Catecholamine Detection Using a Functionalized Poly(l‑dopa)-Coated Gate Field-Effect Transistor

A highly sensitive catecholamine (CA) sensor was created using a biointerface layer composed of a biopolymer and a potentiometric detection device. For the detection of CAs, 3-aminophenylboronic acid (3-NH₂-PBA) was reacted with the carboxyl side chain of l-3,4-dihydroxyphenylalanine (l-dopa, LD) and the PBA-modified l-dopa was directly copolymerized with LD on an Au electrode, resulting in a 3.5 nm thick PBA-modified poly­(PBA–LD/LD) layer-coated Au electrode. By connecting the PBA–LD-coated Au electrode to a field-effect transistor (FET), the molecular charge changes at the biointerface of the Au electrode, which was caused by di-ester binding of the PBA–CA complex, were transduced into gate surface potential changes. Effective CAs included LD, dopamine (DA), norepinephrine (NE), and epinephrine (EP). The surface potential of the PBA–LD-coated Au changed after the addition of 40 nM of each CA solution; notably, the PBA–LD-coated Au showed a higher sensitivity to LD because the surface potential change could already be observed after 1 nM of LD was added. The fundamental parameter analyses of the PBA–LD to CA affinity from the surface potential shift against each CA concentration indicated the highest affinity to LD (binding constant (<i>K</i>_s): 1.68 × 10⁶ M^–1, maximum surface potential shift (<i>V</i>_max): 182 mV). Moreover, the limit of detection for each CA was 3.5 nM in LD, 12.0 nM in DA, 7.5 nM in NE, and 12.6 nM in EP. From these results, it is concluded that the poly­(PBA–LD/LD)-coated gate FET could become a useful biosensor for neurotransmitters, hormones, and early detection of Parkinson’s disease

Structural Transformation of Guanine Coordination Motifs in Water Induced by Metal Ions and Temperature

The transformation effects of metal ions and temperature on the DNA base guanine (G) metal–organic coordination motifs in water have been investigated by scanning tunneling microcopy (STM). The G molecules form an ordered hydrogen-bonded structure at the water–highly oriented pyrolytic graphite interface. The STM observations reveal that the canonical G/9H form can be transformed into the G/(3H,7H) tautomer by increasing the temperature of the G solution to 38.6 °C. Moreover, metal ions bind with G molecules to form G₄Fe₁³⁺, G₃Fe₃²⁺, and the heterochiral intermixed G₄Na₁⁺ metal–organic networks after the introduction of alkali-metal ions in cellular environment

Data File 1.csv

Statistical results of radii and lattice constants in both x and y directions. SEM images are obtained throughout the sample area uniformly, and 64 disks are captured (4 disks per image)

Retraining and Optimizing DNA-Hydrolyzing Deoxyribozymes for Robust Single- and Multiple-Turnover Activities

Recently, we reported two classes of Zn²⁺-dependent DNA-hydrolyzing deoxyribozymes. The class I deoxyribozymes can adopt a secondary structure of either hairpin or stem-loop-stem. The corresponding most active representatives, I-R1 and I-R3, exhibit single-turnover <i>k</i>_obs values of ∼0.059 and ∼1.0 min^–1 at 37 °C, respectively. Further analysis revealed that I-R3 could perform slow multiple-turnover catalysis with a <i>k</i>_cat of ∼0.017 min^–1 at 37 °C. In this study, we sought to retrain and optimize the class I deoxyribozymes for robust single- and multiple-turnover cleavage activities. Refined consensus sequences were derived based on the data of <i>in vitro</i> reselection from the degenerate DNA pools. By examining individual candidates, we obtained the I-R1 mutants I-R1a-c with improved single-turnover <i>k</i>_obs values of 0.68–0.76 min^–1 at 37 °C, over 10 times faster than I-R1. Meanwhile, we further demonstrated that I-R1a–c and I-R3 are thermophilic. As temperature went higher beyond 45 °C, I-R3 cleaved faster with the <i>k</i>_obs value reaching its maximum of ∼3.5 min^–1 at 54 °C. Using a series of the <i>k</i>_obs values of I-R3 from 37 to 54 °C, we calculated the apparent activation energy <i>E</i>_a to be ∼15 ± 3 kcal/mol for the DNA-catalyzed hydrolysis of DNA phosphodiester bond. In addition, we were able to design a simple yet efficient thermal-cycling protocol to boost the effective <i>k</i>_cat of I-R3 from 0.017 to 0.50 min^–1, which corresponds to an ∼30-fold improvement of the multiple-turnover activity. The data and findings provide insights on the enzymatic robustness of DNA-catalyzed DNA hydrolysis and offer general strategies to study various DNA enzymes

