Inhibition of HIV Replication by RNAi
The introduction of combination antiretroviral therapy has resulted in a remarkable improvement of the life expectancy of individuals infected with HIV and has significantly reduced their likelihood of developing AIDS. However, despite this progress, HIV infection remains incurable. Toxicity problems associated with current drug therapies and the emergence of drug resistance clearly indicate the need for alternative therapeutic approaches. Retroviral infection with HIV results in the stable...
References Tfh
Allawi HT, Dong F, Ip HS, Neri BP, Lyamichev VI 2001 Mapping of RNA accessible sites by extension of random oligonucleotide libraries with reverse transcriptase. RNA 7 314-327 Barroso-DelJesus A, Berzal-Herranz A 2001 Selection of targets and the most efficient hairpin ribozymes for inactivation of mRNAs using a self-cleaving RNA library. EMBO Rep 2 1112-1118 Berns K, Hijmans EM, Mullenders J, Brummelkamp TR, Velds A, Heimerikx M, Kerk-hoven RM, Madiredjo M, Nijkamp W, Weigelt B, Agami R, Ge W,...
RNA Targeting by LNAzymes
DNAzymes are catalytically active DNA molecules that are able to cleave RNA in a sequence-specific manner after binding to complementary sequences. The so-called 10-23 DNAzyme Fig. 3 was found by in vitro selection Santoro and Joyce 1997 . It consists of a 15-nt catalytic core flanked by two binding arms that lead to the sequence selectivity of a given DNAzyme. LNAzymes are LNA-modified DNAzymes, and incorporation of two LNA nucleotides in each of the binding arms yielded an LNAzyme with a...
Detection Methods for Small Molecules and Advantages of Aptamers
Small molecules are involved in innumerable biochemical processes in life and can operate as substrate, catalyst or inhibitor in biochemical reactions. Because of these properties, small molecules are valuable as drugs in medicine or in biotechnological applications. In addition, in all cases the feasibility of quickly and reliably detecting them is essential. Different and versatile techniques have been developed for the detection of small molecules. Classic detection methods are based on...
LNA Hybridization Properties and Structural Features
We have defined LNA as an oligonucleotide containing at least one LNA monomer, i.e., one 2 -0,4 -C-methylene-P-d-ribofuranosyl nucleotide see Fig. 1 Singh et al. 1998 Koshkin et al. 1998b . The LNA monomers adopt N-type sugar puckers, also termed C3 -endo conformations Singh et al. 1998 Obika et al. 1997 . The vast majority of reports on LNA-mediated RNA targeting have dealt with mixmer LNA oligonucleotides, i.e., LNAs containing a limited number of LNA monomers in combination with other types...
siRNA Agents Work as Ligands for TollLike Receptors
Surprisingly, recent studies have indicated that siRNAs can induce global up-regulation ofthe expression of IFN-stimulated genes Bridge et al. 2003 Jackson et al. 2003 Sledz et al. 2003 Kariko et al. 2004 Persengiev et al. 2004 Fig. 5 . This effect was detected with synthetic siRNAs that were transfected into cells, and with siRNAs that were produced within cells by the expression of shRNAs. Both of these papers documented significant non-specific changes in gene expression as a consequence of...
Inhibition of HCV by RNAi
HCV is a major cause of chronic hepatitis and hepatocellular carcinoma. Currently, no vaccines are available for HCV, and several groups have used RNAi to target HCV replication. HCV belongs to the family Flaviviridae, and its genome is encoded by a 9.6-kb RNA of positive polarity. Because there is no cell culture system for HCV replication, all studies have used replicon systems in Huh-7 cells as a model for HCV replication. These replicons support HCV RNA transcription and protein synthesis,...
RNA Aptamers that Recognize the VariantSurface Glycoprotein
The aim of the SELEX experiment published by Lorger and co-workers 2003 was to select RNA aptamers that specifically recognize the VSG protein on the surface of bloodstream-stage African trypanosomes. The bloodstream lifecycle stage represents the infectious phase of the parasite, and VSG is the most abundant surface protein during that period. Since the parasite undergoes antigenic variation, which is characterized by the expression of different VSG variants, a selection scheme was designed to...
