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L K Savinkova

Publications and source records attributed to L K Savinkova.

At least 19 recordsLinked to original sources
PubMed2000

Affinity labeling of RNA-polymerase II in the transcriptionally active complex by a phosphorylating analog of the initiation substrate.

Affinity modification of RNA-polymerase II by a phosphorylating analog of the initiation substrate carrying a zwitterionic 5;-terminal phosphate group with a 4-N,N-dimethylaminopyridine residue (DMAP-pA) was studied during specific transcription initiation controlled by the late adenoviral promotor. Super-selective affinity labeling and standard conditions of affinity modification resulted in labeling a polypeptide with molecular weight corresponding to that of the third subunit of the enzyme, RPB3 (45 kD). The initiation substrate (ATP) protects RNA-polymerase II from modification. The third subunit may be involved in the formation of the substrate-binding site of the enzyme.

4-Aminopyridine↗
PubMedDate not supplied

Identification of sequence-dependent DNA features correlating to activity of DNA sites interacting with proteins.

MOTIVATION: The commonly accepted statistical mechanical theory is now multiply confirmed by using the weight matrix methods successfully recognizing DNA sites binding regulatory proteins in prokaryotes. Nevertheless, the recent evaluation of weight matrix methods application for transcription factor binding site recognition in eukaryotes has unexpectedly revealed that the matrix scores correlate better to each other than to the activity of DNA sites interacting with proteins. This observation points out that molecular mechanisms of DNA/protein recognition are more complicated in eukaryotes than in prokaryotes. As the extra events in eukaryotes, the following processes may be considered: (i) competition between the proteins and nucleosome core particle for DNA sites binding these proteins and (ii) interaction between two synergetic/antagonist proteins recognizing a composed element compiled from two DNA sites binding these proteins. That is why identification of the sequence-dependent DNA features correlating with affinity magnitudes of DNA sites interacting with a protein can pinpoint the molecular event limiting this protein/DNA recognition machinery. RESULTS: An approach for predicting site activity based on its primary nucleotide sequence has been developed. The approach is realized in the computer system ACTIVITY, containing the databases on site activity and on conformational and physicochemical DNA/RNA parameters. By using the system ACTIVITY, an analysis of some sites was provided and the methods for predicting site activity were constructed. The methods developed are in good agreement with the experimental data. AVAILABILITY: The database ACTIVITY is available at http://wwwmgs.bionet.nsc.ru/systems/Activity/ and the mirror site, http://www.cbil.upenn.edu/mgs/systems/acti vity/.

Algorithms↗
PubMedDate not supplied

[Interaction of Escherichia coli RNA polymerase with eukaryotic TATA-binding protein].

Interaction with eukaryotic TATA-binding protein (TBP) was analyzed for natural Escherichia coli RNA polymerase or the recombinant holoenzyme, minimal enzyme, or its sigma subunit. Upon preincubation of full-sized RNA polymerase with TBP and further incubation with a constant amount of 32P-labeled phosphamide derivative of a TATA-containing oligodeoxyribonucleotide, the yield of the holoenzyme-oligonucleotide covalent complex decreased with increasing TBP concentration. This was considered as indirect evidence for complexing of RNA polymerase with TBP. In gel retardation assays, the holoenzyme, but neither minimal enzyme nor the sigma subunit, interacted with TPB, since the labeled probe formed complexes with both proteins in the reaction mixture combining TBP with the minimal enzyme or the sigma subunit. It was assumed that E. coli RNA polymerase is functionally similar to eukaryotic RNA polymerase II, and that the complete ensemble of all subunits is essential for the specific function of the holoenzyme.

Amino Acid Sequence↗
PubMedDate not supplied

[Interaction of proteins from general transcription complex RNA polymerase II with oligoribonucleotides].

We have analyzed an interaction of the general transcription complex RNA polymerase II proteins (RNA polymerase II, factors TBP, TFIIB, TFIIF, TFIIE and TFIIH) S. cerevisiae with the oligoribonucleotides. With the help of method EMSA was shown that labeled 32P labeled oligoribonucleotide 5'-ACUCUCUUCCGCAUCGC-3' (r-17) binds with the proteins and generates three species of the complexes with the three major shifts. All the three species of the complexes are RNA specific because a total RNA S. cerevisiae was a competitor for all three species but the TATA-containing oligodeoxyribonucleotide (500-fold molar excess) was not a competitor for its. Complexes 32P-r-17 with the proteins belonging to the middle shift are the sequence specific because unlabeled r-17 was a competitor for its binding (100-fold molar excess) but unlabeled UA-rich oligoribonucleotide (5'-AUAUUAUGUUCAAAA-3) was not a competitor for this shift (500-fold molar excess). Complexes belonging to the upper shift are RNA specific probably. We think 32P-r-17 interaction with the proteins belonging to the under shift is nonspecific corresponding to a sorbtion of 32P-r-17 on a protein. The data presented demonstrate that oligoribonucleotide and oligodeoxyribonucleotide don't compete for the binding sites on a basal transcription complex proteins.

