The Sequence and Structure Determine the Function of Mature Human miRNAs.

Micro RNAs (miRNAs) (19-25 nucleotides in length) belong to the group of non-coding RNAs are the most abundant group of posttranscriptional regulators in multicellular organisms. They affect a gene expression by binding of fully or partially complementary sequences to the 3'-UTR of target mRNA. Furthermore, miRNAs present a mechanism by which genes with diverse functions on multiple pathways can be simultaneously regulated at the post-transcriptional level.

Global methylation status of sperm DNA in carriers of chromosome structural aberrations.

Male infertility might be clearly associated with aberrant DNA methylation patterns in human spermatozoa. An association between oxidative stress and the global methylation status of the sperm genome has also been suggested. The aim of the present study was to determine whether the global sperm DNA methylation status was affected in the spermatozoa of carriers of chromosome structural aberrations.

tRNA--the golden standard in molecular biology.

Transfer RNAs (tRNAs) represent a major class of RNA molecules. Their primary function is to help decode a messenger RNA (mRNA) sequence in order to synthesize protein and thus ensures the precise translation of genetic information that is imprinted in DNA. The discovery of tRNA in the late 1950's provided critical insight into a genetic machinery when little was known about the central dogma of molecular biology.

Effect of desiccation on the dynamics of genome-wide DNA methylation in orthodox seeds of Acer platanoides L.

5-methylcytosine, an abundant epigenetic mark, plays an important role in the regulation of plant growth and development, but there is little information about stress-induced changes in DNA methylation in seeds. In the present study, changes in a global level of m5C were measured in orthodox seeds of Acer platanoides L. during seed desiccation from a WC of 1.

The crucial elements of the 'last step' of programmed cell death induced by kinetin in root cortex of V. faba ssp. minor seedlings.

Kinetin-induced programmed cell death, manifested by condensation, degradation and methylation of DNA and fluctuation of kinase activities and ATP levels, is an autolytic and root cortex cell-specific process. The last step of programmed cell death (PCD) induced by kinetin in the root cortex of V. faba ssp.

Global changes in DNA methylation in seeds and seedlings of Pyrus communis after seed desiccation and storage.

The effects of storage and deep desiccation on structural changes of DNA in orthodox seeds are poorly characterized. In this study we analyzed the 5-methylcytosine (m(5)C) global content of DNA isolated from seeds of common pear (Pyrus communis L.) that had been subjected to extreme desiccation, and the seedlings derived from these seeds.

Nucleic acid-based technologies in therapy of malignant gliomas.

Malignant gliomas are the deadliest brain tumors, which are characterized by highly invasive growth, a rampant genetic instability and intense resistance to apoptosis. Such an aggressive behavior of malignant gliomas is reflected in the resistance to chemo- and radiotherapy and weak prognosis in spite of cytoreduction through surgery. Brain tumors preferentially express a number of specific protein and RNA markers, that may be exploited as potential therapeutic targets in design of the new treatment modalities based on nucleic acids.

Global DNA methylation changes in blood of patients with essential hypertension.

Background: Hypertension is a common disease of the cardiovascular system and one of the main causes of mortality in the world. Its etiopathogenesis and molecular mechanisms are unknown. Epigenetic changes may play a role in its development.

Promising human brain tumors therapy with interference RNA intervention (iRNAi).

Glioblastoma multiforme (GBM) is the most common type of malignant gliomas, characterized by genetic instability, intratumoral histopathological variability and unpredictable clinical behavior. Disappointing results in the treatment of gliomas with surgery, radiation and chemotherapy have fuelled a search for new treatment modalities. Malignant gliomas express preferentially a number of surface markers that may be exploited as therapeutic targets, such as tenascin-C (TN-C), an extracellular matrix glycoprotein that contributes to tumor cell adhesion, invasion, migration and proliferation.

A new and efficient method for inhibition of RNA viruses by DNA interference.

We report here a new method for inhibition of RNA viruses induced by dsDNA. We demonstrated that both long dsDNA molecules and short interfering DNA with a sequence complementary to that of viral RNA inhibited tobacco mosaic virus expression and prevented virus spread. Also, the expression of the HIV-1 gp41 gene in HeLa cells was inhibited by complementary short interfering DNA.

A multivariate analysis of patients with brain tumors treated with ATN-RNA.

Glioblastoma multiforme (GBM) is the most common form of malignant glioma, characterized by genetic instability, intratumoral histopathological variability, and unpredictable clinical behavior. Malignant gliomas express preferentially a number of surface markers that may be exploited as therapeutic targets, such as tenascin-C, an extracellular matrix glycoprotein contributes to tumor cell adhesion, invasion, migration and proliferation. Disappointing results in the treatment of gliomas with surgery, radiation and chemotherapy have fuelled a search for new treatment modalities.

Highly active low magnesium hammerhead ribozyme.

Hammerhead (HH) ribozymes can be used for highly specific inhibition of gene expression through the degradation of target mRNA. In vitro experiments with minimal HH domains demonstrated that the efficiency of catalysis is highly dependent on concentration of magnesium ions. Optimal ion requirements for HH-catalysed RNA cleavage are far from these found in the cell.

The mechanism of acidic hydrolysis of esters explains the HDV ribozyme activity.

