Imaging nanoscale nuclear structures with expansion microscopy.

Commonly applied super-resolution light microscopies have provided insight into subcellular processes at the nanoscale. However, imaging depth, speed, throughput and cost remain significant challenges, limiting the numbers of three-dimensional (3D) nanoscale processes that can be investigated and the number of laboratories able to undertake such analysis. Expansion microscopy (ExM) solves many of these limitations, but its application to imaging nuclear processes has been constrained by concerns of unequal nuclear expansion. Here, we demonstrate the conditions for isotropic expansion of the nucleus at a resolution equal to or better than 120-130 nm (pre-expansion). Using the DNA damage response proteins BRCA1, 53BP1 (also known as TP53BP1) and RAD51 as exemplars, we quantitatively describe the 3D nanoscale organisation of over 50,000 DNA damage response structures. We demonstrate the ability to assess chromatin-regulated events and show the simultaneous assessment of four elements. This study thus demonstrates how ExM can contribute to the investigation of nanoscale nuclear processes.

Safety and feasibility of same-day discharge following uncomplicated transvenous lead extraction.

INTRODUCTION: Transvenous lead extraction (TLE), while mostly a safe procedure, has risk of serious periprocedural complications. As such, overnight hospitalization remains a routine practice. In our center, we routinely discharge patients on the same day following an uncomplicated TLE. METHODS: This is a retrospective study of 265 consecutive patients who underwent uncomplicated TLE in our center between 2019 and 2021. Same-day discharge (SDD) patients are compared with those who stayed at least overnight for observation after the TLE procedure (non-SDD group). To assess the safety of an SDD strategy after uncomplicated TLE, the main study endpoint was to compare the rate of major procedure-related complications at 1-, 7-, and 30-days. To identify the factors influencing the operator's decision to discharge the patient on the same day, the secondary endpoint was to analyze clinical and procedural predictors of SDD. RESULTS: A total of 153 patients were discharged the same day after uncomplicated TLE (SDD), while 112 stayed at least overnight after the procedure (non-SDD). There was no significant difference in major procedure-related complications at 1-day (SDD 0% vs. non-SDD 1.8%, p value = ns), while patients in the SDD group had a lower rate of 7- and 30-day complications when compared with those in the non-SDD group (2.1% vs. 8.2%, p value = .0308; and 3.5% vs. 16%, p value = .0049, respectively). Noninfectious indication for TLE (OR 16.1, 95% confidence interval [CI] 4.29-77.6) and procedure end time before 12:00 (OR 2.82, 95% CI 1.11-7.27) were the only independent predictors of SDD. CONCLUSION: SDD discharge following uncomplicated TLE in selected patients (i.e., those without device infection and when the TLE procedure is completed in the morning) is feasible and safe.

Sterically Enhanced Control of Enzyme-Assisted DNA Assembly.

Traditional methods for the assembly of functionalised DNA structures, involving enzyme restriction and modification, present difficulties when working with small DNA fragments (<100 bp), in part due to a lack of control over enzymatic action during the DNA modification process. This limits the design flexibility and range of accessible DNA structures. Here, we show that these limitations can be overcome by introducing chemical modifications into the DNA that spatially restrict enzymatic activity. This approach, sterically controlled nuclease enhanced (SCoNE) DNA assembly, thereby circumvents the size limitations of conventional Gibson assembly (GA) and allows the preparation of well-defined, functionalised DNA structures with multiple probes for specific analytes, such as IL-6, procalcitonin (PCT), and a biotin reporter group. Notably, when using the same starting materials, conventional GA under typical conditions fails. We demonstrate successful analyte capture based on standard and modified sandwich ELISA and also show how the inclusion of biotin probes provides additional functionality for product isolation.

FRET-Based Method for Direct, Real-Time Measurement of DNA Methyltransferase Activity.

DNA methyltransferase activity is associated with a host of diseases, including cancers, where global hypomethylation of the genome, as well as marked changes in local DNA methylation patterns, can be both diagnostic and prognostic for the disease. Despite this, we currently lack a method for directly measuring the activity of the DNA methyltransferases, which would support the development of DNA methyltransferase-targeted therapies. Here, we demonstrate an assay for the direct measurement of methyltransferase activity, in real time. We employ a fluorescent methyltransferase cofactor analogue, which when bound by the enzyme to a labeled target DNA sequence results in fluorescence resonance energy transfer (FRET) between the donor dye (DNA) and the acceptor dye (cofactor). We demonstrate that the method can be used to monitor the activity of DNA MTases in real time and can be applied to screen inhibitors of the DNA methyltransferases. We show this in both bulk phase and single molecule imaging experiments, highlighting the potential application of the assay in screening and biophysical studies of methyltransferase function.

