Jan Barciszewski

From Nucleic Acids Sequences to Molecular Medicine

Half a century ago, at the dawn of molecular biology, few investigators realized the potential of RNA in cellular regulation and function. After a very long lag phase, the quantitative and qualitative evidence for the significance of nonprotein-coding RNA (npcRNA) is now overwhelming. In the search for diseasecausing gene alterations, RNA genes must be considered equally with proteincoding genes.

DNA and RNA nanobiotechnologies in medicine : diagnosis and treatment of diseases

Introduction.- RNA Nanotechnology: methods for synthesis, conjugation, assembly and application of RNA nanoparticles.- Adsorption of double-stranded DNA to graphene oxide preventing enzymatic digestion.- Electrogenerated chemiluminescence of conjugated polymer films from patterned electrodes.- Use of RNA structure flexibility data in nanostructure modeling.- Informatic resources for identifying and annotating structural RNA motifs.- A nanostructure made of a bacterial noncoding RNA.- HAPIscreen, a method for high-throughput aptamer identification.- Characterization of photophysical and base-mimicking properties of a novel fluorescent adenine analogue in DNA.- Bifacial nucleoside as a surrogate for both T and A in duplex DNA.- Functionally important structural elements of U12 snRNA.- Self-assembling RNA nanorings based on RNAI/II inverse kissing complexes.- Automatic molecular weaving prototyped by using single-stranded DNA.- Nucleic Acid Aptamers: Clinical Applications and Promising New Horizons.- Nanotextured Substrates With Immobilized Aptamers for Cancer Cell Isolation and Cytology.- Targeting cancer with peptide aptamers.- Synthetic, biofunctional nucleic acid-based molecular devices.- Inducible site-selective bottom-up assembly of virus-derived nanotube arrays on RNA-equipped wafers.- Special delivery: targeted therapy with small RNAs, RNAi nanomedicines: challenges and opportunities within the immune system.- Pyrene-functionalized oligonucleotides and locked nucleic acids (LNAs): Tools for fundamental research, diagnostics, and nanotechnology.- Stabilizing RNA by the sonochemical formation of RNA nanospheres. Sonochemical synthesis of DNA nanospheres.- Nucleic acid based molecular devices.- Nanoparticle therapeutics: FDA approval, clinical trials, regulatory pathways, and case study.- A sol-gel-based microfluidics system enhances the efficiency of RNA aptamer selection.- Hierarchical nanotextured microelectrodes overcome the molecular transport barrier to achieve rapid, direct bacterial detection.- Recent developments in lipid-based pharmaceutical nanocarriers.- Targeted delivery of RNAi therapeutics for cancer therapy.- DNAsomes: Multifunctional DNA-based nanocarriers.- Reversible and Controllable Nanolocomotion of an RNA-Processing Machinery.- Scavenger receptors mediate cellular uptake of polyvalent oligonucleotide-functionalized gold nanoparticles.- A highly sensitive microRNA biosensor based on ruthenium oxide nanoparticle-initiated polymerization of aniline.- Preparation and high-resolution microscopy of gold cluster labeled nucleic acid conjugates and nanodevices.- Kinetically grafting G-quadruplexes onto DNA nanostructures for structure and function encoding via a DNA machine.- Synthesis of glycerol nucleic acid (GNA) phosphoramidite monomers and oligonucleotide polymers.- Cancer immunotherapy and nanomedicine.- RNA nanotechnology: inspired by DNA.- From nanotechnology to nanomedicine: applications to cancer research.- Comparative structural and functional studies of nanoparticle formulations for DNA and siRNA delivery.- Advances in novel drug delivery strategies for breast cancer therapy.- DNA origami: a history and current perspective.- Nanoparticles: a promising modality in the treatment of sarcomas.- Gold nanorod delivery of an ssRNA immune activator inhibits pandemic H1N1 influenza viral replication.- Recent developments in oligonucleotide conjugation.- In vivo delivery of small interfering RNA to tumors and their vasculature by novel dendritic nanocarriers.- DNA and carbon nanotubes as medicine.- LHRH-targeted nanoparticles for cancer therapeutics.- Nanoparticle-aptamer conjugates for cancer cell targeting and detection.- Evaluation of targets for ovarian cancer gene silencing therapy: in vitro and in vivo approaches.- Prediction and design of DNA and RNA structures.- siRNA applications in nanomedicine.

RNA technologies and their applications

The Key Features of RNA Silencing.- Selected Strategies for the Delivery of siRNA In Vitro and In Vivo.- RNAi Suppression and Its Application.- Strategies to Prevent siRNA-Triggered Cellular Toxicity.- RNAi in Malignant Brain Tumors: Relevance to Molecular and Translational Research.- Silencing Huntingtons Disease Gene with RNAi.- Application of Dicer-Substrate siRNA in Pain Research.- RNAi Treatment of HIV-1 Infection.- Application of RNA Interference to Treat Conditions Associated with Dysregulation of Transient Receptor Potential Vanilloid 1 Channel.- Harnessing RNAi-Based Functional Genomics to Unravel the Molecular Complexity Underlying Skin Pigment Variation.- mRNA Structure and its Effects on Posttranscriptional Gene Silencing.- Antisense RNA-Mediated Regulation of the p53 Tumor Suppressor.- Antisense Oligonucleotides: Insights from Preclinical Studies and Clinical Trials.- What can the New Hammerhead Ribozyme Structures Teach us About Design?.- microRNA Biogenesis and its Impact on RNA Interference.- MicroRNAs in Epithelial Antimicrobial Immunity.- Emerging Roles of Long Noncoding RNAs in Gene Expression and Intracellular Organization.- Noncoding RNAs as Therapeutic Targets.- Noncoding RNAs at H19/IGF2 Locus: Role in Imprinting, Gene Expression, and Associated Pathologies.

RNA Technologies for Mitochondrial Genetics

Mitochondria ensure fundamental functions in eukaryotic cells. They possess their own genetic system that provides a number of essential polypeptides of the oxidative phosphorylation chain. As a consequence, the respiratory complexes are built from both nuclear-encoded and organellar-encoded subunits. Mitochondrial biogenesis and response to the energetic or metabolic demands of the cell thus relies on elaborate regulation networks and continuous cross talk with the nucleus, as well as with plastids in plants. Main questions remain open regarding these control mechanisms and their relation with the complex transcriptional and posttranscriptional processes that take place in mitochondria. In particular, the field of organelle noncoding RNAs is growing and points to an involvement of mitochondria in cellular RNA interference. To gain further knowledge, manipulating the organelle genetic system is the obvious way to go, but mitochondrial transformation remains restricted to a couple of unicellular organisms. The scientific challenge is of wide relevance, as mutations or rearrangements in the mitochondrial genome cause incurable neurodegenerative diseases in human or lead to cytoplasmic male sterility in plants. RNA technologies may provide another path, as mitochondria naturally import several types of RNA, depending on the organism. Exploiting the natural mechanisms to target customized RNAs to or into mitochondria has begun. Considering their high specificity versus interfering RNAs, catalytic RNAs are of particular interest for such strategies. Major breakthrough has already been obtained in silencing mitochondrial RNAs through the import of trans-cleaving hammerhead ribozymes.