Synthetic Genes For Dynamic Regulation Of DNA-Based Receptors.

We present a strategy to control dynamically the loading and release of molecular ligands from synthetic nucleic acid receptors using in vitro transcription. We demonstrate this by engineering three model synthetic DNA-based receptors: a triplex-forming DNA complex, an ATP-binding aptamer, and a hairpin strand, whose ability to bind their specific ligands can be cotranscriptionally regulated (activated or inhibited) through specific RNA molecules produced by rationally designed synthetic genes. The kinetics of our DNA sensors and their genetically generated inputs can be captured using differential equation models, corroborating the predictability of the approach used. This approach shows that highly programmable nucleic acid receptors can be controlled with molecular instructions provided by dynamic transcriptional systems, illustrating their promise in the context of coupling DNA nanotechnology with biological signaling.

Protein-Protein Communication Mediated by an Antibody-Responsive DNA Nanodevice.

We report here the rational design and optimization of an antibody-responsive, DNA-based device that enables communication between pairs of otherwise non-interacting proteins. The device is designed to recognize and bind a specific antibody and, in response, undergo a conformational change that leads to the release of a DNA strand, termed the "translator," that regulates the activity of a downstream target protein. As proof of principle, we demonstrate antibody-induced control of the proteins thrombin and Taq DNA polymerase. The resulting strategy is versatile and, in principle, can be easily adapted to control protein-protein communication in artificial regulatory networks.

Synthetic Antigen-Conjugated DNA Systems for Antibody Detection and Characterization.

Antibodies are among the most relevant biomolecular targets for diagnostic and clinical applications. In this Perspective, we provide a critical overview of recent research efforts focused on the development and characterization of devices, switches, and reactions based on the use of synthetic antigen-conjugated DNA strands designed to be responsive to specific antibodies. These systems can find applications in sensing, drug-delivery, and antibody-antigen binding characterization. The examples described here demonstrate how the programmability and chemical versatility of synthetic nucleic acids can be used to create innovative analytical tools and target-responsive systems with promising potentials.

Rational Control of the Activity of a Cu2+-Dependent DNAzyme by Re-engineering Purely Entropic Intrinsically Disordered Domains.

The function and activity of many proteins is finely controlled by the modulation of the entropic contribution of intrinsically disordered domains that are not directly involved in any recognition event. Inspired by this mechanism, we demonstrate here that we could finely regulate the catalytic activity of a model DNAzyme (i.e., a synthetic DNA sequence with enzyme-like properties) by rationally introducing intrinsically disordered nucleic acid portions in its original sequence. More specifically, we have re-engineered here the well-characterized Cu2+-dependent DNAzyme that catalyzes a self-cleavage reaction by introducing a poly(T) linker domain in its sequence. The linker is not directly involved in the recognition event and connects the two domains that fold to form the catalytic core. We demonstrate that the enzyme-like activity of this re-engineered DNAzyme can be modulated in a predictable and fine way by changing the length, and thus entropy, of such a linker domain. Given these attributes, the rational design of intrinsically disordered domains could expand the available toolbox to achieve a control of the activity of DNAzymes and, in analogy, ribozymes through a purely entropic contribution.

Publisher Correction: Orthogonal regulation of DNA nanostructure self-assembly and disassembly using antibodies.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

International normalized ratio (INR) values in patients receiving oral vitamin K antagonists and undergoing oral surgery: A clinical audit.

INTRODUCTION: Dental extractions can be safely carried out on patients under vitamin K antagonists (VKAs) therapy, without stopping or changing the dosage, but the international normalized ratio (INR) needs to be monitored on the day of the intervention, showing adequate rates before proceeding. OBJECTIVES: This study aims at evaluating INR values, measured before oral surgery procedures, to assess the rate of patients, under VKAs therapy, outside the therapeutic range. MATERIALS AND METHODS: A clinical audit was carried out involving patients under VKAs, who needed minor oral surgery procedures, over a period of 18 months. The patient was instructed to not modify or suspend VKAs prior to the intervention. Before surgery, each patient fulfilled a questionnaire on dietary and oral hygiene habits, and a blood sample was collected for INR assessment (cut-off value for surgical procedure ≤3.5). RESULTS: One hundred twenty-two patients were enrolled: 69 (56.6%) had an INR value within the established therapeutic range, 53 (43.4%) were out of range. No intra- or postsurgical major bleeding was recorded. CONCLUSIONS: INR, measured on the same day of oral surgery, has the potential to prevent bleeding complications by the identification of those patients out of range, who may require adjusting the drug therapeutic dosage.

