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Impact of a Single Nucleotide Change or Non-Nucleoside Modifications in G-Rich Region on the Quadruplex–Duplex Hybrid Formation

&bdquo;Impact of a Single Nucleotide Change or Non-Nucleoside Modifications in G-Rich Region on the Quadruplex–Duplex Hybrid Formation”. In article, a method to discriminate between two target RNA sequences that differ by one nucleotide only is presented. The method relies on the formation of alternative structures, i.e., quadruplex–duplex hybrid (QDH) and duplex with dangling ends (Dss), after hybridization of RNA G-rich oligonucleotides with target sequences containing 5′–GGGCUGG–3′ (UT) or 5′–GGGCGGG–3′ (GT) fragments. Using biophysical methods, the effect of covalently attached G4 ligand on the ability of G-rich oligonucleotides to assemble a G-quadruplex motif was studied. The sequence-guided o-BMVC G4-ligand acted as a quadruplex stabilizer but not duplex. The use of such conjugates (o-BMVC-RNA) creates the possibility of inducing and stabilizing the bimolecular quadruplexes on the G-rich mRNA template in a sequence-specific manner. The formation of QDH or Dss structures is dependent on a single nucleotide change in the target sequence, and the possibility to selectively stabilize the G-quadruplex domain by attaching the G4 ligand may become an attractive alternative therapy for patients with an EGFR-L858R mutation. <a href="https://www.mdpi.com/2218-273X/11/8/1236">https://www.mdpi.com/2218-273X/11/8/1236</a>, <a href="https://doi.org/10.3390/biom11081236">https://doi.org/10.3390/biom11081236</a> Files are available in original formats: .xlsx, .opi, bruker, MultiGauge raw-image file (.img), JPG file (.jpg), text document (.txt)

opennotspecifiedOct 2022View details →

Fig. 2 in Three unusual hybrid sorbicillinoids with anti-inflammatory activities from the deep-sea derived fungus Penicillium sp. SCSIO06868

Fig. 2. Global natural products social molecular networking analysis of HR- MS/MS of culture extracts derived from Penicillium sp. SCSIO06868 and the cluster corresponding to undescribed sorbicillinoids in this study.

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Fig. 6 in Three unusual hybrid sorbicillinoids with anti-inflammatory activities from the deep-sea derived fungus Penicillium sp. SCSIO06868

Fig. 6. Linear regression analysis of calculated 13C NMR shifts of (1′S)-1 (right) and (1′R)-1 (left) against the experimental shifts of 1 and the DP4 probability for + assignment of 1 to the candidate stereoisomers.

A Hybrid Deep Learning-Based Forecasting Model for the Peak Height of Ionospheric F2 Layer

The data for paper.

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FIGURE 2 in Teucrium × gutierrezii a new hybrid from Southeast Iberian Peninsula, a hotspots of natural hybridization of subfamily Ajugoideae (Lamiaceae)

FIGURE 2. Leaves (out side) (1) and dissected calyx (inner side) (2) morphology of parental and hybrid Teucrium taxa. A. Teucrium lusitanicum subsp. lusitanicum; B. Teucrium × gutierrezii; C. T. eriocephalum subsp. eriocephalum.

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FIGURE 1 in Teucrium × gutierrezii a new hybrid from Southeast Iberian Peninsula, a hotspots of natural hybridization of subfamily Ajugoideae (Lamiaceae)

FIGURE 1. Habitus (A) and floral stem details (B) of parental and hybrid Teucrium taxa. 1. Teucrium lusitanicum subsp. lusitanicum; 2. Teucrium × gutierrezii; 3. T. eriocephalum subsp. eriocephalum. All from the type locality Antenas de Aguadulce, Almería Province, Spain.

A real dataset for evaluating hybrid clustering algorithm

This is a real dataset for testing our hybrid clustering algorithm, and details can be found in our manuscript.

