Nucleobase Recognition by Truncated α-Hemolysin Pores.

The α-hemolysin (αHL) protein nanopore has been investigated previously as a base detector for the strand sequencing of DNA and RNA. Recent findings have suggested that shorter pores might provide improved base discrimination. New work has also shown that truncated-barrel mutants (TBM) of αHL form functional pores in lipid bilayers. Therefore, we tested TBM pores for the ability to recognize bases in DNA strands immobilized within them. In the case of TBMΔ6, in which the barrel is shortened by ∼16 Å, one of the three recognition sites found in the wild-type pore, R1, was almost eliminated. With further mutagenesis (Met113 → Gly), R1 was completely removed, demonstrating that TBM pores can mediate sharpened recognition. Remarkably, a second mutant of TBMΔ6 (Met113 → Phe) was able to bind the positively charged ß-cyclodextrin, am7ßCD, unusually tightly, permitting the continuous recognition of individual nucleoside monophosphates, which would be required for exonuclease sequencing mediated by nanopore base identification.

Distribution properties of polymononucleotide repeats in molluscan genomes.

A total of 635 DNA sequences from 35 species of mollusks were used as taxonomic support to investigate several distribution features of polymononucleotides in genomic regions of different functionality. We show that all polymononucleotide types in mollusks fit to expectations in exons but not in nonexonic regions, in agreement with a leading role of negative selection on expansions/contractions of transcription-linked poly-(A/T) repeats. The fit of all repeat length types to an exponential decay precludes the existence of a threshold size for replication slippage, a popular but unsatisfactorily explained concept in mutation models for single repeats. The genomic density of poly-(A/T) repeats is not correlated with the DNA content of species, suggesting that the differential density of repeats between species could be better explained by the species-specific performance of its repair mechanisms. This research allows a better understanding of the distribution patterns of single repeats in eukaryotes.

Microanalysis of nucleic acids using the limulus G test.

The limulus G test has been used as a quantitative analysis of (1-->3)-beta-D-glucans, including schizophyllan (SPG) and curdlan. The present work extended the limulus G test to detect polynucleotide/SPG complexes. The complex showed an extremely sensitive response to the test, compared with SPG itself. The minimum concentration of the complex to show the response is almost 10-times as small as that of SPG itself, indicating the possibility to detect (1-->3)-beta-D-glucans or/and polynucleotides on the pico gram/ml scale.

Voltammetric determination of underivatized oligonucleotides on graphite electrodes based on their oxidation products.

A new electrochemical method to determine underivatized oligonucleotides is developed. The electro-oxidation of the adenine moieties of adsorbed oligonucleotides at elevated potentials on pyrolytic graphite electrodes (PGE) in neutral or alkaline media gives rise to electroactive products strongly adsorbed on the electrode surface. The extent of the redox processes of these products, with formal potential close to 0 V (vs Ag /AgCl) at pH 10, correlates well with the amount of parent oligonucleotide. Various electrochemical techniques have been compared and applied to the detection of specific DNA sequences and synthetic homopolynucleotides. Detection limits of 2 and 10 ng for (dA)20 and a 21-mer sequence of HIV-1, respectively, have been achieved using sample volumes of 10 microL. Moreover, the adsorbed oxidized oligonucleotide shows electrocatalytic activity toward the oxidation of NADH. The capability of the new method to detect DNA hybridization is discussed.

Plus-strand DNA synthesis of the yeast retrotransposon Ty1 is initiated at two sites, PPT1 next to the 3' LTR and PPT2 within the pol gene. PPT1 is sufficient for Ty1 transposition.

Long terminal repeat elements and retroviruses require primers for initiation of minus and plus-strand DNA synthesis by reverse transcriptase. Here we demonstrate genetically that plus-strand DNA synthesis of the yeast Ty1 element is initiated at two sites located at the 5' boundary of the 3' long terminal repeat (PPT1) and near the middle of the pol gene in the integrase coding sequence (PPT2). A consequence of the presence of two PPTs is that Ty1 plus-strand DNA exists as segments at some time during replication. Three fragments have been identified: the plus-strand strong-stop DNA initiated at PPT1, a downstream fragment initiated at PPT2 and an upstream fragment spanning the 5'-terminal part of Ty1 and a portion of the TyB gene. Characterization of the 3' ends of the plus-strand DNA fragments reveals (1) that the upstream fragment is elongated beyond PPT2 creating a plus-strand overlap and (2) that the majority of plus-strand strong-stop DNA fragments bear a copy of the minus-strand primer binding site in agreement with the accepted model of retroviral genomic RNA reverse transcription. The two polypurine tracts, PPT1 and PPT2, have an identical sequence GGGTGGTA. Mutations replacing purines by pyrimidines in this sequence significantly diminish or abolish initiation of plus-strand synthesis. Ty1 elements bearing a mutated PPT2 sequence are not defective for transposition whereas mutations in PPT1 abolish transposition.

