J. Ciesiolka - Academia.edu (original) (raw)
Papers by J. Ciesiolka
International Journal of Molecular Sciences
The p53 protein is one of the major transcriptional factors which guards cell homeostasis. Here, ... more The p53 protein is one of the major transcriptional factors which guards cell homeostasis. Here, we showed that poly(C)-binding protein 2 (PCBP2) can bind directly to the 5′ terminus of p53 mRNA by means of electrophoretic mobility shift assay. Binding sites of PCBP2 within this region of p53 mRNA were mapped using Pb2+-induced cleavage and SAXS methods. Strikingly, the downregulation of PCBP2 in HCT116 cells resulted in a lower level of p53 protein under normal and stress conditions. Quantitative analysis of p53 mRNA in PCBP2-downregulated cells revealed a lower level of p53 mRNA under normal conditions suggesting the involvement of PCBP2 in p53 mRNA stabilisation. However, no significant change in p53 mRNA level was observed upon PCBP2 depletion under genotoxic stress. Moreover, a higher level of p53 protein in the presence of rapamycin or doxorubicin and the combination of both antibiotics was noticed in PCBP2-overexpressed cells compared to control cells. These observations indi...
International Journal of Molecular Sciences
The p53 protein is one of the major transcriptional factors which guards cell homeostasis. Here, ... more The p53 protein is one of the major transcriptional factors which guards cell homeostasis. Here, we showed that poly(C)-binding protein 2 (PCBP2) can bind directly to the 5′ terminus of p53 mRNA by means of electrophoretic mobility shift assay. Binding sites of PCBP2 within this region of p53 mRNA were mapped using Pb2+-induced cleavage and SAXS methods. Strikingly, the downregulation of PCBP2 in HCT116 cells resulted in a lower level of p53 protein under normal and stress conditions. Quantitative analysis of p53 mRNA in PCBP2-downregulated cells revealed a lower level of p53 mRNA under normal conditions suggesting the involvement of PCBP2 in p53 mRNA stabilisation. However, no significant change in p53 mRNA level was observed upon PCBP2 depletion under genotoxic stress. Moreover, a higher level of p53 protein in the presence of rapamycin or doxorubicin and the combination of both antibiotics was noticed in PCBP2-overexpressed cells compared to control cells. These observations indi...
Acta Biochimica Polonica, 2001
Although the delta ribozymes have been studied for more than ten years the most important informa... more Although the delta ribozymes have been studied for more than ten years the most important information concerning their structure and mechanism of catalysis were only obtained very recently. The crystal structure of the genomic delta ribozyme turns out to be an excellent example of the extraordinary properties of RNA molecules to fold into uniquely compact structures. Details of the X-ray structure have greatly stimulated further studies on the folding of the ribozymes into functionally active molecules as well as on the mechanism of RNA catalysis. The ability of the delta ribozymes to carry out general acid-base catalysis by nucleotide side chains has been assumed in two proposed mechanisms of self-cleavage. Recently, considerable progress has been also made in characterizing the catalytic properties of trans-acting ribozyme variants that are potentially attractive tools in the strategy of directed RNA degradation.
Acta Biochimica Polonica, 2009
Two early nodulin 40 (enod40) genes, ENOD40-1, the shortest legume ENOD40 gene, and ENOD40-2, wer... more Two early nodulin 40 (enod40) genes, ENOD40-1, the shortest legume ENOD40 gene, and ENOD40-2, were isolated from Lupinus luteus, a legume with indeterminate nodules. Both genes were expressed at similar levels during symbiosis with nitrogen-fixing bacteria. ENOD40 phylogeny clustered the L. luteus genes with legumes forming determinate nodules and revealed peptide similarities. The ENOD40-1 small ORF A fused to a reporter gene was efficiently expressed in plant cells, indicating that the start codon is recognized for translation. The ENOD40-1 RNA structure predicted based on Pb(II)-induced cleavage and modeling revealed four structurally conserved domains, an absence of domain 4 characteristic for legumes of indeterminate nodules, and interactions between the conserved region I and a region located upstream of domain 6. Domain 2 contains Mg(II) ion binding sites essential for organizing RNA secondary structure. The differences between L. luteus and Glycine max ENOD40 RNA models sugg...
