Rapid improvements in sequencing and array-based platforms are resulting in a flood of diverse genome-wide data, including data from exome and whole-genome sequencing, epigenetic surveys, expression profiling of coding and noncoding RNAs, single nucleotide polymorphism (SNP) and copy number profiling, and functional assays. Analysis of these large, diverse data sets holds the promise of a more comprehensive understanding of the genome and its relation to human disease. Experienced and knowledgeable human review is an essential component of this process, complementing computational approaches. This calls for efficient and intuitive visualization tools able to scale to very large data sets and to flexibly integrate multiple data types, including clinical data. However, the sheer volume and scope of data pose a significant challenge to the development of such tools.

Integrative Genomics Viewer

This review describes a multidimensional treatment of molecular recognition phenomena involving aromatic rings in chemical and biological systems. It summarizes new results reported since the appearance of an earlier review in 2003 in host-guest chemistry, biological affinity assays and biostructural analysis, data base mining in the Cambridge Structural Database (CSD) and the Protein Data Bank (PDB), and advanced computational studies. Topics addressed are arene-arene, perfluoroarene-arene, S⋅⋅⋅aromatic, cation-π, and anion-π interactions, as well as hydrogen bonding to π systems. The generated knowledge benefits, in particular, structure-based hit-to-lead development and lead optimization both in the pharmaceutical and in the crop protection industry. It equally facilitates the development of new advanced materials and supramolecular systems, and should inspire further utilization of interactions with aromatic rings to control the stereochemical outcome of synthetic transformations.

Aromatic rings in chemical and biological recognition: energetics and structures.

MODOMICS is a database of RNA modifications that provides comprehensive information concerning the chemical structures of modified ribonucleosides, their biosynthetic pathways, RNA-modifying enzymes and location of modified residues in RNA sequences. In the current database version, accessible at http://modomics.genesilico.pl, we included new features: a census of human and yeast snoRNAs involved in RNA-guided RNA modification, a new section covering the 5′-end capping process, and a catalogue of ‘building blocks’ for chemical synthesis of a large variety of modified nucleosides. The MODOMICS collections of RNA modifications, RNA-modifying enzymes and modified RNAs have been also updated. A number of newly identified modified ribonucleosides and more than one hundred functionally and structurally characterized proteins from various organisms have been added. In the RNA sequences section, snRNAs and snoRNAs with experimentally mapped modified nucleosides have been added and the current collection of rRNA and tRNA sequences has been substantially enlarged. To facilitate literature searches, each record in MODOMICS has been cross-referenced to other databases and to selected key publications. New options for database searching and querying have been implemented, including a BLAST search of protein sequences and a PARALIGN search of the collected nucleic acid sequences.

MODOMICS: a database of RNA modification pathways—2013 update

Cation-π interaction: its role and relevance in chemistry, biology, and material science.

Biogenic calcium carbonate forms the inorganic component of seashells, otoliths, and many marine skeletons, and its formation is directed by an ordered template of macromolecules. Classical nucleation theory considers crystal formation to occur from a critical nucleus formed by the assembly of ions from solution. Using cryotransmission electron microscopy, we found that template-directed calcium carbonate formation starts with the formation of prenucleation clusters. Their aggregation leads to the nucleation of amorphous nanoparticles in solution. These nanoparticles assemble at the template and, after reaching a critical size, develop dynamic crystalline domains, one of which is selectively stabilized by the template. Our findings have implications for template-directed mineral formation in biological as well as in synthetic systems.

The initial stages of template-controlled CaCO3 formation revealed by Cryo-TEM

Protein-based molecular recognition tools for detecting and profiling RNA modifications

Erratum: Total synthesis of (S)-equol (Organic Letters (2006) 8, (5443))

Small molecule contaminants pose a significant threat to the environment and human health. While regulations are in place for allowed limits in many countries, detection and remediation of contaminants in more resource-limited settings and everyday environmental sources remains a challenge. Functional nucleic acids, including aptamers and DNA enzymes, have emerged as powerful options for addressing this challenge due to their ability to non-covalently interact with small molecule targets. The goal of this perspective is to outline recent efforts toward the selection of aptamers for small molecules and describe their subsequent implementation for environmental applications. Finally, we provide an outlook that addresses barriers that hinder these technologies from being widely adopted in field friendly settings and propose a path forward toward addressing these challenges.

/pdf/combating-small-molecule-environmental-contaminants-35qffn4w.pdf

Combating small molecule environmental contaminants: detection and sequestration using functional nucleic acids

Adenosine-to-inosine (A-to-I) editing is a conserved RNA modification that contributes to immune response and overall cellular function. RNA editing patterns can vary significantly between different cell and tissue types, and hyperactive A-to-I signatures are indicative of several diseases, including cancer and autoimmune disorders. Because of the importance of these differences, there is significant need for efficient methods to measure overall A-to-I editing levels in cellular RNA. The current standard approach relies on RNA-seq to indirectly detect editing sites, which requires large investments in time and material as well as extensive computational analysis. Here, we utilize Endonuclease V (EndoV), which binds to inosine in RNA, to develop a protein-based chemiluminescent bioassay to directly profile A-to-I editing activity. We previously showed that EndoV can enrich edited transcripts prior to RNA-seq, and we now leverage this activity to construct an EndoV-linked immunosorbency assay (EndoVLISA) as a rapid chemiluminescent method for measuring global A-to-I editing signatures in cellular RNA. We first optimize and validate our assay, illustrating highly selective and sensitive detection of inosine in RNA. We then demonstrate rapid detection of inosine content in treated cell lines, demonstrating equivalent performance against current standard RNA-seq approaches. Lastly, we deploy our EndoVLISA for profiling differential A-to-I RNA editing signatures in normal and diseased human tissue, illustrating the utility of our platform as a diagnostic bioassay. Together, the EndoVLISA method is cost-effective, straightforward, and utilizes common laboratory equipment, offering a highly accessible new approach for studying A-to-I editing. Moreover, the multi-well plate format makes this the first assay amenable for direct high-throughput quantification of A-to-I editing for applications in disease detection and drug development.

Direct Immunodetection of Global A‐to‐I RNA Editing Activity with a Chemiluminescent Bioassay

The first enantioselective total synthesis of (S)-equol is reported. The described route relies on an Evans alkylation to form the stereocenter and an intramolecular Buchwald etherification to generate the chroman ring. Key features of this method include its brevity, its scalability, and the low cost of starting materials. [reaction: see text].

Jennifer M. Heemstra

Papers

Protein-based molecular recognition tools for detecting and profiling RNA modifications

Erratum: Total synthesis of (S)-equol (Organic Letters (2006) 8, (5443))

Combating small molecule environmental contaminants: detection and sequestration using functional nucleic acids

Direct Immunodetection of Global A‐to‐I RNA Editing Activity with a Chemiluminescent Bioassay

Total Synthesis of (S)-Equol.