Expression of acinar and ductal products in Capan-1 cells growing in synthetic serum and serum-free media.

BACKGROUND: Capan-1 is a human pancreatic adenocarcinoma cell line of presumed ductal origin. This is based on the histologic appearance of the tumor from which it arose. Yet considerable controversy exists regarding the actual cell of origin for these exocrine carcinomas. Two acinar antigens, ribonuclease and trypsin, were analyzed in cells growing in synthetic serum. METHODS: Capan-1 cells were adapted to grow in basal medium supplemented with synthetic serum, because fetal bovine serum (FBS) normally used to culture cells contains bovine ribonuclease, which can interfere with measurements of the ribonuclease secretion. These cells were also adapted to grow in different serum-free media, allowing us to determine its minimal growth requirements. The presence of ribonuclease in Capan-1 and PANC-1 conditioned media was monitored by activity. Other acinar and ductal markers were monitored using Northern blot analysis. RESULTS: Capan-1, PANC-1, IBF-CP3, and MDAAmp-7 cell lines were successfully adapted to grow in synthetic serum by means of the adaptation protocol reported here. The adaptation of Capan-1 to serum-free media showed that the cells are capable of growing in a medium containing insulin, transferrin, selenium, a nonprotein carrier, and lipoic and linoleic acids. Northern blot analysis showed the expression of carbonic anhydrase II, cytokeratin 18, ribonuclease, and trypsin in Capan-1 cells growing in FBS and synthetic serum. No changes in morphology, karyotype, or gene expression were observed in these cells as a result of the adaptation process. CONCLUSION: The cell line Capan-1 is expressing some ductal as well as acinar products despite its supposed ductal origin. The expression of trypsin at the mRNA level and ribonuclease at mRNA and protein levels is shown in Capan-1 cells. The protein expression will be further investigated as the cell line has been adapted to grow in synthetic serum and serum-free media with no apparent changes with respect to their growth in FBS.

Yeast telomere length varies in response to changes in the amount of polyC1-3A in the cell.

Yeast chromosomes terminate in a GC-rich tail of DNA. Previous investigations have shown that the length of this tail can change in response to genetic variation. Here we present data that show that the length can also alter in response to changes in the amount of the GC-rich DNA found elsewhere in the nucleus.

[Calorimetric study of the polyG-polyC complex]. / Kalorimetricheskoe issledovanie kompleksa poliG-poliTs.

Heat effects of polyG-polyC melting in neutral aqueous solutions have been measured using differential scanning microcalorimeter with an extended temperature range. The limiting value of melting enthalpy is 53 +/- 4 kJ per mole of base pairs and melting temperature dependence on the sodium concentration can be expressed by the empiric relation Tm = 13.2 log(Na+) + 420 K.

Implications for the formation of abasic sites following modification of polydeoxycytidylic acid by acrolein in vitro.

Polydeoxycytidylic acid (poly dC) was incubated with excess acrolein. A Nensorb 20 nucleic acid purification cartridge was used to bind the polymeric material in the poly dC/acrolein reaction mixture. The non-polymeric material eluted from this column had a UV absorbance four times higher than that of the control. The fluorescence spectrum of the eluted material did not correspond to that of unmodified cytosine. Separate aliquots of the reaction mixture were digested to deoxynucleotide 3'-monophosphates by incubation with micrococcal nuclease and spleen phosphodiesterase. The products were converted to 32P-labeled deoxynucleotide 3',5'-bisphosphates by incubation with T4 polynucleotide kinase and excess [gamma-32P]ATP. The 3'-monophosphate was selectively removed by incubation with nuclease P1. Two-dimensional thin-layer chromatography (TLC) on polyethyleneimine cellulose (PEI)-cellulose and detection of 32P-labeled deoxynucleotide 5'-monophosphates by autoradiography failed to provide evidence for the formation of an acrolein adduct of deoxycytidine 5'-monophosphate. When acrolein-modified deoxycytidine 3'-monophosphate was 32P post-labeled, a new product, which co-chromatographed with UV markers synthesized by reaction of acrolein with deoxycytidine 5'-monophosphate, was detected. These data show that acrolein-modified deoxycytidine 3'-monophosphates are substrates for 32P labeling by T4 polynucleotide kinase and are stable under the assay conditions employed. The inability to detect the acrolein-modified nucleotides after reaction with poly dC in vitro suggests that the modified bases are lost from poly dC by cleavage of the N-glycosyl bond resulting in the formation of an abasic site.