Combinatorial Chemistry, 1996
Publisher Summary Selection-amplification introduced a new capability to the study of RNA and DNA... more Publisher Summary Selection-amplification introduced a new capability to the study of RNA and DNA. One could ask if any nucleic acid (less than a certain size) existed that could perform a particular biochemical function and recover that molecule for further study, along with its closely related functional relatives. Such exhaustive investigation of nucleic acid capabilities was unprecedented. This chapter discusses some of the methods and considerations required to carry out the purification, potentially ≈10 14 -fold, of a new RNA from a randomized pool of initial sequences. RNAs are fractionated (selected by affinity chromatography in this chapter) and the selected fraction is converted to complementary DNA (cDNA) that is amplified by polymerase chain reaction (PCR). Finally the DNA from the PCR is transcribed and the cycle is repeated. After the desired activity is observed in the pool or when selection has apparently succeeded, RNAs are cloned and sequenced. Individual clones are then characterized by appropriate structural and functional biochemical assays.
Methods in molecular biology (Clifton, N.J.), 2012
During in vitro run-off transcription with T7 RNA polymerase, transcripts with heterogenous 3'... more During in vitro run-off transcription with T7 RNA polymerase, transcripts with heterogenous 3' ends are commonly synthesized. Here, we describe an efficient procedure for correct processing of transcript 3' ends with the use of antigenomic HDV ribozyme. The procedure involves the extension of nascent transcripts with seven nucleotides complementary to the ribozyme's recognition site and, subsequently, the removal of those nucleotides with the HDV ribozyme acting in trans. Sufficient reaction rates and final cleavage extents of approx. 90% can be obtained with just twofold excess of the ribozyme. The highest concentration of RNA substrate suggested for practical applications turns out to be 3 μM. The procedure is an alternative to the use of ribozymes as cis-cleaving autocatalytic cassettes attached to transcript 3' ends.
Postepy biochemii, 2006
At the 5' and 3' end of genomic HCV RNA there are two highly conserved, untranslated regi... more At the 5' and 3' end of genomic HCV RNA there are two highly conserved, untranslated regions, 5'UTR and 3'UTR. These regions are organized into spatially ordered structures and they play key functions in regulation of processes of the viral life cycle. Most nucleotides of the region located at the 5' side of the coding sequence serve as an internal ribosomal entry site, IRES, which directs cap-independent translation. The RNA fragment present at the 3' end of the genome is required for virus replication and probably contributes to translation of viral proteins. During virus replication its genomic strand is transcribed into a strand of minus polarity, the replicative strand. Its 3' terminus is responsible for initiation of synthesis of descendant genomic strands. This article summarizes our current knowledge on the structure and function of the non-coding regions of hepatitis C genomic RNA, 5'UTR and 3'UTR, and the complementary sequences of the r...
Nucleic Acids Research, 2005
Oligoribonucleotides that corresponded to the X regions of the (1) and (À) polarity strands of HC... more Oligoribonucleotides that corresponded to the X regions of the (1) and (À) polarity strands of HCV RNA, as well as several shorter oligomers comprising defined stem-loop motifs of their predicted secondary structure models, were analyzed by Pb 21-induced cleavage, partial digestion with specific nucleases and chemical modification. Patterns characteristic of the motifs were compared with those obtained for the full-length molecules and on the basis of such 'structural fingerprinting' conclusions concerning folding of regions X were formulated. It turned out that the secondary structure model of X(1) RNA proposed earlier, the three-stem-loop model composed of hairpins SL1, SL2 and SL3, was only partially consistent with our experimental data. We confirmed the presence of SL1 and SL3 motifs and showed that the single-stranded stretch adjacent to the earlier proposed hairpin SL2 contributed to the folding of that region. It seemed to be arranged into two hairpins, which might form a hypothetical pseudoknot by changing their base-pairing systems. These data were discussed in terms of their possible biological significance. On the other hand, analysis of the X(À) RNA and its sub-fragments supported a three-stem-loop secondary structure model for this RNA.