Datasets S1 ~ S6 for evaluating hybrid clustering algorithm

These datasets are used to evaluate our hybrid clustering algorithm. For details of our algorithm, please refer to https://github.com/junhaiqi/Hybrid_clustering.git.

Fig. 4 in Molecular cloning, characterization and expression analysis of LoTPS2 and LoTPS4 involved in floral scent formation in oriental hybrid Lilium variety 'Siberia'

Fig. 4. Product analysis of LoTPS4 produced from GGPP and FPP. (a) GC-MS analysis (ion chromatogram) of the LoTPS4 enzyme product from GGPP. (b) GC-MS analysis (ion chromatogram) of products obtained from assays with LoTPS4 and FPP. (c, d, e, f) Mass spectra of Peak 1, Peak 2, Peak 3 and Peak 4. Di-epi-α-cedrene (Peak 1), α-cubebene (Peak 2): trans-α-bergamotene (Peak 3) and (E)-β-farnesene (Peak 4).

Fig. 3 in Molecular cloning, characterization and expression analysis of LoTPS2 and LoTPS4 involved in floral scent formation in oriental hybrid Lilium variety 'Siberia'

Fig. 3. (a) GC-MS analysis of products produced from assays with extracts of the empty vector and GPP. (b) Analysis (total ion chromatogram) of the product of the LoTPS4 enzyme generated from GPP (c) Total ion chromatogram of the D-limonene authentic standard. (d) Mass spectrum of the Peak 3 (e) Mass spectrum of Dlimonene in the floral scent of Lilium 'Siberia' (f) Mass spectrum of the D-limonene authentic standard (g, h, I and j) Mass spectra of Peak 1, Peak 2, Peak 4 and Peak 5. β-Phellandrene (Peak 1), β-myrcene (Peak 2), D-limonene (Peak 3), 3-Carene (Peak 4) and (+)-4-Carene (Peak 5).

Fig. 10 in Molecular cloning, characterization and expression analysis of LoTPS2 and LoTPS4 involved in floral scent formation in oriental hybrid Lilium variety 'Siberia'

Fig. 10. Subcellular localization of LoTPS2 and LoTPS4. Confocal laser scanning microscopy of LoTPS2 and LoTPS4 was performed by using EGFP fusion proteins in Arabidopsis protoplasts. The full-length coding region and the N-terminal 80 amino acids of the coding region of LoTPSs were fused to the GFP reporter gene in the p35 S vector to generate the p35 S-LoTPSs/GFP construct. The red column shows chlorophyll autofluorescence; the green column shows GFP fluorescence; the merged columns show combined GFP fluorescence and chlorophyll autofluorescence; and the BF columns represent bright field images. The names of the constructs are given on the left. HcTPS7 from H. coronarium was used as a marker. Scale bars: 5 μm. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 2 in Molecular cloning, characterization and expression analysis of LoTPS2 and LoTPS4 involved in floral scent formation in oriental hybrid Lilium variety 'Siberia'

Fig. 2. GC-MS analysis of products generated by LoTPS2. (a) GC-MS analysis (total ion chromatogram) of the products obtained by incubating extracts of the empty vector (control) with geranyl pyrophosphate. (b) GC-MS analysis (total ion chromatogram) of the LoTPS2 enzyme with GPP. (c) GC–MS analysis (total ion chromatogram) of the LoTPS2 enzyme with farnesyl pyrophosphate showing (E, E)-α- farnesene as the sole product. (d) Mass spectrum of the peak. (e) Mass spectrum of (E, E)-α-farnesene in the NIST08 library.

