Poly[d(A-T)-Cs+] conformations studied by IR spectroscopy.
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Nucleic Acid Conformation↗
Biomedical subjects
J Liquier
Publications and source records attributed to J Liquier.
Z form of poly d(A-T).poly d(A-T) in solution studied by CD and UV spectroscopies.
Near UV CD spectra, UV absorption spectra and their first derivatives have been recorded on poly d(A-T).poly d(A-T) solutions in presence of high NaCl concentration and various amounts of NiCl2. Comparison of the results presented here with those obtained for poly d(G-C).poly d(G-C) and poly d(A-C).poly d(G-T) in comparable conditions, and the I.R. and Raman data on poly d(A-T).poly d(A-T), allows us to assign the new spectra to the Z conformation of poly d(A-T).poly d(A-T) in solution. The mechanism by which nickel ions induce the B----Z interconversion in the presence of high NaCl concentration is discussed.
Circular Dichroism↗
Right- and left-handed helixes of poly[d(A-T)].poly[d(A-T)] investigated by infrared spectroscopy.
The secondary structures of double-stranded poly[d(A-T)].poly[d(A-T)] in films have been studied by IR spectroscopy with three different counterions (Na+, Cs+, and Ni2+) and a wide variety of water content conditions (relative humidity between 100 and 47%). In addition to the A-, B-, C-, and D-form spectra, a new IR spectrum has been obtained in the presence of nickel ions. The IR spectra of Ni2+-poly[d(A-T)].poly[d(A-T)] films are analyzed by comparison with previously assigned IR spectra of left-handed poly[d(G-C)].poly[d(G-C)] and poly[d(A-C)].poly[d(G-T)], and it is possible to conclude that they reflect a Z-type structure for poly[d(A-T)].poly[d(A-T)]. The Z conformation has been favored by the high polynucleotide concentration, by the low water content of the films, and by specific interactions of the transition metal ions with the purine bases stabilized in a syn conformation. A structuration of the water hydration molecules around the double-stranded Ni2+-poly[d(A-T)].poly[d(A-T)] is shown by the presence of a strong sharp water band at 1615 cm-1.
Nucleic Acid Conformation↗
Interaction of transition metal ions with Z form poly d(A-C).poly d(G-T) and poly d(A-T) studied by I.R. spectroscopy.
Interactions between Ni2+, Co2+ and purine bases have been studied by I.R. spectroscopy in the case of double stranded regularly alternating purine-pyrimidine polynucleotides poly d(A-T), poly d(A-C).poly d(G-T) and poly d(G-C). The spectra of polynucleotide films have been recorded in hydration and salt content conditions which correspond to the obtention of the classical right-handed (A,B) and left-handed (Z) helical conformations. Selective deuteration of the 8C site of purines has been obtained and is used to detect interactions between the transition metal ions and the adenine or guanine bases. The spectral region between 1500 and 1250 cm-1 corresponding to base in-plane vibrations and involving also the glycosidic linkage torsion is discussed in detail. The selective interaction between the transition metal ion and the 7N site of the purine base is considered to be partly responsible for the stabilization of the base in a syn conformation, which favours the adoption by the polynucleotide (poly d(G-C), poly d(A-C).poly d(G-T) or poly d(A-T)) of a Z type conformation.
Cobalt↗
Left-handed helical structure of poly[d(A-C)].poly[d(G-T)] studied by infrared spectroscopy.
Infrared spectroscopic studies demonstrate the ability of poly[d(A-C)].poly[d(G-T)] to adopt a Z-type conformation. The Z form of the unmodified polynucleotide is induced by Ni2+ counterions and not by Na+. The B----Z equilibrium is shifted at room temperature, in the presence of 1 Ni2+/nucleotide, by an increase in the concentration of poly[d(A-C)].poly[d(G-T)]. The importance of specific binding of Ni2+ ions on the N7 site of purines in the stabilization of the Z form is also discussed.
Cations↗
Role of the protein alpha helixes in histone-DNA interactions studied by vibrational spectroscopy.
The localization of structurally important histone-DNA interactions has been investigated by vibrational spectroscopy. Histones H2A, H2B, and H4 and their fragments (H2A, 1-56, 1-89, 73-129; H2B, 1-59, 1-83; H4, 1-53, 1-67, 1-84, 69-84, 85-102) have been prepared, characterized, and used to reconstitute protein-DNA complexes. Evidence is given for the existence of a direct relationship between the presence of ordered alpha-helical structures in the histones and a stabilization of the DNA in a B geometry. Infrared linear and ultraviolet dichroism measurements indicate that the N-terminal fragments, rich in basic residues and mostly in a random conformation, remain without any influence on the secondary structure of the nucleic acid, leaving it free in the complexes to undergo a total B----A conformational transition. On the contrary, histone fragments that involve some alpha-helical parts of the protein partially stabilize the DNA in a B geometry. Histone fragments that contain all of the alpha helixes of the protein block the DNA in the same way as the whole corresponding histone. A model for histone-DNA interactions in the core particle is discussed.
