The potential of oligonucleotides for therapeutic applications

DeNAno: Selectable deoxyribonucleic acid nanoparticle libraries

DNA nanoparticles of approximately 250 nm were produced by rolling circle replication of circular oligonucleotide templates which results in highly condensed DNA particulates presenting concatemeric sequence repeats. Using templates containing randomized sequences, high diversity libraries of particles were produced. A biopanning method that iteratively screens for binding and uses PCR to recover selected particles was developed. The initial application of this technique was the selection of particles that bound to human dendritic cells (DCs). Following nine rounds of selection the population of particles was enriched for particles that bound DCs, and individual binding clones were isolated and confirmed by flow cytometry and microscopy. This process, which we have termed DeNAno, represents a novel library technology akin to aptamer and phage display, but unique in that the selected moiety is a multivalent nanoparticle whose activity is intrinsic to its sequence. Cell targeted DNA nanoparticles may have applications in cell imaging, cell sorting, and cancer therapy.

[Synthesis of 3'-deoxy-3'-carboxymethylnucleosides, precursors of oligonucleotides with an amide internucleoside bond]

An improved method for the synthesis of 3-deoxy-3-carboxymethylnucleosides was suggested. Oxidation of 5-O-benzoyl-l,2-O-isopropylidene-alpha-D-xylofuranose resulted in the 3-keto derivative, which was treated with triethylphosphonoacetate in the presence of sodium hydride to obtain the 3-deoxy-3-ethoxycarbonylmethylene derivative. Hydrogenation of the unsaturated compound proceeded strictly stereospecifically and gave the product with the ribo configuration. Acetolysis of the resulting compound with AcOH-Ac2O-CH3SO3H led to 1,2-di-O-acetyl-5-O-benzoyl-3-deoxy-3-ethoxycarbonylmethyl-D-ribofuranose, whose interaction with persilylated nucleic bases gave 3-deoxy-3-ethoxycarbonylmethylnucleosides in a total yield of 42-49% from the starting compound.

DNA-binding drugs caught in action: the latest 3D pictures of drug-DNA complexes

In this paper, we review recent DNA-binding agents that are expected to influence the field of DNA-targeting. We restrict ourselves to binders for which the three-dimensional structure in complex with DNA or RNA has been determined by X-ray crystallography or NMR. Furthermore, we primarily focus on unprecedented ways of targeting peculiar DNA structures, such as junctions, quadruplexes, and duplex DNAs different from the B-form. Classical binding modes of small molecular weight compounds to DNA, i.e. groove binding, intercalation and covalent addition are discussed in those cases where the structures represent a novelty. In addition, we review 3D structures of triple-stranded DNA, of the so-called Peptide Nucleic Acids (PNAs), which are oligonucleotide bases linked by a polypeptide backbone, and of aptamers, which are DNA or RNA receptors that are designed combinatorially. A discussion on perspectives in the field of DNA-targeting and on sequence recognition is also provided.

Evidences for complex formation between L-dabPNA and aegPNA

Continuing our research on the development of nucleopeptides as ODN analogs for biomedical and bioengineering applications, here we report the synthesis and the chemical-physical characterization of a homoadenine hexamer based on a l-diaminobutyric acid (l-DABA) backbone (dabPNA), and its binding studies with a complementary aegPNA. We demonstrated by CD and UV experiments that the l-dabPNA binds the aegPNA forming a complex with good thermal stability, that we identified as a left-handed triplex.

In vitro selection and characterization of cellulose-binding RNA aptamers using isothermal amplification

We sought to create new cellulose-binding RNA aptamers for use as modular components in the engineering of complex functional nucleic acids. We designed our in vitro selection strategy to incorporate self-sustained sequence replication (3SR), which is an isothermal nucleic acid amplification protocol that allows for the rapid amplification of RNAs with little manipulation. The best performing aptamer representative was chosen for reselection and further optimization. The aptamer exhibits robust binding of cellulose in both the powdered and paper form, but did not show any significant binding of closely related polysaccharides. The minimal cellulose-binding RNA aptamer also can be grafted onto other RNAs to permit the isolation of RNAs from complex biochemical mixtures via cellulose affinity chromatography. This was demonstrated by fusing the aptamer to a glmS ribozyme sequence, and selectively eluting ribozyme cleavage products from cellulose using glucosamine 6-phosphate to activate glmS ribozyme function.