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.

Isoenergetic microarray mapping reveals differences in structure between tRNAiMet and tRNAmMet from Lupinus luteus.

Isoenergetic microarray mapping is shown to be an ideal method for probing subtle structural differences between initiator tRNA(i)(Met) and elongator tRNA(m)(Met) from Lupinus luteus. The differences in structure of both tRNAs cause significant dissimilarities in binding to microarrays probes.

Analysis of 5-methylcytosine in DNA of breast and colon cancer tissues.

5-methylcytosine (m(5)C) can be used as a sensitive marker of progress of the tumor formation induced by the oxidative damage reactions. We have analyzed the amount of m(5)C in DNA of patients with breast and colon cancers. Two dimensional thin layer chromatography (TLC) has been used to monitor 5-methylcytosine level in DNA extracted from cancer tissues.

TLC-based detection of methylated cytosine: application to aging epigenetics.

5-Methylcytosine (m(5)C) has a plethora of functions and roles in various biological processes including human diseases and aging. A TLC-based fast and simple method for quantitative determination of total genomic levels of m(5)C in DNA is described, which can be applicable to aging research with respect to rapid and high throughput screening and comparison. Using this method, an example of the analysis of global alternations of m(5)C in serially passaged human skin fibroblasts is provided, which shows age-related global hypomethylation during cellular aging in vitro.

High hydrostatic pressure approach proves RNA catalytic activity without magnesium.

High hydrostatic pressure (HHP) technique was used to evaluate a mechanism of RNA hydrolysis with RNA. We showed that hammerhead ribozyme specifically cleaves RNA substrate at HHP in the absence of Mg(2+). A deoxyribozyme "10-23" was active in the same conditions.

Leadzyme formed in vivo interferes with tobacco mosaic virus infection in Nicotiana tabacum.

We developed a new method for inhibiting tobacco mosaic virus infection in tobacco plants based on specific RNA hydrolysis induced by a leadzyme. We identified a leadzyme substrate target sequence in genomic tobacco mosaic virus RNA and designed a 16-mer oligoribonucleotide capable of forming a specific leadzyme motif with a five-nucleotide catalytic loop. The synthetic 16-mer RNA was applied with nontoxic, catalytic amount of lead to infected tobacco leaves.

Suppression of human brain tumor with interference RNA specific for tenascin-C.

Glioblastoma multiforme (GBM) accounts for approximately 12-15% of intracranial neoplasms. The GBM remains refractory to therapy because of tumor heterogeneity, local invasion, and non-uniform vascular permeability to drugs. Patients with GBM have the median survival of approximately 8-10 months, and for those cases where tumor recurs, the average time of tumor progression after therapy is only eight weeks.

Evaluation of the dynamic structure of DsrA RNA from E. coli and its functional consequences.

DsrA RNA is an 87-nucleotide regulatory non-protein-coding RNA of Escherichia coli for which two secondary structure models (I and II) have been proposed. We have compared these models by the energy calculations, which revealed that the currently accepted model II should be rejected on the basis of thermodynamics. Here we provide new results of nuclease footprinting analysis and the application of RNA technologies that have not previously been used for DsrA RNA structural studies, such as hydrolysis with RNase H, DNAzyme, hydroxyl radicals and lead.

[Riboswitches].

Riboswitches are RNA structures able to bind small molecules and regulate gene expression at both, transcriptional and translational level. They are present in a wide variety of bacterial species. In Bacillus subtilis more than 2% of the genome is regulated by riboswitches.

A new frontier for molecular medicine: noncoding RNAs.

It is now becoming evident that the variety of noncoding RNA (ncRNA) molecules play important roles in many cellular processes and they are not just mere intermediates in transfer of genetic information from DNA to proteins. Recent data, from the analyses of transcriptional activity of human genome, suggest that it may contain roughly equal numbers of protein- and RNA-encoding transcription units. Many of the ncRNAs described in humans as well as in other mammals have been linked, through specific chromosomal localization or expression patterns, with certain diseases including complex congenital syndromes, neurobehavioral and developmental disorders and cancer.

Lead toxicity through the leadzyme.

Lead is one of the most dangerous toxic agents for all living organisms. In humans, elevated levels of lead have been linked to a number of disorders for which various molecular mechanisms have been proposed. However, none of them has been fully understood.

A simple epigenetic method for the diagnosis and classification of brain tumors.

The new, simple, and reliable method for the diagnosis of brain tumors is described. It is based on a TLC quantitative determination of 5-methylcytosine (m(5)C) in relation to its damage products of DNA from tumor tissue. Currently, there is evidence that oxidative stress through reactive oxygen species (ROS) plays an important role in the etiology and progression of several human diseases.

5S rRNA is a leadzyme. A molecular basis for lead toxicity.

This paper reports that the D-loop sequence of cellular mammalian ribosomal 5S RNAs is a natural leadzyme that specifically binds and cleaves in trans other RNA molecules in the presence of lead. The D-loops of these 5S rRNAs are similar in sequence to the active site of the leadzyme derived from tRNA(Phe), which cleaves a single bond in cis. We have devised a 12 nt model substrate based on the leadzyme sequence cleaved in trans by a 12 nt RNA molecule containing of the D-loop sequence.