Nucleic Acid Aptamers Directed Against Carbohydrates
Nucleic acid interactions with polymeric cellular components, particularly with proteins, are dominated by hydrogen bonds, hydrophobic and ionic interactions between phosphate residues and positively charged amino acids. This is defined by the sequence and tertiary structure of the nucleic acid. Carbohydrate residues are void of basic functional groups that are capable of undergoing ionic interaction with nucleic acids. In addition, they possess a very flexible structure. Such molecules are not...
Ribozymes
In the early 1980s, the research groups of Thomas Cech and Sidney Altman discovered RNA molecules that possess catalytic activity in the absence of any protein moiety. These ribonucleic acids with enzymatic properties were named ribozymes. Meanwhile, several classes of ribozymes have been identified that can roughly be divided into large ribozymes consisting of several hundreds to thousands of nucleotides and small ribozymes that range from 30 to about 150 nucleotides in length Doudna and Cech...
References Gcz
Ahmed N, Thornalley PJ 2003 Quantitative screening of protein biomarkers of early glycation, advanced glycation, oxidation and nitrosation in cellular and extracellular proteins by tandem mass spectrometry multiple reaction monitoring. Biochem Soc Trans 31 1417-1422 Altria KD, Elder D 2004 Overview of the status and applications of capillary electrophoresis to the analysis of small molecules. J Chromatogr A 1023 1-14 Aurup H, Williams DM, Eckstein F 1992 2'-Fluoro- and...
Telomerase
Telomerase seems an obvious candidate for antisense targeting because this enzyme carries within it a template RNA for telomere synthesis. Indeed, it has been found that telomerase is very sensitive to inhibition by PNA and other antisense agents targeting this RNA Shammas et al. 2004 Hamilton et al. 1999 Folini et al. 2003 , and that such anti-telomerase PNAs decrease the viability of cancer cells in culture. Furthermore, it was recently found that photochemical internalization of unmodified...
Efficacy and Target Specificity
The biggest difference between ribozyme and siRNA technologies is the recruitment of endogenous proteins applicable in the latter case which is associated with the maintenance of a high intracellular activity. By contrast, the actions of ribozymes do not depend on intracellular factors Scherer and Rossi 2003 . Thus, siRNAs can exploit many intracellular enzymes, such as he-licases and RNases, in cells for cleavage of target mRNAs, and they can be much more effective tools than ribozymes for the...
G V U U Ag
Fig. 1a-c The effects of 2'-amino modification at position 2.1 upon the cleavage activity of a hammerhead ribozyme. a A representative example of multiple turnover reactions of the wild-type ribozyme Wt-URz and the ribozyme with a single 2'-amino group at position 2.1 2'-NH2 2.1 -URz in the presence of 5 mM Mg2 . b The cleavage reaction was performed in the presence of Mn2 . c Summary of the ribozyme catalytic activity following various site-specific modifications at position 2.1. Primary and...
Info Tup
A Direct Coupling Between the Structure and the Regulatory Activity The astonishing variety of RNA performance is imputable to its peculiar structure capability, and its potentiality to form stable or transient interactions. Thus, RNA function is linked to its dynamic properties and versatile structure. Structure-function relationships have not yet been addressed for many regulatory RNAs. It is expected that their stability and regulatory activities are dictated by their structure. The size of...
Npcrnas In Vibrio Cholerae
Functional Redundancies and How to Find Them The few examples described here show that the pathogenesis-related RNAs are much more prevalent than previously anticipated. One interesting feature that emerges is the functional redundancy of some of these regulatory RNAs in different pathogenic bacteria Table 2 . It is conceivable that these RNAs are differentially expressed upon different environmental niches conditions or that they have evolved independent regulatory functions i.e., different...