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Biomedical subjects

J Kypr

Publications and source records attributed to J Kypr.

At least 19 recordsLinked to original sources
PubMed1992

Nucleotide composition of genes and hydrophobicity of the encoded proteins.

We find that true proteins are generally more hydrophobic than the corresponding hypothetical proteins encoded by the randomized gene nucleotide sequences. Furthermore, the protein hydrophobicity but not its gene nucleotide composition is conserved within evolutionary families of functionally related proteins. These two findings indicate that there is a general drift to modify gene nucleotide composition in the course of evolution. An inspection of codon usage in genes shows that the drift mainly increases the content of adenine at the expense of thymine.

Adenosine↗
PubMed1992

Structures of poly(dA-dT, ip5dU) containing various small amounts of the antiherpetic 5-isopropyl-2'-deoxyuridine.

Three different concentrations of the antiherpetic agent 5-isopropyl-2'-deoxyuridine (ip5dU) were introduced into the synthetic DNA poly(dA-dT) to analyze resulting copolymers by electron microscopy, UV absorption and CD spectroscopy. The poly(dA-dT, ip5dU) containing 1.3 and 4.3% ip5dU did not much differ from the parent poly(dA-dT) but poly (dA-dT, ip5dU) with 7.1% ip5dU behaved in an unusual way. Results are explained by the notion that if bulky isopropyls occur sufficiently close to each other then stable hairpins protruding from the double helix are formed, presumably to accommodate the ip5dU-s into the loops.

Antiviral Agents↗
PubMed1992

Conformational transitions of poly(dA-bromo5dU) and poly(dA-iodo5dU) in solution.

Extensive circular dichroism studies have been conducted with the title polynucleotides under various solution conditions. The studies provided the following information: (i) The halogen atoms in place of thymine methyl hinder the isomerization into X-DNA. (ii) The brominated but not iodinated polynucleotide isomerizes into Z-DNA in concentrated NaCl+NiCl2. The transition takes place at lower NiCl2 concentrations than with poly(dA-dT). (iii) The iodinated polynucleotide forms an unusual conformation in aqueous solution in which it is very stable. It isomerizes from this conformer into the usual B-type double helix in concentrated ethanol solutions. The isomerization is a two-state cooperative process. (iv) Both title polynucleotides undergo still another two-state cooperative transition in trifluorethanol solutions presumably into A-DNA showing a rather unusual circular dichroism spectrum.

Circular Dichroism↗
PubMed1992

GLOBIC: a very fast microcomputer program for fingerprinting, characterization and comparison of long nucleotide sequences.

This paper describes the program GLOBIC, which compares, characterizes and fingerprints even 0.1 Mbase sequences in a few minutes with the aid of an IBM-AT microcomputer. Instead of the nucleotide sequences themselves, GLOBIC compares the local nucleotide or short oligonucleotide compositions. GLOBIC presents two-dimensional maps of contour lines depicting the similarity of two different sequences, a sequence compared to itself, to its complementary sequence or to a random sequence. A vocabulary is presented to translate the typical patterns appearing in the two-dimensional maps into their meanings as relationships between the compared sequences. The application of GLOBIC is demonstrated using several examples from the genomic nucleotide sequences of bacteriophage T7, adenovirus type-2 and Epstein-Barr virus.

Adenoviridae↗
PubMed1992

DNABIND: an interactive microcomputer program searching for nucleotide sequences that may code for conserved DNA-binding protein motifs.

This paper presents a simple program for interactive searching for nucleotide sequences that may code for the helix-turn-helix, zinc finger or leucine zipper motifs in proteins. The helix-turn-helix motifs are predicted using the recently published method of Dodd and Egan, while zinc fingers and leucine zippers are searched for by our original methods. DNABIND is shown to detect all four known helix-turn-helix motifs in bacteriophage lambda genes and both zinc fingers of the adr1 gene of yeast.

Algorithms↗
PubMed1991

Different intrastrand and interstrand contributions to stacking account for roll variations at the alternating purine-pyrimidine sequences in A-DNA and A-RNA.

An explanation is suggested for the roll alternation between low and high values in A-type nucleic acid duplexes containing alternating sequences of purine and pyrimidine residues. The explanation combines two points. (1) Roll inevitably occurs in A-type duplexes due to geometrical reasons. (2) Intrastrand base stacking is much more impaired by roll than interstrand base stacking in A-type duplexes. Therefore purine-pyrimidine steps, whose bases mainly exhibit an intrastrand stacking, resist roll and decrease it. By contrast, bases at pyrimidine-purine steps exhibit a significant interstrand stacking that is tolerant to roll in A-type nucleic acid duplexes. In consequence, it is favourable if the purine-pyrimidine and pyrimidine-purine steps adopt low and high rolls, respectively in A-conformations of DNA and RNA molecules containing alternating purine-pyrimidine sequences. This is actually observed in the relevant molecular crystal structures.