Fig. 7 in Molecular cloning, characterization and expression analysis of LoTPS2 and LoTPS4 involved in floral scent formation in oriental hybrid Lilium variety 'Siberia'

Fig. 7. Relative expression analysis of LoTPS2 and LoTPS4 during different flower development performed by quantitative real-time PCR. (a, b) Transcript levels of the LoTPS2 and LoTPS4 genes during flower development. (c, d) Relative expression analysis of LoTPS2 and LoTPS4 at different flower developmental stages. Flower development was divided into 5 different stages: D1 (bud stage), D2 (little open), D3 (half open), D4 (full-bloom), D5 (senescence). GAPDH was used as an internal control. The root was set as 1. Data are presented as the mean ± SEM (n = 3).

Fig. 8 in Molecular cloning, characterization and expression analysis of LoTPS2 and LoTPS4 involved in floral scent formation in oriental hybrid Lilium variety 'Siberia'

Fig. 8. Relative expression analysis of LoTPS genes and the emission of (E, E)-α-farnesene and D-limonene from Lilium 'Siberia' at different time intervals. (a, b) Expression pattern of LoTPS2 and LoTPS4 for 3 days postanthesis. (c) Emission pattern of (E, E)-α-farnesene from Lilium 'Siberia' (d) Emission pattern of D-limonene from Lilium 'Siberia' flowers over 3 days after full-bloom. The plants were kept under a 12 h light, 12 h dark photoperiod. GAPDH was used as an internal control. Each point is the average of 3 replicates.

Fig. 6 in Molecular cloning, characterization and expression analysis of LoTPS2 and LoTPS4 involved in floral scent formation in oriental hybrid Lilium variety 'Siberia'

Fig. 6. (a) A labeled diagram of a fullbloom Lilium 'Siberia' flower. (b) Pictorial view of Lilium 'Siberia' flowers at different flower developmental stages.

Fig. 5 in Molecular cloning, characterization and expression analysis of LoTPS2 and LoTPS4 involved in floral scent formation in oriental hybrid Lilium variety 'Siberia'

Fig. 5. Relative gene expression analysis of LoTPS2 and LoTPS4 in floraland vegetative tissues of Lilium 'Siberia' (a) relative expression levels of LoTPS2 in different tissues of Lilium 'Siberia' (b) Relative expression levels of LoTPS4 in different tissues of Lilium 'Siberia' analyzed by qRT-PCR. (c, d) Relative expression levels of LoTPS2 and LoTPS4 in full-bloom flowers of different Lilium species. GAPDH was used as an internal control. The highest expression level was set as 1 (100%). Lon: Longiflorum; Bru: Brunello; Sib: Siberia; Aca: Acapulco; Sor: Sorbonne; Man: Manissa. Data are presented as the mean ± SEM (n = 4).

Fig. 1 in Molecular cloning, characterization and expression analysis of LoTPS2 and LoTPS4 involved in floral scent formation in oriental hybrid Lilium variety 'Siberia'

Fig. 1. (a) Alignment of the amino acid sequences of LoTPS2 and LoTPS4, with AdAFS1 from Actinidia deliciosa (FJ265785) and (+)-limonene synthase (Q8L5K3) from Citrus limon. The protein sequences were aligned using ClustalX 2.1 and edited with GeneDoc. RRX8W motifs were present in LoTPS4 and (+)-limonene synthase but were missing in both LoTPS2 and AdAFS1. The conserved RRX8W, DDXXD, and RxR domains are underlined. (b) N-terminal sequence alignment of TPS-f clade terpene synthases. AdAFS1; CbLIS2 (C. breweri, AAD19840); CbLIS (C. breweri, AAC49395); CcLIS (Clarkia concinna, AAD19839). The CDIS (conifer diterpene internal sequence) is indicated by a dotted line. Dashes indicate gaps inserted for optimal alignment. (c) Phylogenetic analysis of LoTPS2 and LoTPS4 from Lilium 'Siberia' with amino acid sequences of other selected terpene synthases. The alignment was performed using ClustalX 2.1, and the tree was built via the neighborjoining method using the MEGA 6 program and iTOL (http://itol.embl.de/). The dot size at the branches of the tree shows bootstrap values. Accession numbers are given in a Supplementary Table 1.