Amino Acids↗
Interaction of Z form poly(dG-dC).poly(dG-dC) with divalent metal ions: localization of the binding sites by I.R. spectroscopy.
The secondary structures of poly(dG-dC).poly(dG-dC) in the presence of alcaline , alcaline earth and first row transition metal ions (Na+, Mg2+, Co2+, Ni2+) are investigated by infrared spectroscopy. The conformational transitions are studied as a function of the hydration of the polynucleotide and counter-ion nature and content. The use of selectively deuterated poly(dG-dC).poly(dG-dC) on the 8-carbon of guanines allows to show that a direct interaction occurs between the N7 site of guanines and the transition metal ions Co2+ and Ni2+. In the case of Mg2+, for high ion/nucleotide ratios, the interaction occurs essentially at the level of the phosphate groups. This interaction leads to a modification of the left-handed conformation. Based on the IR spectroscopy results, an explanation is proposed for the different efficiencies of these various ions to induce the B----Z transition.
Cations, Divalent↗
Z-form induction in DNA by carcinogenic nickel compounds: an optical spectroscopy study.
The B----Z conformational transition of double-stranded poly(dG-dC) induced by various nickel salts (chloride, sulfate, subsulfide, carbonate) has been studied by ultraviolet absorption and circular dichroism. The spectra of the nickel compounds, both free and complexed with DNA, have been obtained in the visible and near infrared regions. In all cases the nickel adopts the hexacoordinated ionic form [Ni(H2O6]2+ and induces the B----Z transition of the nucleic acid at submillimolar concentrations (typically 0.4 mM). The addition to the poly(dG-dC)-poly(dG-dC) of an antitumoral drug, pentaziridinocyclodiphosphathiazene (SOAz), inhibits the B----Z transition even at a ten-fold higher nickel concentration (4 mM). Possible implications for carcinogenesis are discussed.
Antineoplastic Agents↗
In vitro recognition of DNA base pairs by histones in histone-DNA complexes and reconstituted core particles: an ultraviolet resonance Raman study.
Resonance Raman spectra of complexes between DNA and the four core histones, alone or associated, have been investigated in vitro using excitations at 300 and 257 nm, which give complementary informations about the DNA bases. H2A and H2B fractions recognize the G-C base pairs, while H3 and H4 (arginine rich fractions) recognize the A-T base pairs. The associated fractions form complexes with DNA which yield about the same DNA spectral modifications as the DNA-H4 complexes. This reveals the important role of the arginine rich fractions in the core particle formation and confirms the preferential in vitro assembly of nucleosome cores on A-T rich regions of DNA (25).
Animals↗
Site and role of the N-terminal fragment of the nucleosomal core histones in their binding to deoxyribonucleic acid as determined by vibrational spectroscopy.
The site and role of the binding of the 1-53 N-terminal part of H4 on DNA have been studied by optical spectroscopy. The structure of the 1-53 H4 fragment determined by vacuum ultraviolet circular dichroism and infrared spectroscopy is essentially aperiodic. The site of the interacion between the fragment and free DNA is localized by Raman laser spectroscopy in the small groove of the DNA, similar to the interaction site of the whole histone with DNA in nucleosomes. Infrared linear dichroism measurements show that the two 1-53 and 54-102 H4 fragments play a very important role in the histone-DNA interactions, but the roles are extremely different: the N-terminal part of the histone remains effectless on the DNA conformational flexibility and it is proposed that the structurally important interaction occurs between the globular part of the histone and the DNA. The N-terminal fragment appears to be responsible for finding the correct place on the DNA of the nucleosomal core particles.
Amino Acid Sequence↗
Particular structural role of H1 in complexes with DNA and comparison with H2A- and H4-DNA complexes investigated by IR linear dichroism.
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Chemical Phenomena↗
Conformation of DNA in chromatin protein-DNA complexes studied by infrared spectroscopy.
