Mini-ribozymes and freezing environment: a new scenario for the early RNA world

International audienceThe RNA World hypothesis states that the present-day life, which is based on DNA genomes and protein enzymes, was preceded by a simpler life form based primarily on RNA. During this era, the genetic information resided in the sequence of RNA molecules and the phenotype derived from the catalytic properties of RNA. Though it is a widely accepted scenario, a number of problems remain unsolved. One of the biggest questions is how complex RNAs could evolve, survive and replicate under typically assumed ''warm and wet'' conditions, taking into account that the RNA phosphodiester backbone is chemically unstable under these conditions. We suggest that prebiotic conditions associated with freezing could have been of key importance in the early RNA World, and discuss the role of primitive catalytic RNA in the evolution of RNA size and complexity

Biomedical journals and databases in Russia and Russian language in the former Soviet Union and beyond

In the 20th century, Russian biomedical science experienced a decline from the blossom of the early years to a drastic state. Through the first decades of the USSR, it was transformed to suit the ideological requirements of a totalitarian state and biased directives of communist leaders. Later, depressing economic conditions and isolation from the international research community further impeded its development. Contemporary Russia has inherited a system of medical education quite different from the west as well as counterproductive regulations for the allocation of research funding. The methodology of medical and epidemiological research in Russia is largely outdated. Epidemiology continues to focus on infectious disease and results of the best studies tend to be published in international periodicals. MEDLINE continues to be the best database to search for Russian biomedical publications, despite only a small proportion being indexed. The database of the Moscow Central Medical Library is the largest national database of medical periodicals, but does not provide abstracts and full subject heading codes, and it does not cover even the entire collection of the Library. New databases and catalogs (e.g. Panteleimon) that have appeared recently are incomplete and do not enable effective searching

Circulating microRNAs in lung cancer: prospects for diagnosis, prognosis, and prediction of antitumor treatment efficacy

The review considers the main techniques to extract microRNA (miRNA) from various biological fluids (in particular, the serum and plasma), approaches to the analysis of miRNA concentration and composition, and methods to normalize the results in data analyses. Advantages and drawbacks of the methods are described. Special attention is given to circulating miRNAs, which can be used as markers for minimally invasive diagnosis, prediction of antitumor treatment efficacy, and disease prognosis in lung cancer. The review discusses the prospects and limitations that arise as the clinical significance is evaluated for miRNAs as potential tumor markers and a better understanding is gained for the roles various miRNAs play in the pathogenesis of lung cancer

Circulating DNA-markers in lung cancer: changes in retrotrasposons methylation status in response therapy and during the post-treatment follow-up

Malignant cell transformation is accompanied by two processes of DNA methylation changes

Site-Selective Artificial Ribonucleases: Oligonucleotide Conjugates Containing Multiple Imidazole Residues in the Catalytic Domain

Design of site-selective artificial ribonucleases (aRNases) is one of the most challenging tasks in RNA targeting. Here, we designed and studied oligonucleotide-based aRNases containing multiple imidazole residues in the catalytic part and systematically varied structure of cleaving constructs. We demonstrated that the ribonuclease activity of the conjugates is strongly affected by the number of imidazole residues in the catalytic part, the length of a linker between the catalytic imidazole groups of the construct and the oligonucleotide, and the type of anchor group, connecting linker structure and the oligonucleotide. Molecular modeling of the most active aRNases showed that preferable orientation(s) of cleaving constructs strongly depend on the structure of the anchor group and length of the linker. The inclusion of deoxyribothymidine anchor group significantly reduced the probability of cleaving groups to locate near the cleavage site, presumably due to a stacking interaction with the neighbouring nucleotide residue. Altogether the obtained results show that dynamics factors play an important role in site-specific RNA cleavage. Remarkably high cleavage activity was displayed by the conjugates with the most flexible and extended cleaving construct, which presumably provides a better opportunity for imidazole residues to be correctly positioned in the vicinity of scissile phosphodiester bond

Dynamics of LINE-1 retrotransposon methylation levels in circulating DNA from lung cancer patients undergoing antitumor therapy

Malignant cell transformation is accompanied with abnormal DNA methylation, such as the hypermethylation of certain gene promoters and hypomethylation of retrotransposons. In particular, the hypomethylation of the human-specific family of LINE-1 retrotransposons was observed in lung cancer tissues. It is also known that the circulating DNA (cirDNA) of blood plasma and cell-surface-bound circulating DNA (csb-cirDNA) of cancer patients accumulate tumor-specific aberrantly methylated DNA fragments, which are currently considered to be valuable cancer markers. This work compares LINE-1 retrotransposon methylation patterns in cirDNA of 16 lung cancer patients before and after treatment. CirDNA was isolated from blood plasma, and csb-cirDNA fractions were obtained by successive elution with EDTA-containing phosphate buffered saline and trypsin. Concentrations of methylated LINE-1 region 1 copies (LINE-1-met) were assayed by real-time methylation-specific PCR. LINE-1 methylation levels were normalized to the concentration of LINE-1 region 2, which was independent of the methylation status (LINE-1-Ind). The concentrations of LINE-1-met and LINE-1-Ind in csb-cirDNA of lung cancer patients exhibited correlations before treatment (r = 0.54), after chemotherapy (r = 0.72), and after surgery (r = 0.83) (P 0.05, respectively). These results suggest a need for the further investigation of dynamic changes in levels of LINE-1 methylation depending on the antitumor therapy

Bulge-Forming miRNases Cleave Oncogenic miRNAs at the Central Loop Region in a Sequence-Specific Manner.

The selective degradation of disease-associated microRNA is promising for the development of new therapeutic approaches. In this study, we engineered a series of bulge-loop-forming oligonucleotides conjugated with catalytic peptide [(LeuArg)(2)Gly](2) (BC–miRNases) capable of recognizing and destroying oncogenic miR-17 and miR-21. The principle behind the design of BC–miRNase is the cleavage of miRNA at a three-nucleotide bulge loop that forms in the central loop region, which is essential for the biological competence of miRNA. A thorough study of mono- and bis-BC–miRNases (containing one or two catalytic peptides, respectively) revealed that: (i) the sequence of miRNA bulge loops and neighbouring motifs are of fundamental importance for efficient miRNA cleavage (i.e., motifs containing repeating pyrimidine–A bonds are more susceptible to cleavage); (ii) the incorporation of the second catalytic peptide in the same molecular scaffold increases the potency of BC–miRNase, providing a complete degradation of miR-17 within 72 h; (iii) the synergetic co-operation of BC–miRNases with RNase H accelerates the rate of miRNA catalytic cleavage by both the conjugate and the enzyme. Such synergy allows the rapid destruction of constantly emerging miRNA to maintain sufficient knockdown and achieve a desired therapeutic effect

Rapid sequence-independent cellular response to oligodeoxynucleotides

AbstractThe presence of receptors for oligodeoxynucleotides (OdN) on the surface of L929 cells has previously been described. To study the possible coupling of the receptor to cellular signal transducing systems, the effect of phosphodiester OdN of different sequences on cellular phospholipase C and protein kinase C (PKC) activities in L929 fibroblasts was studied. Treatment of cells with OdN induced an increase in 32P labeling of phosphatidic acid which was accompanied by a gradual decrease in diacylglycerol. These effects seem to be independent of the OdN sequence. PKC activity in membranes isolated from OdN-treated cells was found to be lower than that in membranes of control cells. SDS-PAGE of the 32P-labeled cellular proteins revealed that OdN treatment caused a decrease in phosphorylation of the 26 and 73 kDa cellular proteins in the cells