Molecular Biology Reports, 2008
The hepatitis delta virus (HDV) ribozyme is an RNA enzyme that catalyzes the site-specific trans-... more The hepatitis delta virus (HDV) ribozyme is an RNA enzyme that catalyzes the site-specific trans-esterification reaction. Using high hydrostatic pressure (HHP) technique we showed that HDV ribozyme catalyzes the reaction of RNA cleavage in the absence of magnesium ions according to mechanism of acidic hydrolysis of esters. HHP induces changes of water structure, lowering pH and effect ribozyme catalytic site structure formation without magnesium. HHP, similarly to magnesium ion at ambient pressure stabilizes the higher order RNA structure of HDV, but Mg(2+) is not involved in the catalysis. Our results clearly support the new mechanism of HDV hydrolysis and show advantages of using HHP in analysis of macromolecules interaction.
Dalton Trans., 2016
Viomycin is a basic peptide antibiotic, which is among the most effective agents against multidru... more Viomycin is a basic peptide antibiotic, which is among the most effective agents against multidrug-resistant tuberculosis.
Journal of Inorganic Biochemistry, 2015
Colistin and transition metal ions are commonly used as feed additives for livestock animals. Thi... more Colistin and transition metal ions are commonly used as feed additives for livestock animals. This work presents the results of an analysis of combined potentiometric and spectroscopic (UV-vis, EPR, CD, NMR) data which lead to conclude that colistin is able to effectively chelate copper(II) ions. In cell-free system the oxidative activity of the complex manifests itself in the plasmid DNA destruction with simultaneous generation of reactive •OH species, when accompanied by hydrogen peroxide or ascorbic acid. The degradation of RNA occurs most likely via a hydrolytic mechanism not only for complexed compound but also colistin alone. Therefore, huge amounts of the used antibiotic for nontherapeutic purposes might have a potential influence on livestock health.
PLoS ONE, 2013
The p53 protein is a key player in cell response to stress events and cancer prevention. However,... more The p53 protein is a key player in cell response to stress events and cancer prevention. However, up-regulation of p53 that occurs during radiotherapy of some tumours results in radio-resistance of targeted cells. Recently, antisense oligonucleotides have been used to reduce the p53 level in tumour cells which facilitates their radiation-induced apoptosis. Here we describe the rational design of antisense oligomers directed against the 59-terminal region of p53 mRNA aimed to inhibit the synthesis of p53 protein and its DNp53 isoform. A comprehensive analysis of the sites accessible to oligomer hybridization in this mRNA region was performed. Subsequently, translation efficiency from the initiation codons for both proteins in the presence of selected oligomers was determined in rabbit reticulocyte lysate and in MCF-7 cells. The antisense oligomers with 29-OMe and LNA modifications were used to study the mechanism of their impact on translation. It turned out that the remaining RNase H activity of the lysate contributed to modulation of protein synthesis efficiency which was observed in the presence of antisense oligomers. A possibility of changing the ratio of the newly synthetized p53 and DNp53 in a controlled manner was revealed which is potentially very attractive considering the relationship between the functioning of these two proteins. Selected antisense oligonucleotides which were designed based on accessibility mapping of the 59-terminal region of p53 mRNA were able to significantly reduce the level of p53 protein in MCF-7 cells. One of these oligomers might be used in the future as a support treatment in anticancer therapy.
Biochemistry and molecular biology international, 1996
The structure of plant 5S rRNA species from lupin and wheat germ as well as the structure of two ... more The structure of plant 5S rRNA species from lupin and wheat germ as well as the structure of two RNA fragments that represent domains beta and gamma of lupin 5S rRNA have been probed by Pb(II)-induced hydrolysis. The lead digestion patterns of 5S rRNA species show that the secondary and tertiary structures of the molecules are very similar. The data suggests that two potential base pairs at the bottom of helix E are destabilized and this causes an enlargement of the hairpin loop e. On the other hand, nucleotides from loop c seem to be involved in the formation of some kind of higher order structure. A comparison of the distribution of cleavages induced in RNA fragments to those in the corresponding regions of the entire 5S rRNA shows that under conditions applied in our studies the structural domains beta and gamma are not involved in formation of any tertiary interaction within 5S rRNA structure.