Orthogonal regulation of DNA nanostructure self-assembly and disassembly using antibodies.

Here we report a rational strategy to orthogonally control assembly and disassembly of DNA-based nanostructures using specific IgG antibodies as molecular inputs. We first demonstrate that the binding of a specific antibody to a pair of antigen-conjugated split DNA input-strands induces their co-localization and reconstitution into a functional unit that is able to initiate a toehold strand displacement reaction. The effect is rapid and specific and can be extended to different antibodies with the expedient of changing the recognition elements attached to the two split DNA input-strands. Such an antibody-regulated DNA-based circuit has then been employed to control the assembly and disassembly of DNA tubular structures using specific antibodies as inputs. For example, we demonstrate that we can induce self-assembly and disassembly of two distinct DNA tubular structures by using DNA circuits controlled by two different IgG antibodies (anti-Dig and anti-DNP antibodies) in the same solution in an orthogonal way.

Enhancing Reactivity and Site-Selectivity in Hydrogen Atom Transfer from Amino Acid C-H Bonds via Deprotonation.

A kinetic study on the reactions of the cumyloxyl radical (CumO•) with N-Boc-protected amino acids in the presence of the strong organic base DBU has been carried out. CO2H deprotonation increases the electron density at the α-C-H bonds activating these bonds toward HAT to the electrophilic CumO• strongly influencing the intramolecular selectivity. The implications of these results are discussed in the framework of HAT-based aliphatic C-H bond functionalization of amino acids and peptides.

Asymptomatic carotid lesions and aging: Role of hypertension and other traditional and emerging risk factors.

BACKGROUND: We evaluated the prevalence of intima-media thickening (IMT) and asymptomatic carotid plaque (ACP) in a group of subjects with or without traditional and/or emerging risk factors (RF). METHODS: There were 631 subjects (313 male and 318 female) aged between 19 and 97 years, asymptomatic for cerebro- and cardiovascular diseases. The following measurements were used: anamnesis, physical examination, height and sitting blood pressure. Biochemistry variables were also considered: total cholesterol, HDL-C, LDL-C, triglycerides, fibrinogen, high sensitive C-reactive protein, IgG antibodies for Helicobacter pylori (HP), cytotoxic HP, cytomegalovirus and Chlamydia pneumoniae. Finally, an echo color Doppler examination of the carotid arteries was performed. We subdivided the population studied in normotensive and hypertensive subjects and evaluated in each group the frequency of IMT and ACP in relation to age. RESULTS: We showed that IMT + ACP was significantly more frequent in patients >65 years in comparison with those <65 years (80.6 vs. 52.1%, p < 0.005) and in hypertensive patients in comparison to normotensive, independent of coexistence of other cardiovascular risk factors (71 vs. 48%, p < 0.005). Another interesting result of our study is a significant presence of IMT and ACP in subjects with emerging but without traditional RF than in subjects with traditional but without emerging RF. CONCLUSIONS: IMT and ACP of carotid arteries are significantly more frequent in patients >65 years vs. those <65 years and in hypertensive patients in comparison to controls. Finally, we have found that the seropositivity of infection and the presence of higher levels of marker of inflammation were correlated with carotid lesion.

Neurocognitive functioning in subjects with eating disorders: the influence of neuroactive steroids.

BACKGROUND: Neuropsychological studies in subjects with eating disorders (EDs) have reported conflicting findings, which might be accounted for by several confounding variables, including neuroendocrine changes. METHODS: General abilities, executive functions, attention, and noneffortful learning were assessed in 45 patients with EDs and 45 healthy comparison subjects (HCS). Plasma levels of 17beta-estradiol, cortisol, allopregnanolone, dehydroepiandrosterone and its sulfate metabolite (DHEA and DHEAS) were evaluated in a subsample of patients and HCS. The influence of clinical, demographic, and neuroendocrine variables on neurocognitive performance was explored. RESULTS: Patients were slower than HCS on noneffortful learning and more accurate on a spatial executive task. DHEA and DHEAS were increased and positively correlated with accuracy on the executive task, while cortisol positively correlated with speed of noneffortful learning. CONCLUSIONS: A subtle impairment of noneffortful learning is the only neuropsychological deficit in patients with EDs. Changes in neuroactive steroids influence neurocognitive performance.