER in seawater.

The role of nucleotide opening dynamics in facilitated target search by DNA-repair proteins

Preserving the genomic integrity stands a fundamental necessity, primarily achieved by the DNA repair proteins through their continuous patrolling on the DNA in search of lesions. However, comprehending how even a single base-pair lesion can be swiftly and specifically recognized amidst millions of base-pair sites remains a formidable challenge. In this study, we employ extensive molecular dynamics simulations using an appropriately tuned model of both protein and DNA to probe the underlying molecular principles. Our findings reveal that the dynamics of a non-canonical base generate an entropic signal that guides the one-dimensional search of a repair protein, thereby facilitating the recognition of the lesion site. The width of the funnel perfectly aligns with the one-dimensional diffusion length of DNA-binding proteins. The generic mechanism provides a physical basis for rapid recognition and specificity of DNA damage sensing and recognition.

Bipartite viral RNA genome heterodimerization influences genome packaging and virion thermostability.

Multi-segmented viruses often multimerize their genomic segments to ensure efficient and stoichiometric packaging of the correct genetic cargo. In the bipartite Nodaviridae family, genome heterodimerization is also observed and conserved among different species. However, the nucleotide composition and biological function for this heterodimer remain unclear. Using Flock House virus as a model system, we developed a next-generation sequencing approach ("XL-ClickSeq") to probe heterodimer site sequences. We identified an intermolecular base-pairing site which contributed to heterodimerization in both wild-type and defective virus particles. Mutagenic disruption of this heterodimer site exhibited significant deficiencies in genome packaging and encapsidation specificity to viral genomic RNAs. Furthermore, the disruption of this intermolecular interaction directly impacts the thermostability of the mature virions. These results demonstrate that the intermolecular RNA-RNA interactions within the encapsidated genome of an RNA virus have an important role on virus particle integrity and thus may impact its transmission to a new host.IMPORTANCEFlock House virus is a member of Nodaviridae family of viruses, which provides a well-studied model virus for non-enveloped RNA virus assembly, cell entry, and replication. The Flock House virus genome consists of two separate RNA molecules, which can form a heterodimer upon heating of virus particles. Although similar RNA dimerization is utilized by other viruses (such as retroviruses) as a packaging mechanism and is conserved among Nodaviruses, the role of heterodimerization in the Nodavirus replication cycle is unclear. In this research, we identified the RNA sequences contributing to Flock House virus genome heterodimerization and discovered that such RNA-RNA interaction plays an essential role in virus packaging efficiency and particle integrity. This provides significant insight into how the interaction of packaged viral RNA may have a broader impact on the structural and functional properties of virus particles.

Reaction Pathways of Gamma-Valerolactone Hydroconversion over Co/SiO2 Catalyst

The hydroconversion of γ-valerolactone (GVL) over Co/SiO2 catalyst proceeds in a complex reaction network, resulting in 2-methyltetrahydrofuran (2-MTHF) as the main product, and C4–C5 alcohol and alkane side-products. The catalyst was shown to contain Co0 sites and Lewis acid (Co2+ ion)/Lewis base (O2− ion) pair sites, active for hydrogenation/dehydrogenation and dehydration reactions, respectively. The initial reaction step was confirmed to be the hydrogenation of GVL to key intermediate 1,4-pentanediol (1,4-PD). Cyclodehydration of 1,4-PD led to the main product 2-MTHF, whereas its dehydration/hydrogenation gave 1-pentanol and 2-pentanol side-products, with about the same yield. In contrast, 2-pentanol was the favored alcohol product of 2-MTHF hydrogenolysis. 2-Butanol was formed by decarbonylation of 4-hydroxypentanal intermediate. The latter was the product of 1,4-PD dehydrogenation. Alkanes were formed from the alcohol side-products via dehydration/hydrogenation reactions.

Programmable DNA Interstrand Crosslinking by Alkene-Alkyne [2+2] Photocycloaddition.