Electrophoretic Mobility Shift Assay↗
PubMedDate not supplied

[Photoactivated analogues of the initiating substrates of RNA polymerase II based on arylazide derivatives of NTP gamma-amidophosphate: synthesis and chemical and photochemical reactions of functional groups].

Photoactivatable derivatives Ar-NH-(CH2)n-NHpppB (where Ar = p-azidophenyl (A1), 5-azido-2-nitrobenzoyl (A2), or 4-azido-2,3,5,6-tetrafluorobenzoyl (A3) group; B = Ado or Guo; n = 2, 3, or 4) were synthesized. The phosphoroamidate bond stability was found to depend on the structure of both the heterocyclic and the photoactivatable groups. The derivative with A3, Ado, and n=3 is hydrolyzed with regeneration of aryl azide and ATP, whereas the other derivatives are stable in aqueous solutions. The photoanalogues with A1 and A2, B = Ado, and n = 2 or 4 were found to behave as initiating substrates toward the RNA polymerase II from Saccharomyces cerevisiae under the conditions of specific transcription initiation and control of the adenovirus late promoter. The photolysis of N-(4-azidophenyl)-1,4-diaminobutane and N-(5-azido-2-nitrobenzoyl)-1,3-diaminopropane, two functional fragments of the photoaffinity reagents, in aqueous solutions was established to result in the formation of p-benzoquinone diimine and p-nitro-N-arylhydroxylamine derivatives, respectively. The arylhydroxylamine derivatives undergo a number of transformations in aqueous solution leading to nitroso derivatives. We concluded that it is these nitroso derivatives (products of nitrene transformation, rather than the nitrene itself) that may modify proteins with reagents containing p-nitrophenylazide fragment.

Adenosine Triphosphate↗
PubMedDate not supplied

[Binding of RNA-polymerase from Escherichia coli with oligodeoxyribonucleotides homologous to transcribed and non-transcribed DNA stands in the "-10"-promoter region of bacterial genes].

By using synthetic oligodeoxynucleotides related to the "-10" regions of spc and lacUV5 E. coli promoters we have shown, that the efficient binding occurs with oligodeoxynucleotides non-transcribed DNA strands. The duplexes containing oligodeoxynucleotides from the non-transcribed and transcribed DNA strands are also bound effectively by RNA polymerase. Oligodeoxynucleotides related to the non-transcribed DNA strands can effectively inhibit the RNA synthesis catalyzed by E. coli RNA polymerase. The data obtained allowed to consider the possible mechanism of selective binding of oligodeoxynucleotides by E. coli RNA polymerase and inhibition of the transcription.

Base Sequence↗
PubMedDate not supplied

[Selective binding of oligoribonucleotides by T7 phage induced RNA-polymerase].

It was shown previously that E. coli RNA-polymerase being incubated with the random oligonucleotide mixtures of definite length binds certain oligoribonucleotides with the length greater than or equal to 5 nucleotides. The data presented demonstrate that T7 phage induced RNA-polymerase (T7 RNA-polymerase) also binds selectively oligoribonucleotides beginning from pentaribonucleotides. From the random mixtures of penta-, hexa-, hepta-, octa-, nona- and decaribonucleotides the hepta- and octaribonucleotides are bound most efficiently. The T7 RNA-polymerase bound oligoribonucleotides can be completely extracted from the random mixture by the addition of the redundant enzyme amounts. As far as E. coli RNA-polymerase and T7 RNA-polymerase do not compete for the oligoribonucleotides the conclusion is made that they bind different oligoribonucleotides. The addition of the T7 DNA to the previously formed T7 RNA-polymerase--heptaribonucleotide complex competitively displace the heptaribonucleotides from the complex; the competitive effect of T4 DNA is very low. The data suggest that the oligoribonucleotides which are selectively bound by the RNA-polymerase are attached to the enzyme site responsible for the interaction with the promotor.

Coliphages↗
PubMedDate not supplied

[Formation of specific T3-RNA-polymerase complexes with oligoribonucleotides and inhibition of DNA-dependent RNA synthesis].

