David Margulies

Digital Analysis of Protein Properties by an Ensemble of DNA Quadruplexes

Here we show how different principles developed in the area of molecular logic gates can be applied to diagnostic technologies for proteins. Simultaneous operation of YES NOT and PASS 1 logic gates, produced by a protein sensing ensemble of DNA G-quadruplexes, is used to encode concentration levels of medicinally important proteins. An AND logic gate is another example, where molecular computation can be used to follow the interaction between proteins and metal ions. Combination of molecular Boolean logic with combinatorial sensing is demonstrated as a general strategy to realizing small scale, real time diagnosis of a variety of protein samples.

Protein Recognition by an Ensemble of Fluorescent DNA G‐Quadruplexes

Sniffing out proteins: Fluorescent DNA G-quadruplexes have been used for building versatile signaling receptors for proteins in a single solution. Introducing a protein sample to the ensemble results in a unique emission signature for unambiguous identification (see scheme, R = fluorophore). The self-assembled, pattern-based protein detection systems are easily fabricated, have the potential for high-throughput operations, and have the ability to handle small protein samples.

Medication Detection by a Combinatorial Fluorescent Molecular Sensor

Working together to uncover the truth: A molecule-sized diagnostic system combining several recognition elements and four fluorescence-emission channels enabled the identification of a wide range of pharmaceuticals on the basis of distinct photophysical processes. The molecular sensor (see simplified representation; ID = identification) was also used to analyze drug concentrations and combinations in urine samples in a high-throughput manner.

Combinatorial protein recognition as an alternative approach to antibody-mimetics.

Current approaches to medical diagnostics and drug design are largely based on the ability of monoclonal antibodies or synthetic molecules to bind proteins with high affinity and selectivity. In recent years, however, an alternative approach to protein recognition has emerged, in which proteins are identified using non-specific receptor arrays that are inspired by the olfactory neural system. An ultimate challenge for such systems is realizing a single, high-throughput analytical device that can effectively diagnose a range of medicinally relevant proteins. Such devices might overcome the difficulties associated with designing potent synthetic receptors for proteins and hence, could open up new possibilities in medical diagnostics, pathogen detection, and proteomics. Here we summarize recent developments in this area and also highlight its limitations and the challenges that this exciting interdisciplinary field faces. In particular, the goal of this review is to underscore the basic parameters required for obtaining combinatorial sensors for proteins and more importantly, to elucidate the rational methodologies that can be applied for systematically improving these promising analytical devices.

Message in a molecule

Since ancient times, steganography, the art of concealing information, has largely relied on secret inks as a tool for hiding messages. However, as the methods for detecting these inks improved, the use of simple and accessible chemicals as a means to secure communication was practically abolished. Here, we describe a method that enables one to conceal multiple different messages within the emission spectra of a unimolecular fluorescent sensor. Similar to secret inks, this molecular-scale messaging sensor (m-SMS) can be hidden on regular paper and the messages can be encoded or decoded within seconds using common chemicals, including commercial ingredients that can be obtained in grocery stores or pharmacies. Unlike with invisible inks, however, uncovering these messages by an unauthorized user is almost impossible because they are protected by three different defence mechanisms: steganography, cryptography and by entering a password, which are used to hide, encrypt or prevent access to the information, respectively.

Surface Binding Inhibitors of the SCF–KIT Protein–Protein Interaction

KIT is a receptor tyrosine kinase (RTK), the interaction of which with its ligand, stem cell factor (SCF), is essential for growth and differentiation of various cells.[1] SCF binding promotes KIT dimerization,[2] transphosphorylation, and activation of downstream cell signaling pathways essential for cell proliferation, differentiation, and survival. Gain-of-function mutations in KIT have been identified in human cancers such as gastrointestinal stromal tumors (GIST).[3,4] It was also demonstrated that autocrine or paracrine mechanisms mediated by aberrant expression of SCF and/or KIT might also lead to oncogenesis.[5–7] Because most cases of GIST are driven by oncogenic KIT mutations resulting in enhanced tyrosine kinase activity, inhibitors of the tyrosine kinase[8] activity of KIT, such as Gleevec® (imatinib mesylate) and Sutent® (sunitinib), have been successfully applied for the treatment of GIST patients.

Enzyme−Artificial Enzyme Interactions as a Means for Discriminating among Structurally Similar Isozymes

We describe the design and function of an artificial enzyme-linked receptor (ELR) that can bind different members of the glutathione-S-transferase (GST) enzyme family. The artificial enzyme-enzyme interactions distinctly affect the catalytic activity of the natural enzymes, the biomimetic, or both, enabling the system to discriminate among structurally similar GST isozymes.

Analyzing Amyloid Beta Aggregates with a Combinatorial Fluorescent Molecular Sensor

Different amyloid beta (Aβ) aggregates can be discriminated by a combinatorial fluorescent molecular sensor. The unique optical fingerprints generated by the unimolecular analytical device provide a simple means to differentiate among aggregates generated from different alloforms or through distinct pathways. The sensor has also been used to track dynamic changes that occur in Aβ aggregation states, which result from the formation of low molecular weight oligomers, high molecular weight oligomers, protofibrils, and fibrils.

User Authorization at the Molecular Scale

Electronic user authorization systems help us maintain our privacy in many aspects of everyday life. However, the increasing difficulty to secure access and/or information digitally has inspired chemists to devise alternative, molecular approaches, in which users are identified by chemical means. The potential advantages of using molecular user authentication systems over conventional electronic devices are their versatility and unusual operating principles, which complicate replicating and, consequently, breaking into molecular security devices. Their molecular scale is another unique property that enables hiding such systems and, consequently, applying steganography as an additional layer of protection. Although the area of molecular-based user authorization is still in its infancy, the development of various molecular keypad locks and, more recently, a password-protected molecular cryptographic machine, indicate the possibility of protecting information at the molecular scale.

Sensing Protein Surfaces with Targeted Fluorescent Receptors.

A methodology for creating fluorescent molecular sensors that respond to changes that occur on the surfaces of specific proteins is presented. This approach, which relies on binding cooperatively between a specific His-tag binder and a nonspecific protein-surface receptor, enabled the development of a sensor that can track changes on the surface of a His-tag-labeled calmodulin (His-CaM) upon interacting with metal ions, small molecules, and protein binding partners. The way this approach was used to detect dephosphorylation of an unlabeled calmodulin-dependent protein kinase II (CaMKII), and the binding of Bax BH3 to His-tagged B-cell lymphoma 2 (Bcl-2) protein is also presented.