Covalent crosslinking of DNA strands provides a useful tool for medical, biochemical, and DNA nanotechnology applications. Here we present a light-induced interstrand DNA crosslinking reaction using the modified nucleoside 5-phenylethynyl-2'-deoxyuridine (PhedU). The crosslinking ability of PhedU was programmed by base pairing and by metal ion interaction at the Watson-Crick base pairing site. Rotation to intrahelical positions was favored by hydrophobic stacking and enabled an unexpected photochemical alkene-alkyne [2 + 2] cycloaddition within the DNA duplex, resulting in efficient formation of a PhedU dimer after short irradiation times of a few seconds. A PhedU-dimer-containing DNA was shown to efficiently bind a helicase complex, but the covalent crosslink completely prevented DNA unwinding, suggesting possible applications in biochemistry or structural biology.

Synergistic Effects of Lewis Acid-Base Pair Sites─Hf-MOFs with Functional Groups as Distinguished Catalysts for the Cycloaddition of Epoxides with CO2.

The incorporation of Lewis acid-base sites in catalysts has been considered as a significant approach to fabricating bifunctional catalysts with efficient catalytic activity for CO2 fixation. In this paper, a series of Hafnium-based metal-organic frameworks (Hf-MOFs), NU-912(Hf) and NU-912-X(Hf)-X (X = -NH2, -Br, -CN, and -I) derivatives assembled by Lewis acidic Hf6(μ3-O)4(μ3-OH)4(H2O)4(OH)4 (Hf6) clusters and Lewis base-attached organic linkers, are successfully synthesized by a facile ligand functionalization method. These isostructural Hf-MOFs, which exhibit diamond channels of 1.3 nm diameter, great chemical stability, and CO2 adsorption capacity, have been evaluated as catalysts for the CO2 cycloaddition reaction with epoxides. Catalytic experiments reveal that the micropore environments of these MOFs have an outstanding impact on catalytic activity. Remarkably, NU-912(Hf)-I serves as an efficient heterogeneous catalyst for this catalytic reaction under mild conditions due to the high density of Lewis acid Hf6 cluster centers and strong Lewis base functional groups, surpassing most of the reported MOF-based catalysts.

Antileukemia Activity and Mechanism of Platinum(II)-Based Metal Complexes.

Transition metal complexes have continued to constitute an appealing class of medicinal compounds since the exceptional discovery of cisplatin in the late 1960s. Pt(II)-based complexes are endowed with a broad range of biological properties, which are mainly exerted by targeting DNA. In this study, we report a significant biological investigation into and computation analyses of four Pt(II)-complexes, namely, LDP-1-4, synthesized and characterized according to previously reported procedures. Molecular-modelling studies highlighted that the top two LDP compounds (i.e., LDP-1 and LDP-4) might bind to both matched and mismatched base pair sites of the oligonucleotide 5'-(dCGGAAATTACCG)2-3', supporting their anticancer potential. These two complexes displayed noteworthy cytotoxicity in vitro (sub-micromolar-micromolar range) against two leukaemia cell lines, i.e., CCRF-CEM and its multi-drug-resistant counterpart CEM/ADR5000, and remarkable anti-angiogenic properties (in the sub-micromolar range) evaluated in an in vivo model, i.e., a chick embryo chorioallantoic membrane (CAM) assay.

Effects of N7-Alkylguanine Conformation and Metal Cofactors on the Translesion Synthesis by Human DNA Polymerase η.