It was shown previously that E. coli RNA polymerase and T7 RNA polymerase being incubated with oligonucleotides of different length derived from RNA endonuclease hydrolysate bind selectively to certain oligonucleotides with the length larger than or equal to 5. The data presented demonstrate that T3 RNA polymerase also binds selectively from the isoplith mixtures certain oligonucleotides starting from pentanucleotides. Adding of excess of T3 RNA polymerase it was possible to exhaustively extract the recognizable oligonucleotides from the isoplith mixture. However, the exhausted by T3 RNA polymerase mixture of pentanucleotides still contained those which are bound selectively by T7 and E. coli RNA polymerases. The data suggest that various RNA-polymerases recognize different oligoribonucleotides. It was shown that T3 DNA inhibits the selective binding of penta-or heptaribonucleotides to T3 RNA polymerase competing obviously for the enzyme. The T3 RNA polymerase bound penta- or heptanucleotides inhibit DNA-dependent RNA synthesis carried out by the enzyme; the isoplith mixtures which do not contain T3 RNA polymerase bound oligonucleotides are deprived of the inhibitory properties. Only those isoplith mixtures contain T3 RNA polymerase bound oligonucleotides which were derived from symmetrically transcribed RNA which have obviously promoter simulating sequences. The data provide evidence that T2 RNA polymerase binds selectively the oligonucleotides mimicking the promotor recognition sites.

Binding Sites↗
PubMedDate not supplied

[Selective binding of oligodeoxyribonucleotides with Escherichia coli RNA-polymerase and their effect on DNA-dependent RNA synthesis].

It was shown previously, that E. coli RNA polymerase selectively binds certain fractions of oligoribonucleotides with the length greater than or equal to 5 nucleotides from the mixtures of random oligonucleotides of definite length. The data presented demonstrate, that E. coli RNA polymerase from the mixtures of random oligodeoxynucleotides of various length selectively binds oligodeoxynucleotides with the length greater than or equal to 9. The activity of the enzyme correlates with its ability to bind oligodeoxynucleotides. The enzyme which has selectively bound oligodeoxynucleotides, manifests sedimentation position characteristic for E. coli RNA polymerase engaged in transcription. The oligodeoxynucleotides with high affinity to the enzyme act as competitive inhibitors of transcription catalyzed by E. coli RNA polymerase. The data suggest that E. coli RNA polymerase bound oligodeoxynucleotides mimic the nucleotide sequences of the promoter responsible for the binding of the enzyme. It was found that selectively bound oligoribo - and oligodeoxynucleotides do not compete for the site on the enzyme. This property of E. coli RNA polymerase is assumed to play a certain role in the regulation of transcription.

Binding, Competitive↗
PubMedDate not supplied

[Interaction of Escherichia coli RNA polymerase with oligoribonucleotides, homologous to "10"- and "35"- segments of the SPC promotor of bacterial genes].

It was shown previously that E. coli RNA polymerase in a highly selective manner recognizes and binds 11-14-mere oligodeoxyribonucleotides related to the "-10" region of the nontranscribed DNA strand of bacterial gene promoters. The oligodeoxyribonucleotides cover the Pribnow box with flanking nucleotides up to the transcription start. These affinity oligodeoxyribonucleotides inhibit competitively the transcription of bacterial DNA carried out by E. coli RNA polymerase. The present work has demonstrated that E. coli RNA polymerase is not capable of binding the oligoribonucleotides homologous to the affinity oligodeoxyribonucleotides related to the "-10" area of the spc promoter, but binds the oligoribonucleotides which are complementary to the latter. The oligoribonucleotides with a high affinity for the E. coli RNA polymerase strongly inhibit transcription of the bacterial DNA. Attachment of alkylating groups to the 5'-ends of the affinity oligodeoxy- and oligoribonucleotides provides their covalent binding to the E. coli RNA polymerase subunits. It was shown that the modified affinity 32P-labelled oligodeoxyribonucleotide is covalently bound to the sigma-subunit while the modified affinity 32P-labelled oligoribonucleotide is covalently bound to the beta'beta-subunits of the E. coli RNA polymerase. It is suggested that the affinity oligoribonucleotides can be transcribed from the non-transcribed DNA strand in the region of the open complex and functions presumably as a primer which is splitted later from the nascent RNA or as a regulator of transcription.

Base Sequence↗
PubMedDate not supplied

[Conditions for specific oligoribonucleotide binding with E. coli RNA-polymerase].

RNA polymerase of E. coli (EC 2.7.7.6) is able to bind certain oligoribonucleotides with the length greater than or equal to 5 from the corresponding isoplith mixtures (Knorre V.L., Vasilenko S.V., Salganik R.I., FEBS Letters 30, 229, 1973). It has been shown in this study that all pentaribonucleotides able to be bound by RNA polymerase can be extracted from the random mixture by the enzyme saturation procedure. Loosely and tightly bound pentaribonucleotides subfractions were isolated and each was separated by chromatography into 3-4 isopliths. Blocking of the enzyme SH groups by p-chloromercurium benzoate (10(-3) M) and denaturation by urea (6.3 M) prevent formation of the enzyme-pentaribonucleotides complexes. Complexes are destroyed by heat denaturation. Removal of sigma-subunit does not influence the enzyme capacity for pentaribonucleotides binding.

Catalysis↗