Progress in the Synthesis of Cyclic Deoxyribo- and Oligoribonucleotides

Abstract

The preparation of purine-rich sequences of cyclic DNA, up to a 28-mer, has been achieved. The products were purified by HPLC and PAGE (larger circles) and fully characterized. Cyclic RNA synthesis can be carried out using the same methodology as for cyclic DNA, provided that a single deoxynucleoside or a 2′-O-methylribonucleoside is placed at the 3′-end of the linear precursor.     

A New Approach to the Synthesis of a N-Acetyl-lincosamine Isomer

A novel synthesis of a N-acetyllincosamine isomer (8) was accomplished.     

Some Aspects of the Chemical Synthesis of Oligoribonucleotides

Abstract

The present position regarding the protection of the 2′- and 5′-hydroxy functions in the chemical synthesis of oligoribonucleotides is discussed.     

A New Approach to Oligonucleotide Synthesis in Solution

Abstract

A new approach, based on the use of 3′-H-phosphonate building blocks, is described for the synthesis of oligonucleotides and their phosphorothioate analogues in solution.

     

Stable Earliest Starting Schedules for Cyclic Job Shops: A Linear System Approach

We consider a cyclic job shop where an identical mixture of parts of different types, called a minimal part set (MPS), is produced repetitively in the same processing order. The precedence relationships among events (start of operation) are represented by a directed graph that has a recurrent structure. Each operation starts as soon as all its preceding operations are complete (called earliest starting). There is a class of desirable schedules that has the minimum cycle time and an identical schedule pattern for every MPS. By using linear system theory on minimax algebra, we characterize the set of all possible such schedules. We develop an efficient algorithm to find one among such schedules that minimizes a performance measure related to work-in-progress inventory. We also discuss an application to a flexible manufacturing system.     

Synthesis of Fused Oligoribonucleotides with Trideoxyribonucleotide Containing Phosphorothioate to Stabilize Against Nuclease Activity

Abstract

Fused oligonucleotides(21mer) consisting of RNA(18mer) and DNA(3mer) were synthesized by combined use of the phosphotriester and phosphoramidite methods. The RNA(18mer) corresponds to the leader sequence of phage fl coat protein mRNA containing initiation codon. The RNA was stabilized against 3′-exonucleases by joining with trideoxy-ribonucleotides containing phosphorothioate linkages and it would be applied to the studies on the initiation complex formation in prokaryotic translation.     

Improvements in the Synthesis of L-Ribonucleosides for the Preparation of Mirror-Image Oligoribonucleotides

Abstract

Different improvements are described for the chemical synthesis of L-ribonucleosides corresponding to the four natural bases. These nucleosides properly protected were used to synthesize successfully a 27-base long L-oligoribonucleotide.     

A New Cyclic Phosphoramidate D4T Prodrug Approach cycloAmb-D4T-Phosphoramidates

Abstract

A new potential phosphoramidate prodrug approach for d4T 1 is described. In hydrolyses studies the cycloAmb-d4T-phosphoramidates 2 and 3 proved to deliver d4TMP following a tandem reaction.     

Oligoribonucleotides with Functionalized Nucleobases as New Modifiers of Biopolymers

Abstract

Synthesis and evaluation of hybridization and modification abilities of the new types of photoactivatable oligoribonucleotide conjugates are presented.     

A Direct Approach to the Synthesis of Famciclovir and Penciclovir

Abstract

Reaction of 2-amino-6-chloropurine with triethyl 3-bromopropane-1,1,1-tricarboxylate followed by decarbethoxylation/transesterification of the unpurified product was the key sequence in synthesising both the anti-herpesvirus agent penciclovir and its oral from famciclovir in three isolated steps.     

Synthesis of the Oligoribonucleotides Incorporating 8-Oxo-Guanosine and Evaluation of their Base Pairing Properties

6-O-7-N-Bis(diphenylcarbamoyl)-2-N-phenoxyacetyl-5′-O-dimethoxytrityl-2′-O-{[(triisopropyl- silyl)oxy]methyl}-8-oxoguanosine-3′-yl-β-cyanoethyl-N,N-diisopropylphosphoramidite (5) was synt- hesized as a new phosphoramidite precursor unit for the synthesis of RNA. Compound 5 was successfully incorporated into the middle of the RNA sequences, and the synthesized RNAs were identified by MALDI-TOF mass measurements. Their properties were evaluated for formation of the RNA duplex and RNA/DNA heteroduplex. ORNs 1 and 4 containing 8-oxo-G can form base pairs with rC or dC in an anti conformation, while it can also interact with rA or dA in a syn conformation in the RNA duplex or RNA/DNA heteroduplex. The described synthetic method is therefore a useful procedure for the synthesis of ORN containing 8-oxo-G and contributes to the study of 8-oxo-G in RNA.     