Non-enzymatic alkylation on DNA often generates N7-alkyl-2'-deoxyguanosine (N7alkylG) adducts as major lesions. N7alkylG adducts significantly block replicative DNA polymerases and can be bypassed by translesion synthesis (TLS) polymerases such as polymerase η (polη). To gain insights into the bypass of N7alkylG by TLS polymerases, we conducted kinetic and structural studies of polη catalyzing across N7BnG, a genotoxic lesion generated by the carcinogenic N-nitrosobenzylmethylamine. The presence of templating N7BnG in the polη catalytic site decreased the replication fidelity by ∼9-fold, highlighting the promutagenicity of N7BnG. The catalytic efficiency for dCTP incorporation opposite N7BnG decreased ∼22-fold and ∼7-fold compared to the incorporation opposite undamaged guanine in the presence of Mg2+ and Mn2+, respectively. A crystal structure of the complexes grown with polη, templating N7BnG, incoming dCTP, and Mg2+ ions showed the lack of the incoming nucleotide and metal cofactors in the polη catalytic site. Interestingly, the templating N7BnG adopted a syn conformation, which has not been observed in the published N7alkylG structures. The preferential formation of syn-N7BnG conformation at the templating site may deter the binding of an incoming dCTP, causing the inefficient bypass by polη. In contrast, the use of Mn2+ in place of Mg2+ in co-crystallization yielded a ternary complex displaying an anti-N7BnG:dCTP base pair and catalytic metal ions, which would be a close mimic of a catalytically competent state. We conclude that certain bulky N7-alkylG lesions can slow TLS polymerase-mediated bypass by adopting a catalytically unfavorable syn conformation in the replicating base pair site.

Interfacial Tandem Catalysis for Ethylene Carbonylation and C–C Coupling to 3-Pentanone on Rh/Ceria

Alkene carbonylation holds the promise to provide atom-efficient, clean routes for the production of ester, aldehyde, amide, etc., and CO insertion followed by C–C bond coupling is an ideal route for ketone synthesis. However, alkoxycarbonylation and hydroformylation, in which ester and aldehyde are produced via CO insertion followed by C–O and C–H bond formation, respectively, overwhelmingly dominate the alkene carbonylation reactions. Herein, a promising approach to realize the ethylene carbonylation followed by C–C bond formation to produce 3-pentanone was developed by coupling with alcohol dehydrogenation–transfer–hydrogenation (DTH) reactions on a ceria-supported Rh catalyst. The interfacial Lewis acid–base pair site (Rhδ+–O–Ce3+–Ov), which is constituted by Lewis acidic Ce3+–Ov (oxygen vacancy) and basic interfacial oxygen of Rhδ+–O–Ce3+, dissociatively activates alcohol and its DTH reactions, which promotes the tandem reaction of ethylene carbonylation and C–C coupling to 3-pentanone. This route provides an alternative way to selectively synthesize higher ketones by one-step olefin carbonylation.

A Novel Non-Coding RNA CsiR Regulates the Ciprofloxacin Resistance in Proteus vulgaris by Interacting with emrB mRNA.

Bacterial non-coding RNAs (ncRNAs) play important regulatory roles in various physiological metabolic pathways. In this study, a novel ncRNA CsiR (ciprofloxacin stress-induced ncRNA) involved in the regulation of ciprofloxacin resistance in the foodborne multidrug-resistant Proteus vulgaris (P. vulgaris) strain P3M was identified. The survival rate of the CsiR-deficient strain was higher than that of the wild-type strain P3M under the ciprofloxacin treatment condition, indicating that CsiR played a negative regulatory role, and its target gene emrB was identified through further target prediction, quantitative real-time PCR (qRT-PCR), and microscale thermophoresis (MST). Further studies showed that the interaction between CsiR and emrB mRNA affected the stability of the latter at the post-transcriptional level to a large degree, and ultimately affected the ciprofloxacin resistance of P3M. Notably, the base-pairing sites between CsiR and emrB mRNAs were highly conserved in other sequenced P. vulgaris strains, suggesting that this regulatory mechanism may be ubiquitous in this species. To the best of our knowledge, this is the first identification of a novel ncRNA involved in the regulation of ciprofloxacin resistance in P. vulgaris species, which lays a solid foundation for comprehensively expounding the antibiotic resistance mechanism of P. vulgaris.