[Study of poly(C) and poly(I)-poly(C) complexes with model phospholipid membranes by infrared spectroscopy]. / Izuchenie kompleksov poly(C) i poly(I)-poly(C) s model'nymi fosfolipidnymi membranami metodom IK-spektroskopii.

The temperature dependence of poly(C) is shown by the infrared spectroscopy to be different for the free polynucleotide and for the polynucleotide in complexes with membranes. The intensity of stretching vibrations of C = 0 bond of poly(C) in the complex appears to be sensitive to the temperature. The intensity of this band is sharply decreased by increasing the temperature. This effect depends upon concentration of Mg2+-cations. Adsorption of poly(I)-poly(C) on the surface of vesicles from phosphatidylcholine results in the increase of the double helix.

Search for promoter sites of prokaryotic DNA using learning techniques.

Using learning techniques previously described in this journal, we have built an expert system able to point to the start DNA point of a sequence and therefore to recognize a promoter. However, to build this system, we have focused on the TATA box and its environment. We have used this expert system to look for new promoters and also to construct new promoters. The results obtained are discussed.

[Evaluation of the size of the continuous poly(G) site necessary for the biological activity of the poly(G).poly(C) complex]. / Otsenka razmera nepreryvnogo uchastka poli(G), neobkhodimogo dlia biologicheskoi aktivnosti kompleksa (G).poli(Ts).

On the basis of synthesis of a series of poly(G, A).poly(C) copolymers with changing G:A ratio from 15:1 to 90:1 and trials of their biological activity in comparison with poly(G).poly(C), the size of poly(G) in it was evaluated within the range of a continuous double-stranded area necessary for the activity. The antiviral activity close to that of poly(G).poly(C) in experimental tick-borne encephalitis of mice and vesicular stomatitis virus infection of chick embryo cells was found only in poly(G,A).poly(C) complexes with a G:A ratio equal to or higher than 90:1. Consequently, the high activity of poly(G).poly(C) is present at an average length of poly(G) equal to 90-100 nucleotides within the limits of the continuous double-stranded area.

Glutathione plus cytosol- and microsome-mediated binding of 1,2-dichloroethane to polynucleotides.

1,2-[1,2-14C]Dichloroethane was metabolized by rat hepatic microsomes to products that irreversibly bound polynucleotides. The polynucleotides were then enzymatically hydrolyzed and the products separated by a high-performance liquid chromatograph (HPLC) equipped with an ODS or a SCX column. The products of microsome-mediated binding were identified in the HPLC eluate as 1,N6-ethenoadenosine to polyadenylic acid, 3,N4-ethenocytidine to polycytidylic acid, and two cyclic derivatives to polyguanylic acid. 1,2-[1,2-14C]Dichloroethane was also metabolized in the presence of a glutathione (GSH)-cytosolic fraction and a polynucleotide. After enzymatic hydrolysis of the polynucleotide, the major peak of radioactivity was eluted from a Sephadex G-25 column in the salt volume which would exclude the presence of a product containing both GSH and a nucleoside. Chromatography by ODS-HPLC of the major peak from Sephadex G-25 indicated the presence of a GSH metabolite of 1,2-dichloroethane that did not contain a nucleoside. A similar hydrophilic peak was obtained for the hydrolysis products of polynucleotides from a glutathione plus cytosol incubation in which the polynucleotide instead of being added prior to the incubation was added after the incubation. The products of the glutathione plus cytosol metabolism of 1,2-[1,2-14]dichloroethane appear to be glutathione metabolites that coisolated with the polynucleotides rather than covalently bound adducts. In conclusion, covalently bound adducts were identified for microsome-mediated binding of 1,2-dichlorethane to polynucleotides, while no evidence was obtained for glutathione plus cytosol-mediated covalent binding to polynucleotides.

Genetic control of chromosome length in yeast.

The chromosomes of the yeast Saccharomyces cerevisiae terminate with sequences that have the form poly(C1-3-A). In this paper, we show that within an individual yeast strain all chromosomes end with tracts of poly(C1-3-A) of similar lengths; however, different strains can have tracts that vary in length by a factor of two. By a genetic analysis, we demonstrate that yeast cells have a mechanism that allows them to change rapidly the length of their chromosomes by altering the length of the poly(C1-3-A) tract.

Heterogeneity of the polyribocytidylic acid tract in aphthovirus: biochemical and biological studies of viruses carrying polyribocytidylic acid tracts of different lengths.

