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In Vitro Selected RNA-Cleaving DNA Enzymes From Combinatorial Libraries

The selective inactivation of a target gene by antisense mechanisms is an important biological tool in the delineation of gene functions. Ribozymes and RNA-cleaving DNA enzymes-mediated approaches are more attractive because of their ability to catalytically cleave the target RNA. ...

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Ribozyme- and siRNA-Mediated mRNA Degradation: A General Introduction

A number of recent discoveries in the RNA field have opened up a wealth of opportunities to specifically target mRNA for the development of therapeutics and/or the elucidation of gene function. Novel agents such as ribozymes, DNAzymes, and siRNAs are emerging as effective strategies that are a ...

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An Experimental Method for Selecting Effective Target Sites and Designing Hairpin Ribozymes

The proper selection of target sites and the correct design of specific ribozymes are decisive initial steps in any attempt to perform ribozyme-mediated gene silencing. Combinatorial methodologies can be used to improve ribozyme targeting and design. The in vitro selection strategy ...

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Crystallization of the Hairpin Ribozyme: Illustrative Protocols

Conditions and techniques that result in successful crystallization differ from RNA to RNA. However, there are some general principles that facilitate crystallization of most RNAs. Three procedures that were instrumental in obtaining well-ordered crystals of the hairpin riboz ...

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Design and Optimization of Sequence-Specific Hairpin Ribozymes

The hairpin ribozyme belongs to a group of small catalytic RNAs that have been extensively used to trans-cleave RNA molecules. Many efforts have been made to elucidate its reaction mechanism, and there is great interest in designing hairpin ribozymes with improved catalytic activity for u ...

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Design, Targeting, and Initial Screening of sTRSV-Derived Hairpin Ribozymes for Optimum Helix 1 Length and Catalytic Efficiency In Vitro

Hairpin ribozymes derived from the negative strand of satellite RNAs from the tobacco ringspot virus (sTRSV) can be engineered to target and cleave a variety of heterologous RNAs from both cellular and viral transcripts. Attention to design and targeting rules and optimization of helix 1 le ...

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Repair of Myotonic Dystrophy Protein Kinase (DMPK) Transcripts by Trans-Splicing Ribozymes

The Tetrahymena group I intron ribozyme is an RNA molecule of approx 400 bases that is capable of base-specific RNA trans-splicing. These properties can be applied to repair mutations at the RNA level, and therefore can restore normal cellular functions in diseased cells. The purpose of this cha ...

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Optimization and Application of the Group I Ribozyme Trans-Splicing Reaction

Group I ribozymes are naturally occurring catalytic RNAs that are able to excise themselves as introns (group I introns) from a precursor RNA, and to ligate the flanking exons. Group I ribozymes can be engineered to act in trans by recognizing a separate RNA molecule in a sequence specific manner, and to ...

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General Design and Construction of RNase P Ribozymes for Gene-Targeting Applications

RNase P ribozyme, such as M1 RNA, the catalytic RNA subunit of RNase P from Escherichia coli, cleaves an RNA helix that resembles the acceptor stem and T-stem structure of its natural ptRNA substrate. When covalently linked with a guide sequence, the M1 ribozyme can function as a sequence-specific en ...

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Preparation and Use of Tethered Ligands as Biomaterials and Tools for Cell Biology

The immobilization of biomolecules to various supports has been an important research area for many years. Molecules such as heparin (1,2), as well as various enzymes (3,4), antibodies (5,6), and adhesion ligands (7), have been bound to such supports as silicon or glass, agarose gels, polyethylene ...

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Fabrication of Biodegradable Polymer Foams for Cell Transplantation and Tissue Engineering

Organ transplantation has been successful since the early 1960s as a result of the success in immunologic suppression in the clinical setting (1), and has saved, and is continuing to save, countless lives, but is far from a perfect solution to tissue losses or organ failures. By far the most serious prob ...

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Nondestructive Evaluation of Biodegradable Porous Matrices for Tissue Engineering

Significant advances in transplantation therapy for end stage organ failure or tissue repair have led to a shortage of donor organs and reconstructive tissue. Alternatives to remedy this deficiency are being investigated. In particular, the engineering of tissue using natural or syn ...

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Formation of Highly Porous Polymeric Foams with Controlled Release Capability: A Phase-Separation Technique

The success of many tissue engineering applications depends on a scaffold with the suitable physical properties, one of which might be a macroporous structure that allows cellular ingrowth. Such a porous implant further raises the possibility of delivering chemotactic or growth fact ...

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Magnetic-Induced Alignment of Collagen Fibrils in Tissue Equivalents

The use of reconstituted type I collagen gel as a scaffold for engineered soft tissues is a highly attractive prospect, given that collagen is the principal component of the extracellular matrix (ECM) in vivo, providing a mechanically suitable and information-rich scaffold for cell-ECM i ...

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Preparation and Use of Thermosensitive Polymers

Restoration of organ structure and function, utilizing tissue engineering technologies, often requires the use of a temporary porous scaffold. The function of the scaffold is to direct the growth of cells migrating from the surrounding tissue (tissue conduction), or of cells seeded wit ...

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In Situ Photopolymerized Hydrogels for Vascular and Peritoneal Wound Healing

The process of wound healing in internal organs lined with mesothelial cells is different in some respects from healing in cutaneous injuries. Hertzler (1) noted that cutaneous wound re-epithelialization takes place from the wound borders, but peritoneal defects become re-mesothe ...

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Quantitative Assessment of Autocrine Cell Loops

Regeneration of functioning tissue essentially involves recapitulating relevant aspects of organogenesis, so that the starting composite of cells, matrix, and molecular factors develops into the desired structure and physiology. A crucial aspect of development is local cell ...

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Fabrication and Implantation of Gel-Filled Nerve Guidance Channels

In human adults, the peripheral nervous system (PNS) is capable of healing and regeneration. In order to reestablish function, nerve tissue must heal by true regeneration of a functional structure, since healing by simple scar will not reestablish electrical connectivity. Nerve guidan ...

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Isolation and In Vitro Proliferation of Chondrocytes, Tenocytes, and Ligament Cells

In recent years it has become possible to grow large numbers of selected cell types in vitro from relatively small tissue samples. This capability has served as the foundation for using autogenous, as well as allogeneic, cells expanded in culture for engineering tissues that display little po ...

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Preparation of Immortalized Human Chondrocyte Cell Lines

The chondrocyte is responsible for synthesis of cartilage matrix proteins, and, thereby, the specialized mechanical properties of articular cartilage, including tensile strength and resistence to mechanical loading (1). The limited repair response by chondrocytes accounts ...

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