Decreased Growth Rate Associated with Tissue Contaminants in Juvenile Chinook Salmon Out-Migrating through an Industrial Waterway.

The industrial waterway in Portland Harbor, Oregon, is a migration corridor for a distinct population segment of Chinook Salmon (Upper Willamette River) currently protected by the U.S. Endangered Species Act. Juveniles are exposed to a suite of contaminants during outmigration including polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs), and dichlorodiphenyltrichloroethanes. We collected natural origin subyearling Chinook salmon from sites in and around the industrial harbor to evaluate growth (otolith microstructural analysis) in relation to measured chemical concentrations in tissue. A reduced growth rate was associated with higher tissue contaminant concentrations, particularly mixtures represented by PAHs and certain PCBs, which were elevated in juvenile Chinook collected throughout sites within Portland Harbor relative to those captured upstream. First-year growth is an established predictor of individual survival and eventual reproductive success in Chinook salmon. Therefore, our results indicate that legacy pollution may be limiting the population abundance of threatened Willamette River Chinook salmon, and future habitat remediation or restoration actions may benefit ongoing species recovery efforts.

DNA barcodes for rapid, whole genome, single-molecule analyses.

We report an approach for visualizing DNA sequence and using these 'DNA barcodes' to search complex mixtures of genomic material for DNA molecules of interest. We demonstrate three applications of this methodology; identifying specific molecules of interest from a dataset containing gigabasepairs of genome; identification of a bacterium from such a dataset and, finally, by locating infecting virus molecules in a background of human genomic material. As a result of the dense fluorescent labelling of the DNA, individual barcodes of the order 40 kb pairs in length can be reliably identified. This means DNA can be prepared for imaging using standard handling and purification techniques. The recorded dataset provides stable physical and electronic records of the total genomic content of a sample that can be readily searched for a molecule or region of interest.

The clinical and laboratory investigation of dysbetalipoproteinemia.

Familial dysbetalipoproteinemia (type III hyperlipoproteinemia) is a potentially underdiagnosed inherited dyslipidemia associated with greatly increased risk of coronary and peripheral vascular disease. The mixed hyperlipidemia observed in this disorder usually responds well to appropriate medical therapy and lifestyle modification. Although there are characteristic clinical features such as palmar and tuberous xanthomata, associated with dysbetalipoproteinemia, they are not always present, and their absence cannot be used to exclude the disorder. The routine lipid profile cannot distinguish dysbetalipoproteinemia from other causes of mixed hyperlipidemia and so additional investigations are required for confident diagnosis or exclusion. A range of investigations that have been proposed as potential diagnostic tests are discussed in this review, but the definitive biochemical test for dysbetalipoproteinemia is widely considered to be beta quantification. Beta quantification can determine the presence of "ß-VLDL" in the supernatant following ultracentrifugation and whether the VLDL cholesterol to triglyceride ratio is elevated. Both features are considered hallmarks of the disease. However, beta quantification and other specialist tests are not widely available and are not high-throughput tests that can practically be applied to all patients with mixed hyperlipidemia. Using apolipoprotein B (as a ratio either to total or non-HDL cholesterol or as part of a multi-step algorithm) as an initial test to select patients for further investigation is a promising approach. Several studies have demonstrated a high degree of diagnostic sensitivity and specificity using these approaches and apolipoprotein B is a relatively low-cost test that is widely available on high-throughput platforms. Genetic testing is also important in the diagnosis, but it should be noted that most individuals with an E2/2 genotype do not suffer from remnant hyperlipidemia and around 10% of familial dysbetalipoproteinemia cases are caused by rarer, autosomal dominant mutations in APOE that will only be detected if the gene is fully sequenced. Wider implementation of diagnostic pathways utilizing apo B could lead to more rational use of specialist investigations and more consistent detection of patients with dysbetalipoproteinemia. Without the application of a consistent evidence-based approach to identifying dysbetalipoproteinemia, many cases are likely to remain undiagnosed.

A general strategy for direct, enzyme-catalyzed conjugation of functional compounds to DNA.