A study of the mechanism of triglyceride hydrodeoxygenation over alumina-supported and phosphatized-alumina-supported Pd catalysts

The mechanism of catalytic hydrodeoxygenation (HDO) of fats, vegetable oils, and fatty acids was studied using alumina-supported Pd catalysts and tricaprylin and valeric acid as model reactants. The chemistry of fatty acid/catalyst interaction was studied by quasi-operando Diffuse Reflectance Infrared Fourier Transform Spectroscopy (DRIFTS). The Pd/γ–Al2O3 catalyst showed good activity in the hydrogenolysis reaction of the ester bonds to convert tricaprylin to caprylic acid, but they were of poor activity in the consecutive hydrodeoxygenation (HDO) of the acid to paraffin. The surface modification of the support alumina by phosphate groups significantly increased the HDO activity of the Pd catalyst and, consequently, the paraffin yield. The activity change was accounted partly for the partial replacement of the weak base Al–OH groups by weak acid P–OH groups but mainly for the partial elimination of Lewis acid (Al⊕) – Lewis base (O⊝) pair sites on the surface of the support. Both surface Al–OH and P–OH groups were shown to participate in the reaction with carboxylic acid and formed bidentate surface carboxylate species, which further reacted with hydrogen to give paraffin. Carboxylates of less basic surface sites were found to be more prone to HDO reaction than those of strong base sites. Monodentate carboxylates, formed on Al⊕ O⊝ pair sites were of low reactivity. Phosphatizing eliminated most of the Lewis type acid-base pair sites, therefore, reactive bidentate carboxylates represented the most abundant surface intermediate (MASI) during the HDO reaction of triglyceride. The hydroxyl coverage of the carboxylated surface was shown to become somewhat higher under steady-state reaction conditions. The increased hydroxyl coverage implies that C–O bond hydrogenolysis of the surface carboxylate proceeds, regenerating OH groups and forming aldehyde that could be intermediate of paraffin formation.

Anti-Proliferative Effect of Doxorubicin-Loaded AS1411 Aptamer on Colorectal Cancer Cell.

Background:Doxorubicin (Dox) inhibits DNA replication and causes DNA damage resulting in cell death. It is a common drug for treatment of many cancers. Treatment efficacy and side effects of Dox are critical issues in using it because the drug lacks of specificity. The objective of this study was to improve the specificity of Dox by the incorporation of this drug with AS1411 aptamer (ASA). Methods:Dox was intercalated into the duplex sites of ASA, a recognition molecule for a number of cancer cells, and formed Dox-loaded ASA. The recognition ability proceeded through specific binding between the aptamer and nucleolin overexpressed in the cancer cells. The tested cells were human colorectal adenocarcinoma cell line (SW480) and human normal colon cell CCD841 CoN (CCD841). Binding of ASA to the cells was tested using flow cytometer and fluorescence microscope. Intercalation of Dox into DNA duplex was confirmed by fluorescence spectrometry. Effect of ASA, Dox, and Dox-loaded ASA on cell viability was examined by cell proliferation assay. Caspase-3 activation was analyzed by western blotting. Results:ASA bound specifically to SW480 cells via interaction between the aptamer and nucleolin because the nucleolin was highly expressed in SW480 cells. ASA decreased the viability of SW480 cells in a dose-dependent manner. Dox was more toxic than ASA. Fluorescence quenching revealed that Dox was able to intercalate in base pairing sites of the aptamer. Dox-loaded ASA inhibited the proliferation of SW480 cells, because the aptamer facilitated the Dox uptake into these cells which caused the cell apoptosis, indicated by the significant decrease in procaspase-3, apoptosis marker protein. Conclusion:This study succeeded to prepare Dox-loaded ASA by intercalation of the drug that inherited the binding function from the aptamer and anti-cancer activity from Dox. Dox-loaded ASA showed promise for effective cancer treatment with lower level of side effects.

