Co-crystal structures of the fluorogenic aptamer Beetroot show that close homology may not predict similar RNA architecture.

Beetroot is a homodimeric in vitro selected RNA that binds and activates DFAME, a conditional fluorophore derived from GFP. It is 70% sequence-identical to the previously characterized homodimeric aptamer Corn, which binds one molecule of its cognate fluorophore DFHO at its interprotomer interface. We have now determined the Beetroot-DFAME co-crystal structure at 1.95 Å resolution, discovering that this RNA homodimer binds two molecules of the fluorophore, at sites separated by ~30 Å. In addition to this overall architectural difference, the local structures of the non-canonical, complex quadruplex cores of Beetroot and Corn are distinctly different, underscoring how subtle RNA sequence differences can give rise to unexpected structural divergence. Through structure-guided engineering, we generated a variant that has a 12-fold fluorescence activation selectivity switch toward DFHO. Beetroot and this variant form heterodimers and constitute the starting point for engineered tags whose through-space inter-fluorophore interaction could be used to monitor RNA dimerization.

Characterizing Fluorescence Properties of Turn-on RNA Aptamers.

Fluorescent RNA aptamers are tools for studying RNA localization and interactions in vivo. The photophysical properties of these in vitro selected RNAs should be characterized prior to cellular imaging experiments. Here, we describe the process of determining the fluorophore affinity, fluorescence enhancement, and fluorescence lifetime(s) of the Mango-III fluorescence turn-on aptamer. Parameters determined through these protocols will aid in establishing conditions for live-cell imaging.

Computational Modeling and Imaging of the Intracellular Oxygen Gradient.

Computational modeling can provide a mechanistic and quantitative framework for describing intracellular spatial heterogeneity of solutes such as oxygen partial pressure (pO2). This study develops and evaluates a finite-element model of oxygen-consuming mitochondrial bioenergetics using the COMSOL Multiphysics program. The model derives steady-state oxygen (O2) distributions from Fickian diffusion and Michaelis-Menten consumption kinetics in the mitochondria and cytoplasm. Intrinsic model parameters such as diffusivity and maximum consumption rate were estimated from previously published values for isolated and intact mitochondria. The model was compared with experimental data collected for the intracellular and mitochondrial pO2 levels in human cervical cancer cells (HeLa) in different respiratory states and under different levels of imposed pO2. Experimental pO2 gradients were measured using lifetime imaging of a Förster resonance energy transfer (FRET)-based O2 sensor, Myoglobin-mCherry, which offers in situ real-time and noninvasive measurements of subcellular pO2 in living cells. On the basis of these results, the model qualitatively predicted (1) the integrated experimental data from mitochondria under diverse experimental conditions, and (2) the impact of changes in one or more mitochondrial processes on overall bioenergetics.

Intracellular imaging of metmyoglobin and oxygen using new dual purpose probe EYFP-Myoglobin-mCherry.

The biological relevance of nitric oxide (NO) and reactive oxygen species (ROS) in signaling, metabolic regulation, and disease treatment has become abundantly clear. The dramatic change in NO/ROS processing that accompanies a changing oxygen landscape calls for new imaging tools that can provide cellular details about both [O2 ] and the production of reactive species. Myoglobin oxidation to the met state by NO/ROS is a known sensor with absorbance changes in the visible range. We previously employed Förster resonance energy transfer to read out the deoxygenation/oxygenation of myoglobin, creating the subcellular [O2 ] sensor Myoglobin-mCherry. We now add the fluorescent protein EYFP to this sensor to create a novel probe that senses both met formation, a proxy for ROS/NO exposure, and [O2 ]. Since both proteins are present in the construct, it can also relieve users from the need to measure fluorescence lifetime, making [O2 ] sensing available to a wider group of laboratories.

Fluorogenic aptamers resolve the flexibility of RNA junctions using orientation-dependent FRET.

