Detecting RNA-Protein Interactions With EGFP-Cy3 FRET by Acceptor Photobleaching

Förster Resonance Energy Transfer (FRET) is a great tool for cell biologists to investigate molecular interactions in live specimens. FRET is a distance-dependent phenomenon which can detect molecular interactions at distances between 1-10 nm. Several FRET approaches are reported in the literature for live and fixed cells to study protein-protein interactions; this protocol provides details of acceptor photobleaching as a FRET method to study RNA-Protein interactions. Cy3-labeled RNA foci (FRET acceptors) are photobleached at the intra-cellular site of interest (the nuclei) and the intensity of the EGFP-tagged proteins (FRET donors) at that same site are measured pre- and post- photobleaching. In principle, FRET is detected if the intensity of EGFP increases after photobleaching of Cy3. This protocol describes necessary steps and appropriate controls to conduct FRET measurements by the acceptor photobleaching method. Successful applications of this protocol will provide data to support the conclusion that EGFP-labeled proteins directly interact with Cy3-labeled RNA at the site of photobleaching. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol: FRET in fixed cells Alternate Protocol: FRET in live cells.

Perylene-Cy3 FRET System to Analyze Photoactive DNA Structures

We report a new Förster resonance energy transfer (FRET) system for structural analyses of DNA duplexes using perylene and Cy3 as donor and acceptor, respectively, linked at the termini of a DNA duplex via D-threoninol. Experimentally obtained FRET efficiencies were in good agreement with theoretical values calculated based on canonical B-form DNA. Due to the relatively long Förster radius, this system can be used to analyze large DNA structures, and duplexes containing photo-reactive molecules can be analyzed since perylene can be excited with visible light. The system was used to analyze a DNA duplex containing stilbene, demonstrating that in the region of the stilbene cluster the duplex adopts a ladder-like structure rather than helical one. Upon photodimerization between stilbene residues, FRET efficiencies indicated the reaction does not disturb DNA duplex. This FRET system will be useful for analysis of photoreactions of nucleobases as well as a wide range of nucleic acid structures.

Hopping and Flipping of RNA Polymerase on DNA during Recycling for Reinitiation after Intrinsic Termination in Bacterial Transcription

Two different molecular mechanisms, sliding and hopping, are employed by DNA-binding proteins for their one-dimensional facilitated diffusion on nonspecific DNA regions until reaching their specific target sequences. While it has been controversial whether RNA polymerases (RNAPs) use one-dimensional diffusion in targeting their promoters for transcription initiation, two recent single-molecule studies discovered that post-terminational RNAPs use one-dimensional diffusion for their reinitiation on the same DNA molecules. Escherichia coli RNAP, after synthesizing and releasing product RNA at intrinsic termination, mostly remains bound on DNA and diffuses in both forward and backward directions for recycling, which facilitates reinitiation on nearby promoters. However, it has remained unsolved which mechanism of one-dimensional diffusion is employed by recycling RNAP between termination and reinitiation. Single-molecule fluorescence measurements in this study reveal that post-terminational RNAPs undergo hopping diffusion during recycling on DNA, as their one-dimensional diffusion coefficients increase with rising salt concentrations. We additionally find that reinitiation can occur on promoters positioned in sense and antisense orientations with comparable efficiencies, so reinitiation efficiency depends primarily on distance rather than direction of recycling diffusion. This additional finding confirms that orientation change or flipping of RNAP with respect to DNA efficiently occurs as expected from hopping diffusion.

High-Throughput Protein-Nucleic Acid Interaction Assay Based on Protein-Induced Fluorescence Enhancement

Molecular processes involved in gene expression encompass multitudes of interactions between proteins and nucleic acids. Quantitative description of these interactions is crucial for delineating the mechanisms governing transcription, genome duplication, and translation. Here we describe a detailed protocol for the quantitative analysis of protein-nucleic acid interactions based on protein-induced fluorescence enhancement (PIFE). While PIFE has mainly been used in single-molecule studies, we modified its application for bulk measurement of protein-nucleic acid interactions in microwell plates using standard fluorescent plate readers. The microwell plate PIFE assay (mwPIFE) is simple, does not require laborious protein labeling, and is high throughput. These properties predispose mwPIFE to become a method of choice for routine applications that require multiple parallel measurements such as buffer optimization, competition experiments, or screening chemical libraries for binding modulators.

A stem-less probe using spontaneous pairing between Cy3 and quencher for RNA detection

We herein report a stem-less probe for the detection of RNA that depends on pairing between Cy3 and nitro methyl red. In our design, two Cy3 residues and two nitro methyl red residues were introduced into an oligonucleotide. In the absence of the target, these dyes formed a complex, and emission of Cy3 was efficiently quenched. Hybridization with the target RNA disrupted this interaction and resulted in Cy3 emission. Under optimized conditions, the signal to background ratio was as high as 180. We demonstrated specific detection of target RNA in cells using a wash-free FISH protocol.

