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F Quadrifoglio

Publications and source records attributed to F Quadrifoglio.

At least 55 records · Page 3Linked to original sources
PubMed1988

The duplex-hairpin conformational transition of d(CGCGCGATCGCGCG) and d(CGCGCGTACGCGCG): a thermodynamic and kinetic study.

We have studied the duplex-hairpin conformational transition in two perfectly palindromic sequences, d(CGCGCGATCGCGCG)(I) and d(CGCGCGTACGCGCG)(II), by means of UV-melting, electrophoretic and T-jump experiments. Both tetradecamers exhibit biphasic thermal profiles. The lower temperature transition is concentration dependent whereas the higher temperature transition is not. The former transition has been characterized by gel electrophoresis and shows two distinct bands, whose intensity depends on temperature. This behavior is due to the occurrence of a slow premelting interconversion between the duplex and hairpin forms in both tetradecamers. The kinetics of hairpin formation from the duplex is studied by T-jump experiments. Relaxation spectra are well reproduced by a single relaxation time with rate constants characterized by a high temperature coefficient. In 10 mM NaCl, the duplex-hairpin conversion of I is characterized by an apparent activation energy of 96 +/- 6 kcal/mol, a value rather close to the expected denaturation enthalpy. In 1 mM NaCl a value slightly lower has been obtained. The rate of duplex-hairpin interconversion has been found to decrease as the salt concentration is raised. These data suggest that the transformation from the duplex to the hairpin form should imply a transition state with a simultaneous breaking of most base pairs, if not total strand separation.

Base Sequence↗
PubMed1987

Base specificity in the interaction of ethidium with synthetic polyribonucleotides.

Base specificity in the interaction of ethidium with double stranded synthetic RNA homopolymers has been studied by means of spectroscopic (UV-visible absorption and fluorescence), microcalorimetric and dilatometric techniques. The results show a strong base specificity in this interaction, the association constant with poly A:poly U being more than three order of magnitude higher than with poly O:poly C. The interaction is mainly enthalpy driven, the differences in affinity being essentially entropic in origin. These evidences along with the dilatometric data suggest that the observed base specificity may arise from the different extent of water release upon intercalation.

Ethidium↗
PubMed1987

dC-dG alternating oligonucleotides: thermodynamic and kinetic aspects of the B-Z transformation.

The alternating cytosine-guanine oligodeoxyribonucleotides (dCdG)n, (dGdC)n, (dCdG)ndC (n = 3,4), (dGdC)7 and dG(dCdG)3 have been studied by UV and CD spectroscopy at different temperatures and NaCl concentrations. The analysis of the melting data, assuming an all-or-none model, reveals that in the B-conformation the 5'G/C3' stacking interactions are enthalpically favoured with respect to the 5'C/G3' one. The CD investigation of the B-Z equilibrium shows that the Z-conformation is enthalpically stabilized, while the B-conformation is entropically favoured, in the range of NaCl concentration considered (1 to 5 M). The kinetic data for the B-Z transformation, obtained with a salt-jump technique for the hexamer (dCdG)3, support a mechanism by which the Watson-Crick hydrogen bonds are broken before the bases flip over separately and eventually stack, reforming the H-bonds, in the new helix.

Base Sequence↗
PubMed1986

Thermodynamic behaviour of the heptadecadeoxynucleotide d(CGCGCGTTTTTCGCGCG) forming B and Z hairpins in aqueous solution.

UV and CD data of the partially self-complementary heptadecadeoxynucleotide d(CGCGCGTTTTTCGCGCG), obtained as a function of temperature, salt and strand concentration, show that: at low NaCl and strand concentration the oligomer exhibits, on increasing the temperature, a biphasic thermal profile which is indicative of two structural transitions, from dimeric duplex to hairpin and from hairpin to coil; the loop stabilizes enthalpically both B and Z hairpin structures with respect to the corresponding unconstrained hexamer d(CGCGCG) by a few Kcal/mol; the oligomer undergoes a B-Z transition which appears to be complete, at 0 degree C, when induced by NaClO4; by contrast the B-Z transition induced by NaCl does not reach completeness even at salt saturation. The independence of the denaturation temperature, at high salt conditions, on the oligomer concentration indicates that the Z structure is present also in the hairpin.

Circular Dichroism↗
PubMed1986

Biochemical and biological activity of the anthracycline analog, 4-demethyl-6-O-methyl-doxorubicin.

The chromophore-modified derivative of doxorubicin, 4-demethyl-6-O-methyl-doxorubicin, has been tested for antitumor activity in a range of experimental murine tumor systems. In contrast to the inactive 6-O-methyl derivative of daunorubicin, 4-demethyl-6-O-methyl-doxorubicin provided antitumor effects comparable to that of the parent compound. In addition, detailed DNA-interaction studies showed that the doxorubicin derivative retains the ability to bind DNA by the intercalation mechanism. However, the binding affinity was appreciably reduced following structural modification in the anthraquinone chromophore. On the basis of the proposed models of intercalation, these results could be rationalized in terms of steric influence of the bulky methoxy group. The results of this study are in agreement with the correlation already observed between DNA binding and relative antitumor activity of anthracyclines.