Base Composition↗
PubMed1991

Caesium fluoride-induced changes in the c.d. spectra of synthetic DNA fragments.

Ten DNA fragments containing self-complementary alternating sequences of adenine and thymine differing in length and the starting nucleotide were studied by c.d. spectroscopy. It was found that d(TATATATA) but not d(ATATATAT), d(TATATA), d(CTATATAG) or (dT-dA)20 isomerized into the unusual X-DNA double helix at molar concentrations of CsF in solution. But in contrast to poly(dA-dT), the octamer (dT-dA)4, isomerized very slowly, at relatively low CsF concentrations and the isomerization was strongly dependent on the octamer concentration. A model is proposed to account for the observed properties of the B-to-X isomerization on the oligomer level.

Adenine Nucleotides↗
PubMed1991

Destabilization of the duplex and the high-salt Z-form of poly(dG-methyl5dC) by substitution of ethyl for the 5-methyl group.

The B-to-Z conformational transition of poly(dG-dC) is highly promoted by 5-methyl substitution of the dC moiety, i.e. in poly(dG-methyl5dC). By the synthesis of a new poly(dG-dC) analogue, poly(dG-ethyl5dC), the effect of a longer alkyl-chain substituent of dC on structure and conformation has been studied with ultraviolet absorption melting profiles and circular dichroism spectroscopy. The 5-ethyl substituent in poly(dG-ethyl5dC) destabilizes the duplex structure against thermal denaturation compared with both poly(dG-methyl5dC) and poly(dG-dC). C.d. studies also reveal that for the high-salt B-Z transition of poly(dG-ethyl5dC) a higher NaCl concentration is required than for that of poly(dG-methyl5dC), although much lower than for poly(dG-dC). However low-salt Z-DNA in poly(dG-ethyl5dC) shows unique features, e.g. it needs no divalent cations to be stable. The low-salt B-Z transition of poly(dG-ethyl5dC) can also be observed by the absorption-temperature melting profile, in contrast to both poly(dG-methyl5dC) and poly(dG-dC). The effects of MgCl2 concentration, temperature, acid pH and trifluorethanol on the conformation of poly(dG-ethyl5dC) have also been determined.

Circular Dichroism↗
PubMed1991

Circular dichroism studies of salt- and alcohol- induced conformational changes in cyanophage S-2L DNA which contains amino 2 adenine instead of adenine.

DNA molecules containing AT pairs exhibit cesium cation specific conformational behavior. This specificity is shown to be cancelled with the title DNA, which not only concerns its conformational alterations in high-salt aqueous solutions but also the B-to-A transition induced by ethanol. S-2L DNA easily adopts the A-conformation in the presence of millimolar concentrations of CsCl which completely destabilize the A-conformation in calf thymus DNA. The present results demonstrate that the specific effects of cesium cations on DNA are connected with their binding to the AT pairs in the DNA minor groove.

Adenine↗
PubMed1991

Alkyl substituent in place of the thymine methyl group controls the A-X conformational bimorphism in poly(dA-dT).

Circular dichroism studies of a family of poly(dA-y5dU) polynucleotides (y = H, methyl, ethyl, propyl, butyl or pentyl) were conducted in water-alcohol solutions containing sodium or cesium counterions. The polynucleotides denatured or adopted A- or X-DNA double helices depending on the concentration and type of alcohol, type of counterions and the length of the aliphatic substituent in place of the thymine methyl group. Short aliphatic substituents and sodium cations favored A-DNA while long aliphatic substituents and cesium cations promoted X-DNA. This study demonstrates delicacy of the conformational equilibrium of poly(dA-dT) between the A- and X-DNA double helices which depends on both intramolecular and intermolecular factors.

Alkylation↗
PubMed1991

Propeller-twisted adenine.thymine and guanine.cytosine base pairs tend to buckle and stagger in opposite directions.

Base pairs are propeller-twisted, buckled and staggered in DNA fragment crystals. These deformations were analyzed with isolated Watson-Crick base pairs using empirical potentials and buckle was found to almost linearly correlate with propeller. Interestingly, the thymine.adenine pair favours negative buckling for propellers mostly observed in DNA crystals while positive buckling is preferred by the cytosine.guanine pair. The propeller also induces opposite staggers in the adenine.thymine and guanine.cytosine base pairs.

Base Composition↗
PubMed1991

Mutual backbone phosphate group interactions promote DNA double helix bending at high salt concentrations in solution.

Results of free energy calculations connected with the backbone phosphate group interactions upon local bending and helical twist modifications of A-, B- or Z-DNA at high salt concentrations have been reported recently (Jursa and Kypr 1990). Here we calculate energies necessary for DNA bending, using three models based on experimentally determined persistence length values. A comparison of energies following from the two quite different approaches suggests that high salt concentrations induce A- and mainly B-DNA bending into the double helix minor groove at least up to 10 degrees.

DNA↗
PubMed1990

CD of the synthetic RNA duplexes poly[r(A-T)] and poly[r(A-U)] in salt and ethanolic solutions.