RNA: A publication of the RNA Society, 1996
From a potentially completely sampled set of randomized 23-mer sequences, we selected RNAs that b... more From a potentially completely sampled set of randomized 23-mer sequences, we selected RNAs that bind a Zn-column and also show KD approximately 100-400 microM for free Zn2+, probably relying on one or two direct ion coordinations. Comparison of selected sequences with previously known divalent sites suggests three or four small RNA motifs repeatedly found to interact with divalent ions. We suggest that the GC cluster, the augmented GC cluster, and the E element may be useful generalized ion-binding structures. Such structures may help identify similar divalent sites in sequenced RNAs and serve as substructures for design of functional RNA metallodomains.
RNA, 1995
We have selected an RNA that depends on zinc for affinity to a column, starting from a pool of ri... more We have selected an RNA that depends on zinc for affinity to a column, starting from a pool of ribooligonucleotides with 50 randomized positions. This RNA's chemical sensitivities, calculated folding thermodynamics, and activity when fragmented suggest that an ion binding site lies within a complex 21-nt hairpin loop, near the junction with an imperfect helical stem. This RNA site has an unselected selectivity among divalents, preferring nickel, cobalt, and cadmium to calcium, magnesium, and manganese, as expected for a simple site of chelation. A moderate zinc-dependent change in loop structure accompanies divalent binding and can be detected by chemical probing and zinc-dependent UV-induced crosslinking. The latter also demonstrates the apposition of loop sequences to make a structure that may be related to the E-loop motif found in a number of other RNA molecules; the E-loop motif, accordingly, may be a divalent site.
RNA (New York, N.Y.), 1996
From a potentially completely sampled set of randomized 23-mer sequences, we selected RNAs that b... more From a potentially completely sampled set of randomized 23-mer sequences, we selected RNAs that bind a Zn-column and also show KD approximately 100-400 microM for free Zn2+, probably relying on one or two direct ion coordinations. Comparison of selected sequences with previously known divalent sites suggests three or four small RNA motifs repeatedly found to interact with divalent ions. We suggest that the GC cluster, the augmented GC cluster, and the E element may be useful generalized ion-binding structures. Such structures may help identify similar divalent sites in sequenced RNAs and serve as substructures for design of functional RNA metallodomains.
International Journal of Molecular Sciences
The p53 protein is one of the major transcriptional factors which guards cell homeostasis. Here, ... more The p53 protein is one of the major transcriptional factors which guards cell homeostasis. Here, we showed that poly(C)-binding protein 2 (PCBP2) can bind directly to the 5′ terminus of p53 mRNA by means of electrophoretic mobility shift assay. Binding sites of PCBP2 within this region of p53 mRNA were mapped using Pb2+-induced cleavage and SAXS methods. Strikingly, the downregulation of PCBP2 in HCT116 cells resulted in a lower level of p53 protein under normal and stress conditions. Quantitative analysis of p53 mRNA in PCBP2-downregulated cells revealed a lower level of p53 mRNA under normal conditions suggesting the involvement of PCBP2 in p53 mRNA stabilisation. However, no significant change in p53 mRNA level was observed upon PCBP2 depletion under genotoxic stress. Moreover, a higher level of p53 protein in the presence of rapamycin or doxorubicin and the combination of both antibiotics was noticed in PCBP2-overexpressed cells compared to control cells. These observations indi...
International Journal of Molecular Sciences
The p53 protein is one of the major transcriptional factors which guards cell homeostasis. Here, ... more The p53 protein is one of the major transcriptional factors which guards cell homeostasis. Here, we showed that poly(C)-binding protein 2 (PCBP2) can bind directly to the 5′ terminus of p53 mRNA by means of electrophoretic mobility shift assay. Binding sites of PCBP2 within this region of p53 mRNA were mapped using Pb2+-induced cleavage and SAXS methods. Strikingly, the downregulation of PCBP2 in HCT116 cells resulted in a lower level of p53 protein under normal and stress conditions. Quantitative analysis of p53 mRNA in PCBP2-downregulated cells revealed a lower level of p53 mRNA under normal conditions suggesting the involvement of PCBP2 in p53 mRNA stabilisation. However, no significant change in p53 mRNA level was observed upon PCBP2 depletion under genotoxic stress. Moreover, a higher level of p53 protein in the presence of rapamycin or doxorubicin and the combination of both antibiotics was noticed in PCBP2-overexpressed cells compared to control cells. These observations indi...