The methyltransferase enzymes can be applied to deliver a range of modifications to pre-determined sites on large DNA molecules with exceptional specificity and efficiency. To date, however, a limited number of modifications have been delivered in this way because of the complex chemical synthesis that is needed to produce a cofactor analogue carrying a specific function, such as a fluorophore. Here, we describe a method for the direct transfer of a series of functional compounds (seven fluorescent dyes, biotin and polyethylene glycol) to the DNA duplex. Our approach uses a functional cofactor analogue, whose final preparative step is performed alongiside the DNA modification reaction in a single pot, with no purification needed. We show that fluorophore conjugation efficiency in these mixtures is significantly improved compared to two-step labeling approaches. Our experiments highlight the remarkable malleability and selectivity of the methyltransferases tested. Additional analysis using high resolution localization of the fluorophore distribution indicates that target sites for the methyltransferase are predominantly labeled on a single strand of their palindromic site and that a small and randomly-distributed probability of off-site labeling exists.

Determination of Real Time in Vivo Drug Receptor Occupancy for a Covalent Binding Drug as a Clinical Pharmacodynamic Biomarker by Immunocapture-LC-MS/MS.

We report a novel immunocapture (IC)-LC-MS/MS methodology to directly measure real time in vivo receptor occupancy (RO) for a covalent binding drug in blood lysate. A small molecule quencher was added immediately after sample collection to convert the free receptor to a quencher-bound receptor (QB-R) which was measured with the drug-bound receptor (DB-R) simultaneously by LC-MS/MS after immunocapture enrichment, followed by trypsin digestion. Addition of the quencher is necessary to prevent the free receptor from ex vivo binding with the drug. The real time RO was calculated based on the concentrations of DB-R and the free receptor (which is now QB-R) that were obtained from each sample. This strategy has been successfully applied to the measurement of the RO for Bruton's tyrosine kinase (BTK) in the blood lysate of monkeys after dosing with branebrutinib (BMS-986195), a covalent BTK inhibitor being evaluated to treat rheumatoid arthritis. A custom-made quencher, which is more reactive to BTK than branebrutinib, was added in excess amount to bind with all available free BTK to form quencher-bound BTK (QB-BTK) during blood sample collection. To measure a wide range of % BTK RO, including those of <5% or >95%, the required LLOQ at 0.125 nM for QB-BTK and 0.250 nM for drug-bound BTK (DB-BTK) in blood lysate were successfully achieved by using this IC-LC-MS/MS strategy. This proof-of-concept assay demonstrated its suitability with high throughput for real time in vivo BTK RO measurement as a pharmacodynamic (PD) biomarker for clinical drug development.

Evaluation of the Non-HDL Cholesterol to Apolipoprotein B Ratio as a Screening Test for Dysbetalipoproteinemia.

BACKGROUND: Familial dysbetalipoproteinemia is associated with the accumulation of remnant lipoproteins and premature cardiovascular disease. Identification of dysbetalipoproteinemia is important because family members may be affected. Diagnostic testing involves demonstration of ß-lipoprotein in the VLDL fraction or characterization of apo E3. These investigations are complex and relatively expensive. The ratios of apo B to total cholesterol and triglycerides have been proposed as screening tests. However, the ratio of non-HDL cholesterol to apo B (NHDLC/apoB) could offer improved performance as the confounding effect of variations in HDL cholesterol is removed. METHODS: We evaluated NHDLC/apoB as a screening test for dysbetalipoproteinemia, using ß-quantification analysis as a reference standard. Data from 1637 patients referred over a 16-year period for ß quantification were reviewed retrospectively. In 63 patients, diagnostic criteria for dysbetalipoproteinemia (VLDL cholesterol/triglyceride ratio ≥0.69 and presence of ß-VLDL) were fulfilled, and 1574 patients had dysbetalipoproteinemia excluded. RESULTS: Mean NHDLC/apoB in patients with dysbetalipoproteinemia was 7.3 mmol/g (SD, 1.5 mmol/g) and with dysbetalipoproteinemia excluded was 4.0 mmol/g (SD, 0.5 mmol/g). The optimum cutoff of >4.91 mmol/g achieved a diagnostic sensitivity of 96.8% (95% CI, 89.0-99.6) and specificity of 95.0% (95% CI, 93.8-96.0). NHDLC/apoB offered improved performance compared to total cholesterol/apoB [diagnostic sensitivity 92.1% (95% CI, 82.4-97.4) and specificity 94.5% (95% CI, 93.2-95.6) with a cutoff of >6.55 mmol/g]. NHDL/apoB reference ranges were not sex-dependent, although there was a significant difference between men and women for total cholesterol/apoB. CONCLUSIONS: NHDLC/apoB offers a simple first-line test for dysbetalipoproteinemia in selecting patients with mixed hyperlipidemia for more complex investigations.

