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Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure.
A dynamic programming algorithm for prediction of RNA secondary structure has been revised to accommodate folding constraints determined by chemical modification and to include free energy incrementsExpand
Promoter-Bound Trinucleotide Repeat mRNA Drives Epigenetic Silencing in Fragile X Syndrome
The data link trinucleotide-repeat expansion to a form of RNA-directed gene silencing mediated by direct interactions of the trin nucleotide- Repeat RNA and DNA to fragile X syndrome. Expand
Sequestration of DROSHA and DGCR8 by expanded CGG RNA repeats alters microRNA processing in fragile X-associated tremor/ataxia syndrome.
It is identified that the double-stranded RNA-binding protein DGCR8 binds to expanded CGG repeats, resulting in the partial sequestration of DG CR8 and its partner, DROSHA, within CGG RNA aggregates, which supports a model in which a human neurodegenerative disease originates from the alteration, in trans, of the miRNA-processing machinery. Expand
Discovery of a Biomarker and Lead Small Molecules to Target r(GGGGCC)-Associated Defects in c9FTD/ALS
It is suggested that c9RAN proteins could potentially serve as a pharmacodynamic biomarker to assess efficacy of therapies that target r(GGGGCC)exp and poly(GP) c9 RAN proteins are specifically detected in c9ALS patient cerebrospinal fluid. Expand
The use of carbohydrate microarrays to study carbohydrate-cell interactions and to detect pathogens.
This system is ideal for whole-cell applications because microarrays present carbohydrate ligands in a manner that mimics interactions at cell-cell interfaces, which allows microarray-based screening of biological samples for contaminants and combinatorial libraries for antiadhesion therapeutics. Expand
A superfolding Spinach2 reveals the dynamic nature of trinucleotide repeat RNA
Using Spinach2, the dynamics of the CGG trinucleotide repeat–containing 'toxic RNA' associated with Fragile X–associated tremor/ataxia syndrome are detailed and show that these RNAs form nuclear foci with unexpected morphological plasticity that is regulated by the cell cycle and by small molecules. Expand
A mannan binding lectin is involved in cell–cell attachment in a toxic strain of Microcystis aeruginosa
This study provides the first experimental evidence that microcystins may have an impact on Microcystis colony formation that is highly important for the competitive advantage of MicroCystis over other phytoplankton species. Expand
Sequence-based design of bioactive small molecules that target precursor microRNAs
Inforna was applied to all human microRNA precursors and identified bioactive small molecules that inhibit biogenesis by binding to nuclease processing sites (41% hit rate) and shows that 1 only significantly effects microRNA-96 biogenesis and is more selective than an oligonucleotide. Expand
Inforna 2.0: A Platform for the Sequence-Based Design of Small Molecules Targeting Structured RNAs.
Inforna 2.0 is described, which incorporates all known RNA motif-small molecule binding partners reported in the scientific literature, a chemical similarity searching feature, and an improved user interface and is freely available via an online web server. Expand
A small molecule that targets r(CGG)(exp) and improves defects in fragile X-associated tremor ataxia syndrome.
A bioactive small molecule probe that targets expanded r(CGG) repeats, or r( CGG)(exp), that causes Fragile X-associated Tremor Ataxia Syndrome (FXTAS) is described and is efficacious in FXTAS model cellular systems as evidenced by its ability to improve FXTas-associated pre-mRNA splicing defects and to reduce the size and number of r (C GG)(exp)-containing nuclear foci. Expand