CELL-SELEX: Novel perspectives of aptamer-based therapeutics

Aptamers, single stranded DNA or RNA molecules, generated by a method called SELEX (systematic evolution of ligands by exponential enrichment) have been widely used in various biomedical applications. The newly developed Cell-SELEX (cell based-SELEX) targeting whole living cells has raised great expectations for cancer biology, -therapy and regenerative medicine. Combining nanobiotechnology with aptamers, this technology opens the way to more sophisticated applications in molecular diagnosis. This paper gives a review of recent developments in SELEX technologies and new applications of aptamers.

Identification of differentially expressed genes in human lymphoblastoid cells exposed to irradiation and suppression of radiation-induced apoptosis with antisense oligonucleotides against caspase-4

To identify candidate genes in response to ionizing radiation (IR) and discover new targets for basic research and radiation protection, whole human genome bioarrays were used to examine gene expression profiles in human lymphoblastoid AHH-1 cells exposed to IR. The results were confirmed by semiquantitative reverse transcription-polymerase chain reaction (RT-PCR). In addition, the effects of ionizing radiation on cell growth, cell cycles and apoptosis were also examined. The microarray analysis revealed a set of IR responsive genes, including 906 genes at 4 hours and 789 genes at 24 hours after exposure to 5 Gy IR. The processes of cell cycles, apoptosis, signal transduction, and DNA repair involved a high percentage of IR responsive genes, among which, caspase-4 was most strongly induced by irradiation. Consistent with this, downregulation of caspase-4 expression by antisense oligonucleotides significantly increased cell viability and protected cells from undergoing apoptosis induced by IR. Taken together, the results suggested that caspase-4 plays an important role in radiation-induced apoptosis.

Potential Use of Gene Transfer in Athletic Performance Enhancement

After only a short history of three decades from concept to practice, gene therapy has recently been shown to have potential to treat serious human diseases. Despite this success, gene therapy remains in the realm of experimental medicine, and much additional preclinical and clinical study will be necessary for proving the efficacy and safety of this approach in the treatment of diseases in humans. However, a potential complicating factor is that advances in gene transfer technology could be misused to enhance athletic performance in sports, in a practice termed "gene doping". Moreover, gene doping could be a precursor to a broader controversial agenda of human "genetic enhancement" with the potential for a significant long-term impact on society. This review addresses the possible ways in which knowledge and experience gained in gene therapy in animals and humans may be abused for enhancing sporting prowess. We provide an overview of recent progress in gene therapy, with potential application to gene doping and with the major focus on candidate performance-enhancement genes. We also discuss the current status of preclinical studies and of clinical trials that use these genes for therapeutic purposes. Current knowledge about the association between the natural "genetic make-up" of humans and their physical characteristics and performance potential is also presented. We address issues associated with the safety of gene transfer technologies in humans, especially when used outside a strictly controlled clinical setting, and the obstacles to translating gene transfer strategies from animal studies to humans. We also address the need for development and implementation of measures to prevent abuse of gene transfer technologies, and to pursue research on strategies for its detection in order to discourage this malpractice among athletes.

Gene conversion: mechanisms, evolution and human disease

Gene conversion, one of the two mechanisms of homologous recombination, involves the unidirectional transfer of genetic material from a 'donor' sequence to a highly homologous 'acceptor'. Considerable progress has been made in understanding the molecular mechanisms that underlie gene conversion, its formative role in human genome evolution and its implications for human inherited disease. Here we assess current thinking about how gene conversion occurs, explore the key part it has played in fashioning extant human genes, and carry out a meta-analysis of gene-conversion events that are known to have caused human genetic disease.