The following observations concerning the DNA secondary structures in various nucleohistone complexes were made by infrared spectroscopy: 1/ in chromatin, chromatin extracted by 0.6 M NaCl, nucleosomes, and histone-DNA reconstituted complexes, the DNA remains in a B type conformation at low relative hygrometry; 2/ in chromatin extracted by tRNA and in non histone protein-DNA reconstituted complexes, the DNA can adopt an A type conformation. Infrared linear dichroism data show that in NHP-DNA complexes the low relative hygrometry conformation of DNA may be modified and that the infrared parameter -1090 is close to that measured for RNA's or DNA-RNA hybrids. It is concluded that the histones block the DNA in a B form and that some of the NHP could be involved in the control of the secondary structure of DNA in chromatin.
Animals↗
Infrared linear dichroism investigations of deoxyribonucleic complexes with histones H2B and H3.
Complexes between DNA and histones H2B and H3 were studies by means of infrared linear dichroism in a wide range of histone to DNA ratios and of different relative humidities. The measurement of the dichroic ratios allows one to determine the secondary structure of DNA in the complexes. It is shown that the progressive addition of histone H2B or H3 to DNA inhibits the structural B leads to A transition and DNA remains in a B-type form at low relative humidity. A new simple method is proposed to evaluate the amount of A or B forms of DNA when both structures are present. It is found that the B leads to A transition is fully inhibited when only one molecule of H2B or H3 histone is bound per about three or four turns of DNA helix, respectively. It is proposed that about four to three turns of DNA helix represent the "critical length of DNA" (minimum "cooperative unit") for the B leads to A transition.
Animals↗
Infrared linear dichroism investigations of deoxyribonucleic acid complexes with poly(L-arginine) and poly(L-lysine).
Complexes between DNAs from various sources and poly(L-lysine) and poly(L-arginine) were studied by means of infrared linear dichroism. The measurements of dichroic ratios allowed us to determine the orientation of the phosphate group of DNA in the complexes with basic polypeptides. At high relative humidities (higher than 90%, B form), the bisector of the less than OPO in the complexes forms an angle with respect to the helical axis which has a value lower by about 4 degrees than in the corresponding DNA sample. This change of orientation of the phosphate group of DNA indicates a modification of the B form upon binding of polylysine or polyarginine. The structural transitions B leads to A and B leads to C measured as a function of relative humidities were not affected by formation of complexes with both basic polypeptides. Similar results were obtained for complexes prepared by direct mixing or by salt gradient dialysis. The presence of A and C forms was observed in complexes of DNA with poly(L-lysine) and poly(L-arginine) at lower relative humidity. Thus, the conformational flexibility of DNA in complexes with polylysine and polyarginine is not changed despite a substantial increase in the Tm (melting temperature). These results are considered as a model for the understanding of interactions between DNA and histones particularly of the binding of the N-terminal fragment, lysine or arginine rich.
Arginine↗
Structural transitions in DNAs and nucleohistones studied by I.R. spectroscopy.
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Animals↗
Spectroscopic studies of conformational transitions in double stranded DNAs in the presence of carcinogenic nickel compounds and an antitumoral drug (SOAZ).
The influence of an antitumoral drug, the pentaziridinocyclodiphosphatiazene (SOAZ), on the right----left-handed helix conformational transition of Poly (dG-dC). Poly (dG-dC) induced by carcinogenic or mutagenic Nickel compounds has been studied by ultraviolet absorbance and circular dichroïsm measurements. The B----Z transition of the polynucleotide is induced in two steps, in a similar way whatever the origin of the Nickel ions (NiCl2, NiSO4, Ni3S2, NiCO3). The midpoint of the second step (right----left-transition) is located around 0.4 mM Ni2+. The addition of SOAZ to the Poly (dG-dC). Poly (dG-dC) modifies this transition which is shifted to 2 mM Ni2+ for a 1 SOAZ/10 DNA phosphates ratio. The right-handed helix is stabilized and for a 1.5 SOAZ/phosphate ratio no B----Z transition is observed even for a tenfold amount of added Nickel (4 mM Ni2+). The addition of SOAZ to the DNA initially converted to a Z conformation by the presence of Nickel inhibits the return to the B form.
Antineoplastic Agents↗
[Specificity of DNA-peptide and DNA-histone interactions in ultraviolet Raman resonance spectroscopy].
Resonance Raman spectra of complexes between DNA and peptides on one hand, DNA and histones on the other, were obtained. Our work has clearly shown a DNA-base recognition by various protides. The basic residues selectively modify the environment of DNA bases: G-C bases for the lysine residues, A-T bases for the arginine residues, wether the residues are alone or included in a protein. This selectivity of interaction has allowed us to confirm the particular role played by H4 in the structure of nucleosomes and specially of the arginine residues.
DNA↗