Additional file 8: of IMP1 regulates UCA1-mediated cell invasion through facilitating UCA1 decay and decreasing the sponge effect of UCA1 for miR-122-5p

Figure S5. Effect of UCA1 on the invasive abilities of MCF7 cells. Histograms show the effect of UCA1 on the invasive abilities of MCF7 cells. Values represent the means ± SD from three independent experiments; **P < 0.01, *P < 0.05 as determined by one-way ANOVA followed by Tukey’s multiple comparison tests. (TIFF 992 kb

Additional file 1: of IMP1 regulates UCA1-mediated cell invasion through facilitating UCA1 decay and decreasing the sponge effect of UCA1 for miR-122-5p

Table S1. Primers used for qPCR, RT-PCR and siRNA interference. (DOC 53 kb

MOESM1 of Metabolic engineering of Escherichia coli for the synthesis of polyhydroxyalkanoates using acetate as a main carbon source

Additional file 1: Table S1. Oligonucleotides used in this study. Table S2. P3HB production by E. coli strains cultivated in MM medium supplemented with CSL. Figure S1. Effect of acetate concentration on cell growth and P3HB production

Additional file 6: of IMP1 regulates UCA1-mediated cell invasion through facilitating UCA1 decay and decreasing the sponge effect of UCA1 for miR-122-5p

Table S2. miRNAs associated with UCA1. (DOCX 13 kb

Additional file 5: of IMP1 regulates UCA1-mediated cell invasion through facilitating UCA1 decay and decreasing the sponge effect of UCA1 for miR-122-5p

Figure S3. UCA1 is associated with IMP1 and CNOT1 and with miR-185-5p. (A) Vectors expressing UCA1 or UCA1-MS2 were transiently transfected into MDA231/IMP1-GFP cells. Pulldown assays were performed to analyze the association of IMP1 and CNOT1 with UCA1-MS2. Representative images indicate that both IMP1 and CNOT1 co-precipitated with UCA1. Control: cells transfected with MS2-untagged UCA1. (B) Putative binding site of UCA1 for miR-185-5p. (C) Interaction of miR-185-5p with UCA1-MS2 was examined in the pulldown material. Relative levels of miR-185-5p in the precipitates were statistically analyzed as means ± SD from three independent experiments: **P < 0.01 as determined by Student’s t test. (TIFF 1227 kb

Additional file 7: of IMP1 regulates UCA1-mediated cell invasion through facilitating UCA1 decay and decreasing the sponge effect of UCA1 for miR-122-5p

Figure S4. IMP1 knockdown increases the expression of miR-122-5p target mRNAs. (A) Cellular levels of miR-122-5p are not affected by IMP1-GFP expression. (B) After MS2 pulldown experiments, levels of miR-122-5p in the supernatants were analyzed by qPT-PCR. Levels of miR-122-5p were normalized to GAPDH mRNA from three independent experiments: **P < 0.01 as determined by Student’s t test. (C) RT-qPCR was applied to measure the levels of PKM2 and IGF-1R mRNAs in IMP1 knockdown T47D cells. Levels of the mRNAs were normalized to GAPDH mRNA from three independent experiments: *P < 0.05 as determined by Student’s t test. (TIFF 884 kb