Acta Biochimica Polonica, 2001
Although the delta ribozymes have been studied for more than ten years the most important informa... more Although the delta ribozymes have been studied for more than ten years the most important information concerning their structure and mechanism of catalysis were only obtained very recently. The crystal structure of the genomic delta ribozyme turns out to be an excellent example of the extraordinary properties of RNA molecules to fold into uniquely compact structures. Details of the X-ray structure have greatly stimulated further studies on the folding of the ribozymes into functionally active molecules as well as on the mechanism of RNA catalysis. The ability of the delta ribozymes to carry out general acid-base catalysis by nucleotide side chains has been assumed in two proposed mechanisms of self-cleavage. Recently, considerable progress has been also made in characterizing the catalytic properties of trans-acting ribozyme variants that are potentially attractive tools in the strategy of directed RNA degradation.
Acta Biochimica Polonica, 2009
Two early nodulin 40 (enod40) genes, ENOD40-1, the shortest legume ENOD40 gene, and ENOD40-2, wer... more Two early nodulin 40 (enod40) genes, ENOD40-1, the shortest legume ENOD40 gene, and ENOD40-2, were isolated from Lupinus luteus, a legume with indeterminate nodules. Both genes were expressed at similar levels during symbiosis with nitrogen-fixing bacteria. ENOD40 phylogeny clustered the L. luteus genes with legumes forming determinate nodules and revealed peptide similarities. The ENOD40-1 small ORF A fused to a reporter gene was efficiently expressed in plant cells, indicating that the start codon is recognized for translation. The ENOD40-1 RNA structure predicted based on Pb(II)-induced cleavage and modeling revealed four structurally conserved domains, an absence of domain 4 characteristic for legumes of indeterminate nodules, and interactions between the conserved region I and a region located upstream of domain 6. Domain 2 contains Mg(II) ion binding sites essential for organizing RNA secondary structure. The differences between L. luteus and Glycine max ENOD40 RNA models sugg...
Combinatorial Chemistry, 1996
Publisher Summary Selection-amplification introduced a new capability to the study of RNA and DNA... more Publisher Summary Selection-amplification introduced a new capability to the study of RNA and DNA. One could ask if any nucleic acid (less than a certain size) existed that could perform a particular biochemical function and recover that molecule for further study, along with its closely related functional relatives. Such exhaustive investigation of nucleic acid capabilities was unprecedented. This chapter discusses some of the methods and considerations required to carry out the purification, potentially ≈10 14 -fold, of a new RNA from a randomized pool of initial sequences. RNAs are fractionated (selected by affinity chromatography in this chapter) and the selected fraction is converted to complementary DNA (cDNA) that is amplified by polymerase chain reaction (PCR). Finally the DNA from the PCR is transcribed and the cycle is repeated. After the desired activity is observed in the pool or when selection has apparently succeeded, RNAs are cloned and sequenced. Individual clones are then characterized by appropriate structural and functional biochemical assays.
Methods in molecular biology (Clifton, N.J.), 2012
During in vitro run-off transcription with T7 RNA polymerase, transcripts with heterogenous 3'... more During in vitro run-off transcription with T7 RNA polymerase, transcripts with heterogenous 3' ends are commonly synthesized. Here, we describe an efficient procedure for correct processing of transcript 3' ends with the use of antigenomic HDV ribozyme. The procedure involves the extension of nascent transcripts with seven nucleotides complementary to the ribozyme's recognition site and, subsequently, the removal of those nucleotides with the HDV ribozyme acting in trans. Sufficient reaction rates and final cleavage extents of approx. 90% can be obtained with just twofold excess of the ribozyme. The highest concentration of RNA substrate suggested for practical applications turns out to be 3 μM. The procedure is an alternative to the use of ribozymes as cis-cleaving autocatalytic cassettes attached to transcript 3' ends.
