Precision and accuracy of single-molecule FRET measurements - a multi-laboratory benchmark study

Single-molecule Förster resonance energy transfer (smFRET) is increasingly being used to determine distances, structures, and dynamics of biomolecules in vitro and in vivo. However, generalized protocols and FRET standards to ensure the reproducibility and accuracy of measurements of FRET efficiencies are currently lacking. Here we report the results of a comparative blind study in which 20 labs determined the FRET efficiencies (E) of several dye-labeled DNA duplexes. Using a unified, straightforward method, we obtained FRET efficiencies with s.d. between ±0.02 and ±0.05. We suggest experimental and computational procedures for converting FRET efficiencies into accurate distances, and discuss potential uncertainties in the experiment and the modeling. Our quantitative assessment of the reproducibility of intensity-based smFRET measurements and a unified correction procedure represents an important step toward the validation of distance networks, with the ultimate aim of achieving reliable structural models of biomolecular systems by smFRET-based hybrid methods

Interrater Agreement and Reliability of PERCIST and Visual Assessment When Using 18F-FDG-PET/CT for Response Monitoring of Metastatic Breast Cancer

Response evaluation at regular intervals is indicated for treatment of metastatic breast cancer (MBC). FDG-PET/CT has the potential to monitor treatment response accurately. Our purpose was to: (a) compare the interrater agreement and reliability of the semi-quantitative PERCIST criteria to qualitative visual assessment in response evaluation of MBC and (b) investigate the intrarater agreement when comparing visual assessment of each rater to their respective PERCIST assessment. We performed a retrospective study on FDG-PET/CT in women who received treatment for MBC. Three specialists in nuclear medicine categorized response evaluation by qualitative assessment and standardized one-lesion PERCIST assessment. The scans were categorized into complete metabolic response, partial metabolic response, stable metabolic disease, and progressive metabolic disease. 37 patients with 179 scans were included. Visual assessment categorization yielded moderate agreement with an overall proportion of agreement (PoA) between raters of 0.52 (95% CI 0.44–0.66) and a Fleiss kappa estimate of 0.54 (95% CI 0.46–0.62). PERCIST response categorization yielded substantial agreement with an overall PoA of 0.65 (95% CI 0.57–0.73) and a Fleiss kappa estimate of 0.68 (95% CI 0.60–0.75). The difference in PoA between overall estimates for PERCIST and visual assessment was 0.13 (95% CI 0.06–0.21; p = 0.001), that of kappa was 0.14 (95% CI 0.06–0.21; p < 0.001). The overall intrarater PoA was 0.80 (95% CI 0.75–0.84) with substantial agreement by a Fleiss kappa of 0.74 (95% CI 0.69–0.79). Semi-quantitative PERCIST assessment achieved significantly higher level of overall agreement and reliability compared with qualitative assessment among three raters. The achieved high levels of intrarater agreement indicated no obvious conflicting elements between the two methods. PERCIST assessment may, therefore, give more consistent interpretations between raters when using FDG-PET/CT for response evaluation in MBC

Single Molecule FRET Analysis of the 11 Discrete Steps of a DNA Actuator

DNA hybridization allows the design and assembly of dynamic DNA-based molecular devices. Such structures usually accomplish their function by the addition of fuel strands that drive the structure from one conformation to a new one or by internal changes in DNA hybridization. We report here on the performance and robustness of one of these devices by the detailed study of a dynamic DNA actuator. The DNA actuator was chosen as a model system, as it is the device with most discrete states to date. It is able to reversibly slide between 11 different states and can in principle function both autonomously and nonautonomously. The 11 states of the actuator were investigated by single molecule Förster Resonance Energy Transfer (smFRET) microscopy to obtain information on the static and dynamic heterogeneities of the device. Our results show that the DNA actuator can be effectively locked in several conformations with the help of well-designed DNA lock strands. However, the device also shows pronounced static and dynamic heterogeneities both in the unlocked and locked modes, and we suggest possible structural models. Our study allows for the direct visualization of the conformational diversity and movement of the dynamic DNA-based device and shows that complex DNA-based devices are inherently heterogeneous. Our results also demonstrate that single molecule techniques are a powerful tool for structural dynamics studies and provide a stringent test for the performance of molecular devices made out of DNA

Mutations in Calmodulin Cause Ventricular Tachycardia and Sudden Cardiac Death

Catecholaminergic polymorphic ventricular tachycardia (CPVT) is a devastating inherited disorder characterized by episodic syncope and/or sudden cardiac arrest during exercise or acute emotion in individuals without structural cardiac abnormalities. Although rare, CPVT is suspected to cause a substantial part of sudden cardiac deaths in young individuals. Mutations in RYR2, encoding the cardiac sarcoplasmic calcium channel, have been identified as causative in approximately half of all dominantly inherited CPVT cases. Applying a genome-wide linkage analysis in a large Swedish family with a severe dominantly inherited form of CPVT-like arrhythmias, we mapped the disease locus to chromosome 14q31-32. Sequencing CALM1 encoding calmodulin revealed a heterozygous missense mutation (c.161A>T [p.Asn53Ile]) segregating with the disease. A second, de novo, missense mutation (c.293A>G [p.Asn97Ser]) was subsequently identified in an individual of Iraqi origin; this individual was diagnosed with CPVT from a screening of 61 arrhythmia samples with no identified RYR2 mutations. Both CALM1 substitutions demonstrated compromised calcium binding, and p.Asn97Ser displayed an aberrant interaction with the RYR2 calmodulin-binding-domain peptide at low calcium concentrations. We conclude that calmodulin mutations can cause severe cardiac arrhythmia and that the calmodulin genes are candidates for genetic screening of individual cases and families with idiopathic ventricular tachycardia and unexplained sudden cardiac death

Precision and accuracy of single-molecule FRET measurements-a multi-laboratory benchmark study.

Single-molecule Förster resonance energy transfer (smFRET) is increasingly being used to determine distances, structures, and dynamics of biomolecules in vitro and in vivo. However, generalized protocols and FRET standards to ensure the reproducibility and accuracy of measurements of FRET efficiencies are currently lacking. Here we report the results of a comparative blind study in which 20 labs determined the FRET efficiencies (E) of several dye-labeled DNA duplexes. Using a unified, straightforward method, we obtained FRET efficiencies with s.d. between ±0.02 and ±0.05. We suggest experimental and computational procedures for converting FRET efficiencies into accurate distances, and discuss potential uncertainties in the experiment and the modeling. Our quantitative assessment of the reproducibility of intensity-based smFRET measurements and a unified correction procedure represents an important step toward the validation of distance networks, with the ultimate aim of achieving reliable structural models of biomolecular systems by smFRET-based hybrid methods