RNA helicase-mediated regulation of snoRNP dynamics on pre-ribosomes and rRNA 2′-O-methylation

RNA helicases play important roles in diverse aspects of RNA metabolism through their functions in remodelling ribonucleoprotein complexes (RNPs), such as pre-ribosomes. Here, we show that the DEAD box helicase Dbp3 is required for efficient processing of the U18 and U24 intron-encoded snoRNAs and 2′-O-methylation of various sites within the 25S ribosomal RNA (rRNA) sequence. Furthermore, numerous box C/D snoRNPs accumulate on pre-ribosomes in the absence of Dbp3. Many snoRNAs guiding Dbp3-dependent rRNA modifications have overlapping pre-rRNA basepairing sites and therefore form mutually exclusive interactions with pre-ribosomes. Analysis of the distribution of these snoRNAs between pre-ribosome-associated and ‘free’ pools demonstrated that many are almost exclusively associated with pre-ribosomal complexes. Our data suggest that retention of such snoRNPs on pre-ribosomes when Dbp3 is lacking may impede rRNA 2′-O-methylation by reducing the recycling efficiency of snoRNPs and by inhibiting snoRNP access to proximal target sites. The observation of substoichiometric rRNA modification at adjacent sites suggests that the snoRNPs guiding such modifications likely interact stochastically rather than hierarchically with their pre-rRNA target sites. Together, our data provide new insights into the dynamics of snoRNPs on pre-ribosomal complexes and the remodelling events occurring during the early stages of ribosome assembly.

Promutagenic bypass of 7,8-dihydro-8-oxoadenine by translesion synthesis DNA polymerase Dpo4.

Reactive oxygen species induced by ionizing radiation and metabolic pathways generate 7,8-dihydro-8-oxoguanine (oxoG) and 7,8-dihydro-8-oxoadenine (oxoA) as two major forms of oxidative damage. The mutagenicity of oxoG, which promotes G to T transversions, is attributed to the lesion's conformational flexibility that enables Hoogsteen base pairing with dATP in the confines of DNA polymerases. The mutagenesis mechanism of oxoA, which preferentially causes A to C transversions, remains poorly characterized. While structures for oxoA bypass by human DNA polymerases are available, that of prokaryotic DNA polymerases have not been reported. Herein, we report kinetic and structural characterizations of Sulfolobus solfataricus Dpo4 incorporating a nucleotide opposite oxoA. Our kinetic studies show oxoA at the templating position reduces the replication fidelity by ∼560-fold. The catalytic efficiency of the oxoA:dGTP insertion is ∼300-fold greater than that of the dA:dGTP insertion, highlighting the promutagenic nature of oxoA. The relative efficiency of the oxoA:dGTP misincorporation is ∼5-fold greater than that of the oxoG:dATP misincorporation, suggesting the mutagenicity of oxoA is comparable to that of oxoG. In the Dpo4 replicating base pair site, oxoA in the anti-conformation forms a Watson-Crick base pair with an incoming dTTP, while oxoA in the syn-conformation assumes Hoogsteen base pairing with an incoming dGTP, displaying the dual coding potential of the lesion. Within the Dpo4 active site, the oxoA:dGTP base pair adopts a Watson-Crick-like geometry, indicating Dpo4 influences the oxoA:dGTP base pair conformation. Overall, the results reported here provide insights into the miscoding properties of the major oxidative adenine lesion during translesion synthesis.

Polymorphism of Myostatin Gene and its Association with Body Weight of Iraqi Local Ducks

Myostatin, or growth and differentiation factor-8(GDF-8) is a member of the transforming growth factor (TGF)-ß superfamily. The objective of this study was to investigate the association between genetic polymorphism of the myostatin gene with the body-weight of Iraqi local ducks by DNA sequence analysis. The results of DNA sequence showed nitrogen base change (G?A) at 129 base pair sites of the exon1 of MSTN gene. Therefore, two alleles, G and A and two patterns of genotypes, GG, AG were observed. The observed numbers of GG and AG genotypes were 25 and 6, respectively. The G allele was of the highest frequency (0.9) while A allele showed the lowest frequency (0.1). The GG genotype showed the highest frequency (80.65%) and AG genotype showed the lowest frequency (19.35%). Additionally, the percentages of observed and expected heterozygosity were 0.19 and 0.17 respectively. Moreover, the percentages of observed and expected homozygosity were 0.80 and 0.82, respectively. The average heterozygosity was 0.17. The results revealed no significant (P?0.05) effect of the MSTN gene on body weight.