Postepy biochemii, 2006
At the 5' and 3' end of genomic HCV RNA there are two highly conserved, untranslated regi... more At the 5' and 3' end of genomic HCV RNA there are two highly conserved, untranslated regions, 5'UTR and 3'UTR. These regions are organized into spatially ordered structures and they play key functions in regulation of processes of the viral life cycle. Most nucleotides of the region located at the 5' side of the coding sequence serve as an internal ribosomal entry site, IRES, which directs cap-independent translation. The RNA fragment present at the 3' end of the genome is required for virus replication and probably contributes to translation of viral proteins. During virus replication its genomic strand is transcribed into a strand of minus polarity, the replicative strand. Its 3' terminus is responsible for initiation of synthesis of descendant genomic strands. This article summarizes our current knowledge on the structure and function of the non-coding regions of hepatitis C genomic RNA, 5'UTR and 3'UTR, and the complementary sequences of the r...
Nucleic Acids Research, 2005
Oligoribonucleotides that corresponded to the X regions of the (1) and (À) polarity strands of HC... more Oligoribonucleotides that corresponded to the X regions of the (1) and (À) polarity strands of HCV RNA, as well as several shorter oligomers comprising defined stem-loop motifs of their predicted secondary structure models, were analyzed by Pb 21-induced cleavage, partial digestion with specific nucleases and chemical modification. Patterns characteristic of the motifs were compared with those obtained for the full-length molecules and on the basis of such 'structural fingerprinting' conclusions concerning folding of regions X were formulated. It turned out that the secondary structure model of X(1) RNA proposed earlier, the three-stem-loop model composed of hairpins SL1, SL2 and SL3, was only partially consistent with our experimental data. We confirmed the presence of SL1 and SL3 motifs and showed that the single-stranded stretch adjacent to the earlier proposed hairpin SL2 contributed to the folding of that region. It seemed to be arranged into two hairpins, which might form a hypothetical pseudoknot by changing their base-pairing systems. These data were discussed in terms of their possible biological significance. On the other hand, analysis of the X(À) RNA and its sub-fragments supported a three-stem-loop secondary structure model for this RNA.
Molecular Biology Reports, 2008
The hepatitis delta virus (HDV) ribozyme is an RNA enzyme that catalyzes the site-specific trans-... more The hepatitis delta virus (HDV) ribozyme is an RNA enzyme that catalyzes the site-specific trans-esterification reaction. Using high hydrostatic pressure (HHP) technique we showed that HDV ribozyme catalyzes the reaction of RNA cleavage in the absence of magnesium ions according to mechanism of acidic hydrolysis of esters. HHP induces changes of water structure, lowering pH and effect ribozyme catalytic site structure formation without magnesium. HHP, similarly to magnesium ion at ambient pressure stabilizes the higher order RNA structure of HDV, but Mg(2+) is not involved in the catalysis. Our results clearly support the new mechanism of HDV hydrolysis and show advantages of using HHP in analysis of macromolecules interaction.
Dalton Trans., 2016
Viomycin is a basic peptide antibiotic, which is among the most effective agents against multidru... more Viomycin is a basic peptide antibiotic, which is among the most effective agents against multidrug-resistant tuberculosis.
Journal of Inorganic Biochemistry, 2015
Colistin and transition metal ions are commonly used as feed additives for livestock animals. Thi... more Colistin and transition metal ions are commonly used as feed additives for livestock animals. This work presents the results of an analysis of combined potentiometric and spectroscopic (UV-vis, EPR, CD, NMR) data which lead to conclude that colistin is able to effectively chelate copper(II) ions. In cell-free system the oxidative activity of the complex manifests itself in the plasmid DNA destruction with simultaneous generation of reactive •OH species, when accompanied by hydrogen peroxide or ascorbic acid. The degradation of RNA occurs most likely via a hydrolytic mechanism not only for complexed compound but also colistin alone. Therefore, huge amounts of the used antibiotic for nontherapeutic purposes might have a potential influence on livestock health.