Animals↗
PubMed1985

Interaction of DAPI with double-stranded ribonucleic acids.

The interaction of DAPI with natural and synthetic double-stranded polyribonucleotides was studied with different optical and calorimetric methods. The results were similar to those obtained previously with double-stranded polydeoxynucleotides, i.e. two interaction modes, the first of which shows high affinity for AU clusters and consequent strong fluorescence enhancement. The results suggest caution in the use of DAPI as selective fluorescent staining agent for DNA in the presence of RNA. A narrow groove binding model with hydrogen bonds between DAPI and AU pairs is proposed. An intercalation mechanism can be excluded because of the non planarity of DAPI molecule.

Calorimetry↗
PubMed1984

Short oligodeoxynucleotides with d(G-C)n sequence do not assume left-handed conformation in high salt conditions.

d(G-C)n oligodeoxynucleotides (with n varying from 3 to 7) were studied by the circular dichroism technique in 5 M-NaCl. Contrary to what was previously found with the d(C-G)n series in the same solvent, the left-handed double-stranded Z-conformation appears less stable than the B-form for low n values. The influence of base sequence on the relative stability of B- and Z-conformations for the two series is discussed.

Base Sequence↗
PubMed1983

Interaction of diamidino-2-phenylindole (DAPI) with natural and synthetic nucleic acids.

The interaction of DAPI with natural and synthetic polydeoxynucleotides of different base content and sequences was studied with circular dichroism, ultracentrifugation, viscosity and calorimetry. All the polymers show two types of binding. The strength of the interaction and its resistance to ionic strength are related to the content of AT clusters in the chain. On the other hand, sedimentation measurements rule out an intercalation mechanism. A model of DAPI interaction with DNA, similar to that displayed by distamycin and netropsin, is proposed.

Animals↗
PubMed1982

Simultaneous stability of short alternating Z and B helices in synthetic DNA concatamers.

The conformation of d(TA)3 (CG)3 has been studied in aqueous solution in the presence of high salt concentration. The oligonucleotide forms in solution concatamers. In the presence of 5 M NaC1 the concatamer is built up of d(CG)3 blocks in Z-conformation and of d(TA)3 blocks in B-conformation. In the presence of 4 M LiCl both blocks in the concatamer display a B-type structure.

Circular Dichroism↗
PubMed1981

Conformational stability of alternating d (CG) oligomers in high salt solution.

The conformation of d (CG)n oligomers with n = 2,3 has been studied in aqueous solution in the presence of high salt concentration. A minimum n value of three is necessary to obtain a left-handed Z-helix. When d (CG)3 is flanked by three non Z-helicogenic alternating AT sequences the left-handed helix is unstable and a B-type conformation is obtained also at high salt concentration.

Chlorides↗
PubMed1980

Fluorescence of buried tyrosine residues in proteins.

Histone H1 contains only one tyrosine and no tryptophan. The intrinsic fluorescence of the tyrosine rises by about 400% as the protein folds from a random coil to a globular structure (Giancotti, V., Fonda, M. and Crane-Robinson, C. (1977) Biophys. Chem. 6, 379-383). Measurements of external quenching by a large variety of quenchers shows very much reduced quenching in the folded state as compared to the disordered. It is concluded that the tyrosine is a buried residue. This is supported by the observation that the fluorescence of modified amino-tyrosyl H1 is similar to that of buried tyrosines in ribonuclease. The classification of tyrosine fluorescence in tryptophan-free proteins (Cowgill, R.W. (1976) in Biochemical Fluorescence Concepts, Vol. 2 to include the case of residues buried in a hydrophobic environment and having a relative quantum yield RTyr, greater than unity.

Animals↗
PubMed1977

The interaction of adriamycin and its beta anomer with DNA.

The results of thermal denaturation, fluorescence, calorimetric and viscosimetric studies on the interaction of adriamycin and its beta anomer with DNA are reported. Whereas all equilibrium, hydrodynamic and thermodynamic measurements are consistent with the proposed intercalative binding model for the adriamycin-DNA complex, the binding mechanism for the reaction of the beta anomer with DNA remains uncertaian. All DNA binding properties of this stereoisomer are substantially different from those of the parent compound. The results suggest that the amino sugar residue of the natural antibiotic may interact stero-specifically with the DNA helix, thus dictating the orientation of the tetracvclic chromophore within the intercalation site. The alteration in the DNA binding capacity and the changes in interactions with DNA following in inversion of configuration at C-1', parallel a lack of biological activity observed for the beta anomer.

Binding Sites↗