Determinants of target prioritization and regulatory hierarchy for the bacterial small RNA SgrS.

Small RNA (sRNA) regulators promote efficient responses to stress, but the mechanisms for prioritizing target mRNA regulation remain poorly understood. This study examines mechanisms underlying hierarchical regulation by the sRNA SgrS, found in enteric bacteria and produced under conditions of metabolic stress. SgrS posttranscriptionally coordinates a nine-gene regulon to restore growth and homeostasis. An in vivo reporter system quantified SgrS-dependent regulation of target genes and established that SgrS exhibits a clear target preference. Regulation of some targets is efficient even at low SgrS levels, whereas higher SgrS concentrations are required to regulate other targets. In vivo and in vitro analyses revealed that RNA structure and the number and position of base pairing sites relative to the start of translation impact the efficiency of regulation of SgrS targets. The RNA chaperone Hfq uses distinct modes of binding to different SgrS mRNA targets, which differentially influences positive and negative regulation. The RNA degradosome plays a larger role in regulation of some SgrS targets compared to others. Collectively, our results suggest that sRNA selection of target mRNAs and regulatory hierarchy are influenced by several molecular features and that the combination of these features precisely tunes the efficiency of regulation of multi-target sRNA regulons.

Highly Selective Lanthanum-Modified Zirconia Catalyst for the Conversion of Ethanol to Propylene: A Combined Experimental and Simulation Study

La/ZrO2 catalysts were prepared by co-precipitation method. The physical and chemical properties of the catalysts were characterized by N2 adsorption–desorption method, X-ray diffraction and temperature programmed desorption. The selective conversions of ethanol to propylene over these synthesized La/ZrO2 catalysts were also investigated. The optimum propylene yield reached 42.3% over La(1)/ZrO2 catalyst. A coordination of redox and acid–base properties accounts for the remarkable improvement of reaction performance over La/ZrO2 catalysts. On the basis of calculation results, the introduction of oxygen vacancy or La results in significant charge transfer. The Lewis acid–base (Zr–O) pair sites become more active as a result of charge transfer over La/ZrO2 catalysts. Furthermore, the formation of O vacancies over La/ZrO2 (101) is easier than that over t-ZrO2(101). Therefore, La modification improves the performance of ZrO2 on conversion of ethanol to propylene.

A Neuromorphic Device Implemented on a Salmon-DNA Electrolyte and its Application to Artificial Neural Networks.

A bioinspired neuromorphic device operating as synapse and neuron simultaneously, which is fabricated on an electrolyte based on Cu2+‐doped salmon deoxyribonucleic acid (S‐DNA) is reported. Owing to the slow Cu2+ diffusion through the base pairing sites in the S‐DNA electrolyte, the synaptic operation of the S‐DNA device features special long‐term plasticity with negative and positive nonlinearity values for potentiation and depression (αp and αd), respectively, which consequently improves the learning/recognition efficiency of S‐DNA‐based neural networks. Furthermore, the representative neuronal operation, “integrate‐and‐fire,” is successfully emulated in this device by adjusting the duration time of the input voltage stimulus. In particular, by applying a Cu2+ doping technique to the S‐DNA neuromorphic device, the characteristics for synaptic weight updating are enhanced (|αp|: 31→20, |αd|: 11→18, weight update margin: 33→287 nS) and also the threshold conditions for neuronal firing (amplitude and number of stimulus pulses) are modulated. The improved synaptic characteristics consequently increase the Modified National Institute of Standards and Technology (MNIST) pattern recognition rate from 38% to 44% (single‐layer perceptron model) and from 89.42% to 91.61% (multilayer perceptron model). This neuromorphic device technology based on S‐DNA is expected to contribute to the successful implementation of a future neuromorphic system that simultaneously satisfies high integration density and remarkable recognition accuracy.