In this paper we report a study of a sample of foot-and-mouth disease virus carrying two polyribocytidylic acid [poly(C)] tracts of different lengths. By plaque purification in tissue culture, we isolated two populations of particles, one carrying the long poly(C) tract and the other carrying only the short homopolymer. The fingerprints of both viruses were indistinguishable from each other and from that of the virus present in the original sample, suggesting that the main difference between the two types of particles is limited to the poly(C) tracts of their genomic RNAs, to the flanking sequences of the poly(C) tract, or to both. In addition, some biological properties of these viruses are reported, such as stability upon serial passages in different cell lines, plaque size, and pathogenicity for cattle. The results indicate that the size of the poly(C) tract is not directly related to the virulence of these viruses. However, the size of the homopolymer could play a role in determining their efficiency of replication, and it appears that the particles with the short poly(C) tract might have some replicative advantage over those carrying the long one.

Electrochemistry of double-stranded complexes of synthetic polyribonucleotides having interferonogenic and antiviral activity.

Double-stranded (ds) complexes of poly(C) with poly(G) and poly(G,I) were studied using differential pulse polarography (DPP) and differential pulse voltammetry at a pyrolytic graphite electrode (DPV). The complex formed by copolymer was found to be DPP inactive. On the other hand, poly(G).poly(C) yielded a small DPP peak corresponding to single-stranded (ss) poly(C). It was suggested that ss poly(C) present in the solutions of poly(G).poly(C) appeared due to the existence of segments in poly(G) during the complex-forming process in which guanine residues were unable to be hydrogen-bonded with bases in poly(C). Polynucleotide complexes investigated in this report yielded a DPV peak corresponding to electrooxidation of guanine residues, which was markedly lower than that yielded by ss polymers. Moreover, this DPV peak yielded by the complex prepared from an equimolar mixture of poly(G) and poly(C) was still markedly higher than that yielded by poly(G,I).poly(C), or by poly(G).poly(C) prepared in the excess of poly(C). The lowering of the DPV peak was explained as being particularly due to the presence of the polynucleotide segments with an intact and regular secondary structure. The results of our electrochemical analysis of the complexes investigated were compared with their biological activity reported earlier. This comparison calls attention to the fact that biological effectiveness of these biopolymers may be dependent on details of their secondary structure which may be monitored using the methods of electrochemical analysis.

[Heterogeneity of the poly(C) tract of encephalomyocarditis virus RNA]. / Neodnorodnost' poly(C)-trakta RNK virusa éntsefalomiokardita.

The nucleotide sequence of the RNase T1-resistant fragment of encephalomyocarditis virus RNA that includes the poly(C) tract was determined by gel sequencing and mobility shift methods. This sequence is (5') AC126(127) UCUCUCUC9UAACG (3'). The results show that the poly(C) tract is discontinuous, i.e., it is interrupted by the UCUCUCU-sequence. The tract displays anomalously high mobility in polyacrylamide gels as compared to random polynucleotides, indicating that electrophoretic determination of its length gives underestimated values.

[DNA-binding proteins in human serum]. / DNK-sviazyvaiushchie belki syvorotki krovi cheloveka.

Fractions of acid and base blood serum proteins, separated by ion exchange chromatography on QAE-Sephadex (but not the proteins of the whole blood serum, which had the same charge), reacted with DNA preparations. Separate fractions of blood serum proteins were able to react with DNA after electrophoretic separation. Binding of blood serum proteins with DNA did not depend on ion strength within the range of NaCl concentration from 0.1 M to 0.5 M; it was also stable at pH 5.5 = 8.0. Interaction between acid DNA-binding proteins and native DNA was inhibited by denatured DNA, polyguanilic and polyinosinic acids and by other polyanions: dextran sulfate, polyvinyl sulfate, polyanetol sulphonate, polystyrol sulphonate and heparin. Acid DNA-binding proteins showed only a slight affinity to polyadenilic, polyuridilic and polycytidilic acids. The acid and base DNA-binding proteins appear to be contained in blood serum in the form of a loosely bound complex.

Characterization of Theiler's murine encephalomyelitis virus RNA.

Theiler's murine encephalomyelitis viruses are usually included in the enterovirus genus of the family Picornaviridae, although there is little physicochemical evidence to support this classification. In this report, the size of the RNA of highly virulent and less virulent representatives of the Theiler's group of viruses has been determined by sucrose gradient centrifugation and electrophoresis in agarose to be the same as that of other enteroviruses. The absence of a poly(C) residue provides evidence that these viruses are not cardioviruses or aphthoviruses. The base composition of the two members are similar to each other but differ from those of other enteroviruses. However the one- and two-dimensional maps of the ribonuclease T1 hydrolysates of the two virus RNAs show considerable differences despite their close serological similarity. Virus-specified RNA synthesis in cells infected with the more virulent strain of the virus was almost 10 times greater than that induced by the less virulent strain, in accord with the yields of virus particles.