2-Aminopurine as a fluorescent probe of DNA conformation and the DNA-enzyme interface.

Nearly 50 years since its potential as a fluorescent base analogue was first recognized, 2-aminopurine (2AP) continues to be the most widely used fluorescent probe of DNA structure and the perturbation of that structure by interaction with enzymes and other molecules. In this review, we begin by considering the origin of the dramatic and intriguing difference in photophysical properties between 2AP and its structural isomer, adenine; although 2AP differs from the natural base only in the position of the exocyclic amine group, its fluorescence intensity is one thousand times greater. We then discuss the mechanism of interbase quenching of 2AP fluorescence in DNA, which is the basis of its use as a conformational probe but remains imperfectly understood. There are hundreds of examples in the literature of the use of changes in the fluorescence intensity of 2AP as the basis of assays of conformational change; however, in this review we will consider in detail only a few intensity-based studies. Our primary aim is to highlight the use of time-resolved fluorescence measurements, and the interpretation of fluorescence decay parameters, to explore the structure and dynamics of DNA. We discuss the salient features of the fluorescence decay of 2AP when incorporated in DNA and review the use of decay measurements in studying duplexes, single strands and other structures. We survey the use of 2AP as a probe of DNA-enzyme interaction and enzyme-induced distortion, focusing particularly on its use to study base flipping and the enhanced mechanistic insights that can be gained by a detailed analysis of the decay parameters, rather than merely monitoring changes in fluorescence intensity. Finally we reflect on the merits and shortcomings of 2AP and the prospects for its wider adoption as a fluorescence-decay-based probe.

Aortic root replacement for bicuspid aortopathy following heart transplantation.

Although donors with well-functioning bicuspid aortic valves (BAV) are not a contraindication for transplantation, BAV patients are at risk for long-term aortopathy and valve dysfunction. We report a case of a patient status-post heart transplant 13 years ago who presented to our institution with a BAV and severe aortic regurgitation associated with an aortic root aneurysm and underwent aortic root replacement.

Methyltransferase-Directed Labeling of Biomolecules and its Applications.

Methyltransferases (MTases) form a large family of enzymes that methylate a diverse set of targets, ranging from the three major biopolymers to small molecules. Most of these MTases use the cofactor S-adenosyl-l-Methionine (AdoMet) as a methyl source. In recent years, there have been significant efforts toward the development of AdoMet analogues with the aim of transferring moieties other than simple methyl groups. Two major classes of AdoMet analogues currently exist: doubly-activated molecules and aziridine based molecules, each of which employs a different approach to achieve transalkylation rather than transmethylation. In this review, we discuss the various strategies for labelling and functionalizing biomolecules using AdoMet-dependent MTases and AdoMet analogues. We cover the synthetic routes to AdoMet analogues, their stability in biological environments and their application in transalkylation reactions. Finally, some perspectives are presented for the potential use of AdoMet analogues in biology research, (epi)genetics and nanotechnology.

Super-resolution optical DNA Mapping via DNA methyltransferase-directed click chemistry.

We demonstrate an approach to optical DNA mapping, which enables near single-molecule characterization of whole bacteriophage genomes. Our approach uses a DNA methyltransferase enzyme to target labelling to specific sites and copper-catalysed azide-alkyne cycloaddition to couple a fluorophore to the DNA. We achieve a labelling efficiency of ∼70% with an average labelling density approaching one site every 500 bp. Such labelling density bridges the gap between the output of a typical DNA sequencing experiment and the long-range information derived from traditional optical DNA mapping. We lay the foundations for a wider-scale adoption of DNA mapping by screening 11 methyltransferases for their ability to direct sequence-specific DNA transalkylation; the first step of the DNA labelling process and by optimizing reaction conditions for fluorophore coupling via a click reaction. Three of 11 enzymes transalkylate DNA with the cofactor we tested (a readily prepared s-adenosyl-l-methionine analogue).

Short-term outcomes in adult cardiac surgery in the use of del Nido cardioplegia solution.