Enzymatic manipulations of DNA oligonucleotides on microgel: towards development of DNA-microgel bioassays

We demonstrate that DNA oligonucleotides covalently coupled to colloidal microgel can be manipulated by T4 DNA ligase for DNA ligation and by Phi29 DNA polymerase for rolling circle amplification (RCA). We also show that the long single-stranded RCA product can generate intensive fluorescence upon hybridization with complementary fluorescent DNA probe. We believe DNA-microgel conjugates can be explored for the development of DNA based bioassays and biosensors.

Current Status of Cardiovascular Gene Therapy

Gene transfer for the therapeutic modulation of cardiovascular diseases is an expanding area of gene therapy. During the last decade several approaches have been designed for the treatment of hyperlipidemias, post-angioplasty restenosis, hypertension, and heart failure, and for protection of vascular by-pass grafts and promotion of therapeutic angiogenesis. Adenoviruses (Ads) and adeno-associated viruses (AAVs) are currently the most efficient vectors for delivering therapeutic genes into the cardiovascular system. Gene transfer using local gene delivery techniques have been shown to be superior to less-targeted intra-arterial or intra-venous applications. To date, no gene therapy drugs have been approved for clinical use in cardiovascular applications. In preclinical studies of therapeutic angiogenesis, various growth factors such as vascular endothelial growth factors (VEGFs) and fibroblast growth factors (FGFs), have shown positive results. Gene therapy also appears to have potential clinical applications in improving the patency of vascular grafts and in treating heart failure. Post-angioplasty restenosis, hypertension, and hyperlipidemias (excluding homozygotic familial hypercholesterolemia) can usually be managed satisfactorily by conventional approaches, and are therefore less favored areas for gene therapy. The development of technologies that can ensure long-term, targeted, and regulated gene transfer, and a careful selection of target patient populations, will be very important for the progress of cardiovascular gene therapy in clinical applications.

Specificity protein 1 and Smad-dependent regulation of human heme oxygenase-1 gene by transforming growth factor-beta1 in renal epithelial cells

Excess transforming growth factor-beta1 (TGF-beta1) in the kidney leads to increased cell proliferation and deposition of extracellular matrix, resulting in progressive kidney fibrosis. TGF-beta1, however, stabilizes and attenuates tissue injury through the activation of cytoprotective proteins, including heme oxygenase-1 (HO-1). HO-1 catabolizes pro-oxidant heme into substances with anti-oxidant, anti-apoptotic, anti-fibrogenic, vasodilatory and immune modulatory properties. Little is known regarding the molecular regulation of human HO-1 induction by TGF-beta1 except that it is dependent on de novo RNA synthesis and requires a group of structurally related proteins called Smads. It is not known whether other DNA binding proteins are required to initiate transcription of HO-1 and, furthermore, the promoter region(s) involved in TGF-beta1-mediated induction of HO-1 has not been identified. The purpose of this study was to further delineate the molecular regulation of HO-1 by TGF-beta1 in human renal proximal tubular cells. Actinomycin D and nuclear run-on studies demonstrate that TGF-beta1 augments HO-1 expression by increased gene transcription and does not involve increased mRNA stability. Using transient transfection, mithramycin A, small interfering RNA, electrophoretic mobility shift assays, and decoy oligonucleotide experiments, a TGF-beta1-responsive region is identified between 9.1 and 9.4 kb of the human HO-1 promoter. This approximately 280-bp TGF-beta1-responsive region contains a putative Smad binding element and specificity protein 1 binding sites, both of which are required for human HO-1 induction by TGF-beta1.

Synthetic RNA circuits

Natural and engineered RNA 'parts' can perform a variety of functions, including hybridizing to targets, binding ligands and undergoing programmed conformational changes, and catalyzing reactions. These RNA parts can in turn be assembled into synthetic genetic circuits that regulate gene expression by acting either in cis or in trans on mRNAs. As more parts are discovered and engineered, it should be increasingly possible to create synthetic RNA circuits that are able to carry out complex logical operations in cells, either superimposed on or autonomous to extant gene regulation.