PLoS ONE, 2013
The p53 protein is a key player in cell response to stress events and cancer prevention. However,... more The p53 protein is a key player in cell response to stress events and cancer prevention. However, up-regulation of p53 that occurs during radiotherapy of some tumours results in radio-resistance of targeted cells. Recently, antisense oligonucleotides have been used to reduce the p53 level in tumour cells which facilitates their radiation-induced apoptosis. Here we describe the rational design of antisense oligomers directed against the 59-terminal region of p53 mRNA aimed to inhibit the synthesis of p53 protein and its DNp53 isoform. A comprehensive analysis of the sites accessible to oligomer hybridization in this mRNA region was performed. Subsequently, translation efficiency from the initiation codons for both proteins in the presence of selected oligomers was determined in rabbit reticulocyte lysate and in MCF-7 cells. The antisense oligomers with 29-OMe and LNA modifications were used to study the mechanism of their impact on translation. It turned out that the remaining RNase H activity of the lysate contributed to modulation of protein synthesis efficiency which was observed in the presence of antisense oligomers. A possibility of changing the ratio of the newly synthetized p53 and DNp53 in a controlled manner was revealed which is potentially very attractive considering the relationship between the functioning of these two proteins. Selected antisense oligonucleotides which were designed based on accessibility mapping of the 59-terminal region of p53 mRNA were able to significantly reduce the level of p53 protein in MCF-7 cells. One of these oligomers might be used in the future as a support treatment in anticancer therapy.
Biochemistry and molecular biology international, 1996
The structure of plant 5S rRNA species from lupin and wheat germ as well as the structure of two ... more The structure of plant 5S rRNA species from lupin and wheat germ as well as the structure of two RNA fragments that represent domains beta and gamma of lupin 5S rRNA have been probed by Pb(II)-induced hydrolysis. The lead digestion patterns of 5S rRNA species show that the secondary and tertiary structures of the molecules are very similar. The data suggests that two potential base pairs at the bottom of helix E are destabilized and this causes an enlargement of the hairpin loop e. On the other hand, nucleotides from loop c seem to be involved in the formation of some kind of higher order structure. A comparison of the distribution of cleavages induced in RNA fragments to those in the corresponding regions of the entire 5S rRNA shows that under conditions applied in our studies the structural domains beta and gamma are not involved in formation of any tertiary interaction within 5S rRNA structure.
RNA: A publication of the RNA Society, 1996
From a potentially completely sampled set of randomized 23-mer sequences, we selected RNAs that b... more From a potentially completely sampled set of randomized 23-mer sequences, we selected RNAs that bind a Zn-column and also show KD approximately 100-400 microM for free Zn2+, probably relying on one or two direct ion coordinations. Comparison of selected sequences with previously known divalent sites suggests three or four small RNA motifs repeatedly found to interact with divalent ions. We suggest that the GC cluster, the augmented GC cluster, and the E element may be useful generalized ion-binding structures. Such structures may help identify similar divalent sites in sequenced RNAs and serve as substructures for design of functional RNA metallodomains.
RNA, 1995
We have selected an RNA that depends on zinc for affinity to a column, starting from a pool of ri... more We have selected an RNA that depends on zinc for affinity to a column, starting from a pool of ribooligonucleotides with 50 randomized positions. This RNA's chemical sensitivities, calculated folding thermodynamics, and activity when fragmented suggest that an ion binding site lies within a complex 21-nt hairpin loop, near the junction with an imperfect helical stem. This RNA site has an unselected selectivity among divalents, preferring nickel, cobalt, and cadmium to calcium, magnesium, and manganese, as expected for a simple site of chelation. A moderate zinc-dependent change in loop structure accompanies divalent binding and can be detected by chemical probing and zinc-dependent UV-induced crosslinking. The latter also demonstrates the apposition of loop sequences to make a structure that may be related to the E-loop motif found in a number of other RNA molecules; the E-loop motif, accordingly, may be a divalent site.
RNA (New York, N.Y.), 1996
From a potentially completely sampled set of randomized 23-mer sequences, we selected RNAs that b... more From a potentially completely sampled set of randomized 23-mer sequences, we selected RNAs that bind a Zn-column and also show KD approximately 100-400 microM for free Zn2+, probably relying on one or two direct ion coordinations. Comparison of selected sequences with previously known divalent sites suggests three or four small RNA motifs repeatedly found to interact with divalent ions. We suggest that the GC cluster, the augmented GC cluster, and the E element may be useful generalized ion-binding structures. Such structures may help identify similar divalent sites in sequenced RNAs and serve as substructures for design of functional RNA metallodomains.