OBJECTIVES: Del Nido cardioplegia in adult cardiac surgery has not been studied although it has been in common use as a "single" dose cardioplegia in pediatric heart surgery. We retrospectively assessed the short-term (in-hospital) clinical outcomes of patients undergoing aortic valve replacement (AVR) using del Nido cardioplegia solution, comparing it to conventional multi-dose whole blood cardioplegia. METHODS: We switched our cardioplegia protocol from conventional whole blood cardioplegia exclusively to del Nido solution in May 2011. In 2011, 240 consecutive patients underwent isolated AVR. One hundred and seventy-eight of them were operated on with the use of del Nido cardioplegia (del Nido group) and whole blood cardioplegia (conventional group) was used in the other 62 patients. Isolated AVR was chosen as a cohort because of its relative simplicity and the similarity of surgical techniques among surgeons. Propensity-score matching identified 54 matched pairs for analysis. RESULTS: The retrograde cardioplegia technique was used in 19 cases (35.2%) in the del Nido group and 52 cases (96.3%) in the conventional group (p<0.001). Mean cardiopulmonary bypass time and mean aortic cross-clamp time were significantly shorter in the del Nido group compared to the conventional group: 71 ± 16 min vs. 84 ± 28 min (p<0.01), 52 ± 14 min vs. 60 ± 16 min (p<0.01), respectively. Postoperative inotropic support was required in 11 patients (20.4 %) in the del Nido group and 13 patients (24.1 %) in the conventional group (p=0.82) with no statistical difference. No patient required a postoperative intra-aortic balloon pump and in-hospital mortality was 0% in both groups. There was no significant difference in postoperative complications between the two groups. CONCLUSIONS: Short-term outcomes in adult cardiac surgery using del Nido solution were acceptable and comparable to conventional multi-dose whole blood cardioplegia. The del Nido cardioplegia technique was associated with shortened cross-clamp times and less frequent utilization of the retrograde cardioplegia delivery technique.

The impact of a minimally invasive approach on reoperative aortic valve replacement.

BACKGROUND AND AIM OF THE STUDY: The advantages of minimally invasive aortic valve replacement (AVR) are well documented, but whether the benefits extend to subsequent reoperative aortic valve surgery and beyond is unknown. The study aim was to compare in-hospital outcomes and long-term survival following reoperative AVR between patients who had previous undergone either minimally invasive AVR (mini-AVR) or full sternotomy AVR (sAVR). METHODS: All reoperative, isolated AVRs performed between July 1997 and September 2013 at the authors' institution, with or without non-complex aortic surgery, were identified. Patients were excluded if AVR was not isolated, had occurred prior to July 1997, or if the initial AVR was performed before the patient was aged 18 years. All reoperations were performed through a full sternotomy. The main outcomes of interest were operative results and long-term survival. RESULTS: A total of 101 patients was identified, of which 34 had undergone previous mini-AVR and 67 previous sAVR. The time from the previous AVR was similar in both groups (median 7.6 years overall). Of previous valve implants, 57 were bioprostheses and 44 mechanical; structural valve degeneration was the most common indication for surgery (43/101). Mini-AVR and sAVR patients did not differ significantly with regards to patient demographics and preoperative risk factors. A strong trend towards shorter skin-to-skin operative times was observed for mini-AVR (330 min versus 356 min; p = 0.053). Postoperatively, mini-AVR patients had a shorter ventilation time (5.7 h versus 8.4 h; p = 0.005), intensive care unit stay (37 h versus 63 h; p ≤ 0.001) and hospital length of stay (6.5 days versus 8.0 days; p = 0.038). There was one operative mortality in the sAVR, and none in the mini-AVR group. Mid-term survival at one and five years for mini-AVR was 100% (95% CI 100-100) and 100% (95% CI 100-100), and for sAVR was 93.9% (95% CI 88.2-99.7) and 85.0% (95% CI 75.1-94.9), respectively (p = 0.041). CONCLUSION: Mini-AVR confers benefits during subsequent reoperative AVR, with shorter hospital stays and improved long-term survival. These findings suggest that mini-AVR should be considered for patients at risk for aortic valve reoperation, and describes a previously unreported advantage of this well-established technique.

The Use of Lidocaine Containing Cardioplegia in Surgery for Adult Acquired Heart Disease.