HER4 selectively coregulates estrogen stimulated genes associated with breast tumor cell proliferation

The EGFR-family member HER4 undergoes regulated intramembrane proteolysis (RIP) to generate an intracellular domain (4ICD) that functions as a transcriptional coactivator. Accordingly, 4ICD coactivates the estrogen receptor (ER) and associates with ER at target gene promoters in breast tumor cells. However, the extent of 4ICD coactivation of ER and the functional significance of the 4ICD/ER transcriptional complex is unclear. To identify 4ICD coactivated genes we performed a microarray gene expression analysis of β-estradiol treated cells comparing control MCF-7 breast cancer cells to MCF-7 cells where HER4 expression was stably suppressed using a shRNA. In the MCF-7 cell line, β-estradiol significantly stimulated or repressed by 2-fold or more 726 or 53 genes, respectively. Significantly, HER4/4ICD was an obligate coactivator for 277 or 38% of the β-estradiol stimulated genes. Ingenuity Pathway Analysis of β-estradiol regulated genes identified significant associations with multiple cellular functions regulating cellular growth and proliferation, cell cycle progression, cancer metastasis, decreased hypoplasia, tumor cell migration, apoptotic resistance of tumor cells, and increased transcription. Genes coactivated by 4ICD displayed functional specificity by only significantly contributing to cellular growth and proliferation, cell cycle progression, and decreased hypoplasia. In direct concordance with these in situ results we show that HER4 knockdown in MCF-7 cells results in a loss of estrogen stimulated tumor cell proliferation and cell cycle progression, whereas, estrogen stimulated tumor cell migration was unaffected by loss of HER4 expression. In summary, we demonstrate for the first time that a cell surface receptor functions as an obligate ER coactivator with functional specificity associated with breast tumor cell proliferation and cell cycle progression. Nearly 90% of ER positive tumors coexpress HER4, therefore we predict that the majority of breast cancer patients would benefit from a strategy to therapeutic disengage ER/4ICD coregulated tumor cell proliferation.

Effects of early prebiotic and probiotic supplementation on development of gut microbiota and fussing and crying in preterm infants: a randomized, double-blind, placebo-controlled trial

OBJECTIVE

To evaluate the impact of early prebiotic and probiotic intervention on preterm infants' well-being, crying, growth, and microbiological programming.

STUDY DESIGN

Ninety-four preterm infants (gestational age 32-36 weeks and birth weight >1500 g) randomized to receive prebiotics (mixture of galacto-oligosaccharide and polydextrose 1:1), probiotics (Lactobacillus rhamnosus GG), or placebo during the first 2 months of life were followed up for 1 year. Infants were categorized based on the extent of crying and irritability during the first 2 months of life, and their gut microbiota was investigated by fluorescence in situ hybridization (n = 66) and quantitative polymerase chain reaction (n = 63).

RESULTS

A total of 27 of 94 infants (29%) infants were classified as excessive criers, significantly less frequently in the prebiotic and the probiotic groups than in the placebo group (19% vs 19% vs 47%, respectively; P = .02). The placebo group had a higher percentage of Clostridium histolyticum group bacteria in their stools than did the probiotic group (13.9% vs 8.9%, respectively; P = .05). There were no adverse events related to either supplementation.

CONCLUSIONS

Early prebiotic and probiotic supplementation may alleviate symptoms associated with crying and fussing in preterm infants. This original finding may offer new therapeutic and preventive measures for this common disturbance in early life.

Secretagogin-containing neurons in the mouse main olfactory bulb

Secretagogin (SCGN) is a recently discovered calcium binding protein of the EF hand family. We studied the structural features of SCGN-positive neurons in the mouse main olfactory bulb (MOB). SCGN-positive neurons were localized throughout layers but clustered in the glomerular layer (GL), mitral cell layer (MCL) and granule cell layer (GCL). They were heterogeneous, including numerous juxtaglomerular neurons, granule cells, small to medium-sized neurons in the external plexiform layer (EPL), and a few small cells in the ependymal/subependymal layer. Calretinin and/or tyrosine hydroxylase occasionally colocalized in SCGN-positive juxtaglomerular neurons. Calretinin also frequently colocalized in SCGN-positive EPL and GCL neurons. Morphologically some of juxtaglomerular SCGN-positive neurons were classical periglomerular cells, whereas others were apparently different from those periglomerular cells, although they were further heterogeneous. Some extended one slender process into a glomerulus which passed the glomerulus and further penetrated into another nearby glomeruli, and thus their dendritic processes spanned two or three or more glomeruli. We named this type of juxtaglomerular neurons "transglomerular cells." With the stereological analysis we estimated total number of juxtaglomerular SCGN-positive neurons at about 80,000/single MOB. The present study revealed the diversity of SCGN-positive neurons in the mouse MOB and their particular structural properties hitherto unknown.

Photostability of Cy3 and Cy5-Labeled DNA in the Presence of Metallic Silver Particles

We examined the photostability of a double-stranded DNA oligomer, covalently labeled with Cy3 or Cy5 on one strand, in the presence of metallic silver island films. In our experimental configuration a minor fraction of the labeled DNA was close to the silver particles and the remainder was distant from the particles. Proximity of the fluorophores to silver island films resulted in increased intensity. Upon continuous illumination we found a fraction of the emission that was resistant to the photobleaching. The emission spectra of the residual fractions were identical to the initial spectra. The frequency-domain lifetime measurements of this fraction revealed greatly shortened decay times. These results are consistent with the photostable fraction being close to the silver particles. This results suggest that the number of photons detected per fluorophore, prior to photobleaching, can be increased 5-fold or more by proximity to silver particles. Localization at an optimal distance from the silver surface may result in larger enhancements.