Synthesis and Cell Adhesive Properties of Linear and Cyclic RGD Functionalized Polynorbornene Thin Films

Described herein is the efficient synthesis and evaluation of bioactive arginine-glycine-aspartic acid (RGD) functionalized polynorbornene-based materials for cell adhesion and spreading. Polynorbornenes containing either linear or cyclic RGD peptides were synthesized by ring-opening metathesis polymerization (ROMP) using the well-defined ruthenium initiator [(H(2)IMes)(pyr)(2)(Cl)(2)Ru═CHPh]. The random copolymerization of three separate norbornene monomers allowed for the incorporation of water-soluble polyethylene glycol (PEG) moieties, RGD cell recognition motifs, and primary amines for postpolymerization cross-linking. Following polymer synthesis, thin-film hydrogels were formed by cross-linking with bis(sulfosuccinimidyl) suberate (BS(3)), and the ability of these materials to support human umbilical vein endothelial cell (HUVEC) adhesion and spreading was evaluated and quantified. When compared to control polymers containing either no peptide or a scrambled RDG peptide, polymers with linear or cyclic RGD at varying concentrations displayed excellent cell adhesive properties in both serum-supplemented and serum-free media. Polymers with cyclic RGD side chains maintained cell adhesion and exhibited comparable integrin binding at a 100-fold lower concentration than those carrying linear RGD peptides. The precise control of monomer incorporation enabled by ROMP allows for quantification of the impact of RGD structure and concentration on cell adhesion and spreading. The results presented here will serve to guide future efforts for the design of RGD functionalized materials with applications in surgery, tissue engineering, and regenerative medicine.     

A Convenient Approach to the Synthesis of Azido-Acyclic Nucleosides

Abstract

The azidation of unprotected acyclic nucleosides (4) was carried out in a one-pot reaction by means of the reagent triphenylphosphine-carbon tetraiodide-sodium azide to give the corresponding mono-azido-acyclic nucleosides (6) in good yields without by-products such as the di-azido-acyclic nucleosides.     

Synthesis and Biological Action of a New Cyclic AMP Analogue

Abstract

A new cyclic AMP analogue, adenosine- 3′, 5′-cyclic methyl phosphonate (cAMP-Me) was chemically synthesized. This compound was not a substrate for phosphodiesterase, and it did not activate cAMP-dependent protein kinases (type I or type II). However, it inhibited cAMP phosphodiesterase and protein kinase at milimolar concentration levels. It also inhibited malignant cell proliferation in vitro.     

Large Scale Synthesis of Oligoribonucleotides on High-Loaded Polystyrene (HLP) Support

Abstract

Large quantities of oligoribonucleotides (up to 200 μmole) were synthesized on the high-loaded polystyrene (HLP) support with phosphoramidite nucleosides and 5-ethylthio-1H-tetrazole as activator. The HLP support significantly reduces solvent and reagent consumption. RNA synthesized on HLP support at large scale was shown to have full biological activity by a comparative ribozyme-substrate assay.     

A Solid-Phase Method for the Synthesis of Small to Medium-Sized Cyclic Oligonucleotides

Abstract

Cyclic oligonucleotides (2- to 30-mer) are synthesized by a solid-phase method, for both chain elongation and cyclization, employing a new linker and standard phosphoramidite chemistry. Fairly pure crude products (>90% by HPLC) are obtained.     

A Large Fragment Approach to Gene Synthesis

Abstract

The total synthesis of a 232 base-pair coding sequence of the proteinase inhibitor eglin c from only six synthetic fragments is described.     

A New Approach to Undergraduate Biology

The use of a common pathogenic vegetable soft-rot bacterium Erwinia carotovora is recommended for school student investigations. Suggestions are made about simple ways in which quantitative data can be collected, as well as some suitable investigations that could be carried out by school pupils at Key Stage 4(15–16 years old) or Advanced level.     

A New Approach to Bacterial Vaccines

Immunizing antigens against only 10 bacterial diseases—cholera, diphtheria, paratyphoid, pertussis, plague, scarlet fever, staphylococcal disease, tetanus, tuberculosis and typhoid—have been licensed for sale in Canada and the United States. Convincing evidence of efficacy is available for only four of these—diphtheria and tetanus toxoids, and pertussis and typhoid vaccines.The principles which determine the efficacy of different immunizing antigens are not always the same. Toxoids, for example, stimulate the formation of antitoxin-producing mechanisms which can neutralize toxins produced by invading organisms, thereby rendering them harmless. Conversely, vaccines stimulate the formation of antibacterial mechanisms which stop the growth of organisms before they can produce disease.Use of enzyme-lysed vaccines for prevention of staphylococcal disease represents a new approach in vaccine research. Animal tests have shown lysed vaccines to be 10 to 100 times less toxic, and about eight times more effective, than whole bacterial vaccines. Studies with lysed vaccines for other diseases are now in progress.     

A Boolean Approach to Linear Prediction for Signaling Network Modeling

The task of the DREAM4 (Dialogue for Reverse Engineering Assessments and Methods) “Predictive signaling network modeling” challenge was to develop a method that, from single-stimulus/inhibitor data, reconstructs a cause-effect network to be used to predict the protein activity level in multi-stimulus/inhibitor experimental conditions. The method presented in this paper, one of the best performing in this challenge, consists of 3 steps: 1. Boolean tables are inferred from single-stimulus/inhibitor data to classify whether a particular combination of stimulus and inhibitor is affecting the protein. 2. A cause-effect network is reconstructed starting from these tables. 3. Training data are linearly combined according to rules inferred from the reconstructed network. This method, although simple, permits one to achieve a good performance providing reasonable predictions based on a reconstructed network compatible with knowledge from the literature. It can be potentially used to predict how signaling pathways are affected by different ligands and how this response is altered by diseases.