Klara Birikh - Academia.edu (original) (raw)

Papers by Klara Birikh

Nucleosides and Nucleotides, 1994

ABSTRACT A prokaryotic two-cistron system for gene expression, based on the pGEM1 plasmid and con... more ABSTRACT A prokaryotic two-cistron system for gene expression, based on the pGEM1 plasmid and containing a translation enhancer in the coding part of the first cistron, has been constructed. The gene to be expressed can be inserted into the vector by means of a PCR-mediated approach using type IIS restriction endonucleases (SDL method). Efficiency of the system is exemplified by the expression of a synthetic gene encoding human interleukin lα.

European Journal of Biochemistry, 1997

The hammerhead ribozyme is one of the smallest ribozymes known and catalyses the site-specific hy... more The hammerhead ribozyme is one of the smallest ribozymes known and catalyses the site-specific hydrolysis of a phosphodiester bond. This small ribozyme is of interest for two reasons. It offers a convenient system to study the structure/function relationship of a nucleotide sequence, and is a potential vehicle for the inhibition of gene expression. The first part of the review summarizes the sequence requirements of the hammerhead, its three-dimensional structure and the proposed mechanism, in addition to ribozyme specificity and turnover. The second part of the review focuses on the in vivo application of the ribozyme. The processes involved in designing ribozymes for efficient cleavage in vivo are described, together with possible delivery strategies.

Proceedings of the National Academy of Sciences, 2003

Behavioral reactions to stress are altered in numerous psychiatric and neurodegenerative syndrome... more Behavioral reactions to stress are altered in numerous psychiatric and neurodegenerative syndromes, but the corresponding molecular processes and signal transduction pathways are yet unknown. Here, we report that, in mice, the stress-induced splice variant of acetylcholinesterase, AChE-R, interacts intraneuronally with the scaffold protein RACK1 and through it, with its target, protein kinase C␤II (PKC␤II), which is known to be involved in fear conditioning. In stress-responsive brain regions of normal FVB͞N mice, the mild stress of i.

Oncogene, 2002

To study the regulation of acetylcholinesterase (AChE) gene expression in human brain tumors, 3' ... more To study the regulation of acetylcholinesterase (AChE) gene expression in human brain tumors, 3' splice variants of AChE mRNA and potentially relevant transcription factor mRNAs were labeled in primary astrocytomas and melanomas. AChE-S and AChE-R mRNA, as well as Runx1/AML1 mRNA accumulated in astrocytomas in correlation with tumor aggressiveness, but neither HNF3b nor c-fos mRNA was observed in melanoma and astrocytomas. Immunohistochemistry demonstrated nuclear Runx1/AML1 and cellular AChE-S and AChE-R in melanomas, however, only AChE-S, and not the secreted AChE-R variant, was retained in astrocyte tumor cells. Runx1/AML1 revealed weak linkage with ACHE promoter sequences, yet enhanced ACHE gene expression in co-transfected COS1 cells. The p300 coactivator and the ACHE promoter's distal enhancer facilitated this effect, which was independent of much of the Runx1/AML1 trans-activation domain. Surprisingly, GASP, a fusion product of green fluorescence protein (GFP) and ASP 67 , a peptide composed of the 67 Cterminal amino acid residues of AChE-S, localized to COS1 cell nuclei. However, GARP, the corresponding fusion product of GFP with a peptide having the 51 Cterminal residues of AChE-E or GFP alone, remained cytoplasmic. Runx1/AML1 exhibited improved nuclear retention in GASP-expressing COS1 cells, suggesting modulated nuclear localization processes. Together, these findings reveal brain tumor-specific regulation of both expression and cellular retention of variant ACHE gene products.

Nucleic Acids Research, 2006

To be effective, antisense molecules should be stable in biological fluids, non-toxic, form stabl... more To be effective, antisense molecules should be stable in biological fluids, non-toxic, form stable and specific duplexes with target RNAs and readily penetrate through cell membranes without non-specific effects on cell function. We report herein that negatively charged DNA mimics representing chiral analogues of peptide nucleic acids with a constrained trans-4-hydroxy-N-acetylpyrrolidine-2-phosphonate backbone (pHypNAs) meet these criteria. To demonstrate this, we compared silencing potency of these compounds with that of previously evaluated as efficient gene knockdown molecules hetero-oligomers consisting of alternating phosphono-PNA monomers and PNA-like monomers based on trans-4-hydroxy-L-proline (HypNA-pPNAs). Antisense potential of pHypNA mimics was confirmed in a cell-free translation assay with firefly luciferase as well as in a living cell assay with green fluorescent protein. In both cases, the pHypNA antisense oligomers provided a specific knockdown of a target protein production. Confocal microscopy showed that pHypNAs, when transfected into living cells, demonstrated efficient cellular uptake with distribution in the cytosol and nucleus. Also, the high potency of pHypNAs for down-regulation of Ras-like GTPase Ras-dva in Xenopus embryos was demonstrated in comparison with phosphorodiamidate morpholino oligomers. Therefore, our data suggest that pHypNAs are novel antisense agents with potential widespread in vitro and in vivo applications in basic research involving live cells and intact organisms.