Synthetic RNA poly[r(A-T)] has been synthesized and its CD spectral properties compared to those of poly[r(A-U)], poly[d(A-T)], and poly[d(A-U)] in various salt and ethanolic solutions. The CD spectra of poly[r(A-T)] in an aqueous buffer and of poly[d(A-T)] in 70.8% v/v ethanol are very similar, suggesting that they both adopt the same A conformation. On the other hand, the CD spectra of poly[r(A-T)] and of poly[r(A-U)] differ in aqueous, and even more so in ethanolic, solutions. We have recently observed a two-state salt-induced isomerization of poly[r(A-U)] into chiral condensates, perhaps of Z-RNA [M. Vorlícková, J. Kypr, and T. M. Jovin, (1988) Biopolymers 27, 351-354]. It is shown here that poly[r(A-T)] does not undergo this isomerization. Both the changes in secondary structure and tendency to aggregation are different for poly[r(A-T)] and poly[r(A-U)] in aqueous salt solutions. In most cases, the CD spectrum of poly[r(A-U)] shows little modification of its CD spectrum unless the polymer denatures or aggregates, whereas poly[r(A-T)] displays noncooperative alterations in its CD spectrum and a reduced tendency to aggregation. At high NaCl concentrations, poly[r(A-T)] and poly[r(A-U)] condense into psi(-) and psi(+) structures, respectively, indicating that the type of aggregation is dictated by the polynucleotide chemical structure and the corresponding differences in conformational properties.

Ammonium Chloride↗
PubMed1990

Replication, transcription and nuclease digestion of the unusual X-DNA double helix of poly(amino2dA-dT).

The alternating copolymer poly(amino2dA-dT) isomerizes into the unusual X-DNA double helix at low-salt aqueous conditions (Vorlicková et al., J. Biomolec. Struct. Dyn. 6, 503-510 (1988)). This observation allowed us to start studies on how the X-DNA is recognized, copied and hydrolyzed by various enzymes. In the present paper X-DNA replication, transcription and digestion by various polymerases and nucleases, respectively, are examined and compared to appropriate controls. It is found that X-DNA is a poor primer-template for DNA synthesis by the E. coli Klenow DNA polymerase (12% of the activity observed with B-DNA), the Micrococcus luteus DNA polymerase I (25%) and the AMV reverse transcriptase (51%). In contrast, X-DNA is a better template by 74% than B-DNA for calf thymus DNA polymerase alpha. For transcription by E. coli RNA polymerase enzyme poly(amino2dA-dT) did not serve as a template at all in either B or X conformation. Poly(amino2dA-dT) in its B form proved to be much more stable than poly(dA-dT) against hydrolysis by pancreatic DNase and snake venom phosphodiesterase. Formation of the X conformation in poly(amino2dA-dT) decreased this large difference in nuclease stability.

DNA Replication↗
PubMed1990

Base pair buckling can eliminate the interstrand purine clash at the CpG steps in B-DNA caused by the base pair propeller twisting.

Results of calculations using various empirical potentials suggest that base pair buckling, which commonly occurs in DNA crystal structures, is sufficient to eliminate the steric clash at CpG steps in B-DNA, originating from the base pair propeller twisting. The buckling is formed by an inclination of cytosines while deviations of guanines from a plane perpendicular to the double helix axis are unfavorable. The buckling is accompanied by an increased vertical separation of the base pair centers but the buckled arrangement of base pairs is at least as stable as when the vertical separation is normal and buckle zero. In addition, room is created by the increased vertical separation for the bases to propeller twist as is observed in DNA crystal structures. Further stabilization of base stacking is introduced into the buckled base pair arrangement by roll opening the base pairs into the double helix minor groove. The roll may lead to the double helix bending and liberation of guanines from the strictly perpendicular orientation to the double helix axis. The liberated guanines further contribute to the base pair buckling and stacking improvement. This work also suggests a characteristic very stable DNA structure promoted by nucleotide sequences in which runs of purines follow runs of pyrimidine bases.

Base Composition↗
PubMed1990

Mutual interactions of the phosphate groups in locally deformed backbones of various DNA double helices at high salt concentrations.

Changes in the free energy of mutual phosphate group interactions are calculated that accompany bending of the A-, B- and Z-DNA backbones in 0.7, 2.1 and 4.2 mol/l NaCl aqueous solutions. The bending is often found to be favoured in the direction of the double helix grooves; B-DNA prefers bending into the major groove while minor groove is the preferred bending direction of A-DNA in the presence of 0.7 mol/l NaCl. Interestingly, the preferences are reversed in 4.2 mol/l NaCl. Further stabilization of A-DNA and B-DNA backbones is achieved in some cases if bending is combined with suitable local double helix twist alterations. Bending tendencies of Z-DNA backbone are generally weaker and they decrease, in contrast to B-DNA and A-DNA, with the increasing ionic strength.

DNA↗