BACKGROUND: Del Nido cardioplegia, a crystalloid-based solution with lidocaine as a key element, is given as a single dose and has been used successfully in congenital cardiac surgery. HYPOTHESIS: We retrospectively compared a lidocaine containing "modified del Nido" solution with our standard whole blood cardioplegia to investigate its safety and efficacy in adult cardiac surgery. METHODS: From June 1, 2013 to December 30, 2013, we used a single dose of lidocaine containing cardioplegia (LC group) in 92 consecutive operations. Propensity matching analysis was undertaken to compare the outcomes of such patients with those who underwent their surgery by the same surgeon using standard whole blood cardioplegia (WB group), n = 396. Propensity score matching yielded 79 pairs of patients. RESULTS: After propensity matching, LC and WB groups were similar in baseline operative characteristics including cross-clamp time (LC: 65 minutes [range 54 to 89] vs. WB: 70 minutes [54 to 86], p = 0.993). Postoperative outcomes were similar including inotropic requirements (30.4% [24/72] vs. 25.3% [20/72], p < 0.60), median ventilation time (4.7 hours vs. 5.3, p < 0.74) and median length of stay was seven days for both groups (p < 0.82). Despite higher median postoperative, 24-hour CK-MB levels LC group (LC:22.3 ng/ml, range [15.6 to 40.3] vs. WB:18.4 ng/ml [13.9 to 28.2], p = 0.040), operative and one-year mortality were comparable among study groups (both p > 0.798). CONCLUSIONS: Lidocaine containing cardioplegia appears to be safe in adults undergoing cardiac procedure when administered for the first 60 minutes of aortic cross clamping. Higher CK-MB levels did not translate into adverse clinical outcomes.

Single molecule methods for the study of catalysis: from enzymes to heterogeneous catalysts.

Structural and temporal inhomogeneities can have a marked influence on the performance of inorganic and biocatalytic systems alike. While these subtle variations are hardly ever accessible through bulk or ensemble averaged activity screening, insights into the molecular mechanisms underlying these diverse phenomena are absolutely critical for the development of optimized or novel catalytic systems and processes. Fortunately, state-of-the-art fluorescence microscopy methods have allowed experimental access to this intriguing world at the nanoscale. In this tutorial review we will first provide a broad overview of key concepts and developments in the application of single molecule fluorescence spectroscopy to (bio)catalysis research. In the second part topics specific to both bio and heterogeneous catalysis will be reviewed in more detail.

Priming in the microbial landscape: periphytic algal stimulation of litter-associated microbial decomposers.

Microbial communities associated with submerged detritus in aquatic ecosystems often comprise a diverse mixture of autotrophic and heterotrophic microbes, including algae, bacteria, protozoa, and fungi. Recent studies have documented increased rates of plant litter mass loss when periphytic algae are present. We conducted laboratory and field experiments to assess potential metabolic interactions between natural autotrophic and heterotrophic microbial communities inhabiting submerged decaying plant litter of Typha angustifolia and Schoenoplectus acutus. In the field, submerged plant litter was either exposed to natural sunlight or placed under experimental canopies that manipulated light availability and growth of periphytic algae. Litter was collected and returned to the laboratory, where algal photosynthesis was manipulated (light/dark incubation), while rates of bacterial and fungal growth and productivity were simultaneously quantified. Bacteria and fungi were rapidly stimulated by exposure to light, thus establishing the potential for algal priming of microbial heterotrophic decay activities. Experimental incubations of decaying litter with 14C- and 13C-bicarbonate established that inorganic C fixed by algal photosynthesis was rapidly transferred to and assimilated by heterotrophic microbial decomposers. Periphytic algal stimulation of microbial heterotrophs, especially fungal decomposers, is an important and largely unrecognized interaction within the detrital microbial landscape, which may transform our current conceptual understanding of microbial secondary production and organic matter decomposition in aquatic ecosystems.

Enzyme-promoted base flipping controls DNA methylation fidelity.

A quantitative understanding of how conformational transitions contribute to enzyme catalysis and specificity remains a fundamental challenge. A suite of biophysical approaches was used to reveal several transient states of the enzyme-substrate complexes of the model DNA cytosine methyltransferase M.HhaI. Multidimensional, transverse relaxation-optimized nuclear magnetic resonance (NMR) experiments show that M.HhaI has the same conformation with noncognate and cognate DNA sequences. The high-affinity cognatelike mode requires the formation of a subset of protein-DNA interactions that drive the flipping of the target base from the helix to the active site. Noncognate substrates lacking these interactions undergo slow base flipping, and fluorescence tracking of the catalytic loop corroborates the NMR evidence of a loose, nonspecific binding mode prior to base flipping and subsequent closure of the catalytic loop. This slow flipping transition defines the rate-limiting step for the methylation of noncognate sequences. Additionally, we present spectroscopic evidence of an intermediate along the base flipping pathway that has been predicted but never previously observed. These findings provide important details of how conformational rearrangements are used to balance specificity with catalytic efficiency.