Human Mutation, 1992

The allele-specific PCR approach has been modified by introducing a second mismatch at the 3&... more The allele-specific PCR approach has been modified by introducing a second mismatch at the 3'-penultimate link of the primer and used to identify the sickle cell anemia mutation (A-->T transversion in the sixth codon of the human beta-globin gene causing Glu-->Val substitution in the protein), thus obviating the problem of an interpretationally ambiguous 3'-terminal mismatch including T residue.

Gene, 1995

Synthetic intronless genes, coding for human interleukin 1 alpha (IL 1 alpha) and interleukin 1 r... more Synthetic intronless genes, coding for human interleukin 1 alpha (IL 1 alpha) and interleukin 1 receptor antagonist (IL1ra), have been expressed efficiently in a specially designed prokaryotic vector, pGMCE (a pGEM1 derivative), where the target gene forms the second part of a two-cistron system. The first part of the system is a translation enhancer-containing mini-cistron, whose termination codon overlaps the start codon of the target gene. In the case of the IL1 alpha gene, the high expression level is largely due to the direct efficient translation initiation at the second cistron, whereas with the IL1ra gene in the same system, the proximal translation initiation region (TIR) provides a high level of coupled expression of the target gene. Thus, pGMCE is a potentially versatile vector for direct prokaryotic expression.

Biological Psychiatry, 2006

Background: Cholinergic neurotransmission notably participates in stress-induced motor responses.... more Background: Cholinergic neurotransmission notably participates in stress-induced motor responses. Here we report the contribution of alternative splicing of acetylcholinesterase (AChE) pre-mRNA to modulate these responses. More specifically, we induced stress-associated hypofunction of dopaminergic, mainly D2 dopamine receptor-mediated neurotransmission by haloperidol and explored stress induced hyperlocomotion and catalepsy, an extreme form of immobility, induced in mice with AChE deficiencies. Methods: Conditional transgenic (Tet/AS) mice were created with tetracycline-induced antisense suppression of AChE gene expression. Locomotion and catalepsy times were measured in Tet/AS and strain-matched control mice, under open-field exposure threat and under home-cage safety. Results: In vitro, NGF-treated PC12 cells failed to extend neurites upon Tet/AS suppression. In vivo, Tet/AS but not control mice showed stress-associated hippocampal deposits of heat-shock protein 70 and GRP78 (BiP), predicting posttranscriptional changes in neuronal reactions. Supporting this notion, their striatal cholinergic neurons demonstrated facilitated capacity for neurite extension, attributing these in vivo changes in neurite extension to network interactions. Tet/AS mice presented stress-induced hyperlocomotion. Moreover, the dopamine antagonist haloperidol induced longer catalepsy in threatened Tet/AS than in control mice. When returned to home-cage safety, Tet/AS mice showed retarded release from catalepsy. Conclusions: Acetylcholinesterase modulates stress-induced motor responses and facilitates resumption of normal motor behavior following stress through both catalytic and noncatalytic features.

Analytical Chemistry, 2008

A new method suitable for single nucleotide polymorphism detection and other applications based o... more A new method suitable for single nucleotide polymorphism detection and other applications based on oligonucleotide probe extension has been developed. The method is based on mass spectrometry and utilizes a single surface for affinity purification of extended probes and matrix-independent desorption/ionization of the cleavable labels. A new family of sulfur-linked laser-cleavable trityl labels with vastly improved flying abilities is implemented in this study. Corresponding reagents compatible with automated oligonucleotide synthesis are presented. Utility of this method for SNP genotyping is demonstrated. Darnhofer-Patel, B.; van den Boom, D.; Rodi, C. P. Methods Mol. Biol. 2003, 212, 241-62. (5) Kokoris, M.; Dix, K.; Moynihan, K.; Mathis, J.; Erwin, B.; Grass, P.; Hines, B.; Duesterhoeft, A.

Methods in Molecular Biology, 2009

A new method suitable for single nucleotide polymorphism (SNP) detection using differential oligo... more A new method suitable for single nucleotide polymorphism (SNP) detection using differential oligonucleotide probe extension has been developed. Sulfur-linked laser-cleavable trityl labels are implemented in this protocol. The method is based on mass spectrometry and utilizes a single surface for affinity purification of extended probes and matrix-independent desorption-ionization of the cleavable labels. The usefulness of this method for SNP genotyping is demonstrated.