To further understand the transcriptome, new tools capable of measuring folding, interactions, and localization of RNA are needed. Although Förster resonance energy transfer (FRET) is an angle- and distance-dependent phenomenon, the majority of FRET measurements have been used to report distances, by assuming rotationally averaged donor-acceptor pairs. Angle-dependent FRET measurements have proven challenging for nucleic acids due to the difficulties in incorporating fluorophores rigidly into local substructures in a biocompatible manner. Fluorescence turn-on RNA aptamers are genetically encodable tags that appear to rigidly confine their cognate fluorophores, and thus have the potential to report angular-resolved FRET. Here, we use the fluorescent aptamers Broccoli and Mango-III as donor and acceptor, respectively, to measure the angular dependence of FRET. Joining the two fluorescent aptamers by a helix of variable length allowed systematic rotation of the acceptor fluorophore relative to the donor. FRET oscillated in a sinusoidal manner as a function of helix length, consistent with simulated data generated from models of oriented fluorophores separated by an inflexible helix. Analysis of the orientation dependence of FRET allowed us to demonstrate structural rigidification of the NiCo riboswitch upon transition metal-ion binding. This application of fluorescence turn-on aptamers opens the way to improved structural interpretation of ensemble and single-molecule FRET measurements of RNA.

Cooperative Adsorption of Trehalose to DPPC Monolayers at the Water-Air Interface Studied with Vibrational Sum Frequency Generation.

A combination of surface tension, surface-specific vibrational spectroscopy, and differential scanning calorimetry experiments was performed to examine the ability of lipid films to enrich interfacial organic content by attracting soluble, neutral saccharides from bulk aqueous solution. This "cooperative adsorption" hypothesis has been proposed as a possible source of the high organic fractions found in sea spray aerosols and is believed to be responsible for cryoprotection in some organisms. Experiments described in this work show that the neutral disaccharide trehalose (Tre) is drawn to lipid films composed of dipalmitoylphosphatidylcholine (DPPC), a saturated lipid that is a major component of most eukaryotic cells. The effects of Tre on DPPC monolayer structure and organization were tested with tightly packed monolayers in the two-dimensional solid phase (40 Å2/molecule) and more expanded monolayers in the two-dimensional liquid condensed phase (55 Å2/molecule). Surface tension data show that DPPC monolayer behavior remains largely unchanged until Tre bulk concentrations are sufficiently high (≥50 mM). In contrast, surface-specific vibrational sum frequency spectra show that when Tre bulk concentrations are ≥10 mM, DPPC monolayers in their liquid condensed state (55 Å2/molecule) became more ordered, implying relatively strong noncovalent interactions between the two species. Tre also induces changes in DPPC bilayer behavior as evidenced by a gel-to-liquid crystalline phase transition temperature that increases with increasing Tre concentration. This result suggests that Tre associates with the DPPC headgroups in very specific ways leading to partial dehydration. Together, these results support the cooperative adsorption mechanism under some circumstances, namely, that there is a minimum aqueous phase Tre concentration required to induce observable structural changes in a lipid monolayer and that these effects are most pronounced with DPPC monolayers in their liquid condensed state compared to those of a tightly packed two-dimensional solid.

Organic Enrichment at Aqueous Interfaces: Cooperative Adsorption of Glucuronic Acid to DPPC Monolayers Studied with Vibrational Sum Frequency Generation.

Surface tension, surface-specific vibrational spectroscopy and differential scanning calorimetry measurements were all used to test cooperative adsorption of glucuronic acid (GU) to DPPC monolayers adsorbed to the aqueous/vapor interface. Experiments were performed using GU solutions prepared in Millipore water and in carbonate/bicarbonate solutions buffered to a pH of 9.0. The effects of GU on DPPC monolayer structure and organization were carried out with tightly packed monolayers (40 Å2/DPPC) and monolayers in their liquid condensed phase (55 Å2/molecule). Surface tension data show that GU concentrations of 50 mM lead to expanded DPPC monolayers with diminished surface tensions (or higher surface pressures) at a given DPPC coverage relative to monolayers on pure water. With unbuffered solutions, GU induces significant ordering within liquid condensed monolayers although the effects of GU on tightly packed DPPC monolayers are less pronounced. GU also induces a second, higher melting temperature in DPPC vesicles implying that GU (at sufficiently high concentrations) strengthens lipid-lipid cohesion, possibly by replacing water solvating the DPPC headgroups. Together, these observations all support a cooperative adsorption mechanism. In buffer solutions, the effects of dissolved GU on DPPC structure and organization are muted. Only at sufficiently high GU concentrations (when the solution's buffering capacity has been exceeded) do the data again show evidence of cooperative adsorption. These findings place limits on cooperative adsorption's ability to enrich interfacial organic content in alkaline environmental systems such as oceans.