Differential DNA Methylation of Human Metastable Epialleles in Guatemalan Infants at Birth Due to Timing of a Maternal Lipid-Based Nutrition Supplement and Pre-Pregnancy BMI (P11-139-19)

ObjectivesHuman metastable epialleles (MEs) are specific regions that are systemically methylated (lack tissue specificity), stable over time, and variably expressed between individuals. DNA methylation (DNAme) of MEs have been previously reported to be altered by maternal nutritional status at the time of conception. Here, we examined DNAme of MEs from a subset of Guatemalan mother/infant dyads as part of the Women First study, an international RCT that tested whether timing of a daily lipid-based nutrition supplement (LNS) improved birth length. The 3 study arms are: women consumed LNS ≥ 3 months prior to conception until delivery (Arm 1, N = 45); women consumed the same LNS commencing at 12 weeks gestation until delivery (Arm 2, N = 45); or no LNS (Arm 3, N = 44). The purpose of this study was to test if the timing of maternal LNS and pre-pregnancy BMI (ppBMI, BMI range = 20.1 – 38.4 kg/m2) led to differential DNAme of MEs in infants at birth. MethodsBisulfite-converted DNAme libraries were constructed using NimbleGen SeqCap Epi CpGiant probes from amnion tissue collected at birth. Individuals were sequenced via 2 × 150 paired end reads using the Illumina NovaSeq sequencer. Subjects that passed quality control (131/142 subjects) were used in subsequent statistical analyses. A linear model was used to test for the interaction between maternal LNS and ppBMI on infant DNAme for each base pair site within 296 previously identified candidate ME regions. The number of methylated base pairs per region ranged from 1 – 737. A significance level adjusting for the 296 regions was set at P ≤ 0.000169. ResultsWe identified 6 ME regions with significant interactions, demonstrating differential ME DNAme due to intervention arm was dependent on ppBMI values. Our analyses also identified 3 CpGs associated with ppBMI regardless of LNS status and 1 CpG associated with LNS regardless of ppBMI suggesting a role for independent effects of maternal LNS and ppBMI on ME DNAme. ConclusionsOur findings indicate that timing of maternal LNS and ppBMI contribute to DNAme of candidate MEs in infants at birth, suggesting epigenetic influences due to in utero exposures. Future analyses will identify genes associated with changes in ME DNAme and the role of DNAme on infant growth. Funding SourcesBill & Melinda Gates Foundation and National Institutes of Health.

Small molecule binders recognize DNA microstructural variations via an induced fit mechanism.

Regulation of gene-expression by specific targeting of protein-nucleic acid interactions has been a long-standing goal in medicinal chemistry. Transcription factors are considered "undruggable" because they lack binding sites well suited for binding small-molecules. In order to overcome this obstacle, we are interested in designing small molecules that bind to the corresponding promoter sequences and either prevent or modulate transcription factor association via an allosteric mechanism. To achieve this, we must design small molecules that are both sequence-specific and able to target G/C base pair sites. A thorough understanding of the relationship between binding affinity and the structural aspects of the small molecule-DNA complex would greatly aid in rational design of such compounds. Here we present a comprehensive analysis of sequence-specific DNA association of a synthetic minor groove binder using long timescale molecular dynamics. We show how binding selectivity arises from a combination of structural factors. Our results provide a framework for the rational design and optimization of synthetic small molecules in order to improve site-specific targeting of DNA for therapeutic uses in the design of selective DNA binders targeting transcription regulation.