Biomedical subjects

G Albiser

Publications and source records attributed to G Albiser.

At least 19 recordsLinked to original sources

PubMed2001

The A--B transition: temperature and base composition effects on hydration of DNA.

Natural DNAs and some polynucleotides organised in fiber present the A--B form transition at a relative humidity (r.h.) which depends on the temperature. A shift of the midpoint of that helix--helix transition to higher r.h. values is observed when the temperature is risen. It is shown that the average number of water molecules associated to a nucleotide pair is the relevant parameter for the A-B transition and that this parameter can be given a precise value by a combination of different r.h. and temperature values. The minimum number of water molecules necessary to get the B form depends on the base composition of the DNA. It is observed that AT base pairs have a higher affinity toward water molecules than GC base pairs. In the B form there are 27 water molecules per GC nucleotide pair and 44 per AT pair. Moreover, we noted that the fraction of nucleotides in the B form as a function of the average number of water molecules associated per base pair does not depend on the temperature. The A helical form is obtained with about 11 water molecules per nucleotide pair and this number is not very sensitive to the base composition of DNA.

Base Pairing↗

PubMed2001

A new D-DNA form of poly(dA-dT).poly(dA-dT): an A-DNA type structure with reversed Hoogsteen pairing.

The D-DNA double helix model of poly(dA-dT).poly(dA-dT) proposed in the literature is not in accordance with some notable experimental facts and physicochemical conditions to which it is related. Thus, the fibre X-ray diffraction pattern of D-DNA obtained at a relative humidity lower than that giving the A-DNA form is singularly not taken into account when one assumes that there is only one D structure of B-DNA type. We rather suggest that there are actually two different forms of D-DNA, namely D(A) which partakes in the D-A-B transitions and D(B) associated with the D-B change of conformation. Although these two DNA structures have the same helical parameters (pitch and number of residues per turn), in agreement with X-ray data, their detailed conformations are considerably different. Whereas D(B) is indeed the structure generally defined as D-DNA, a critical analysis based on a comparison between different possible DNA double helices leads us to propose dihedral angles, a set of atomic coordinates and a stereo view of another new form of D-DNA, the D(A) structural model. It is a right-handed double helix with a dinucleotide as the repeat unit. The furanose rings are of the A-DNA type (C3' endo) and the bases are hydrogen bonded according to the reversed Hoogsteen pairing. Such a disposition renders the D(A) model unsuitable for poly(dI-dC).poly(dI-dC), the other alternating polynucleotide observed in the D(B) structure. The consistency of these two different D-DNA structures of poly(dA-dT).poly(dA-dT) with the general aspects of hydration and helix-helix transitions of DNA, as well as with the conformational variability of AT base sequences, is discussed.

Base Composition↗

PubMed1999

Helix-helix transitions in DNA: fibre X-ray study of the particular cases poly(dG-dC). poly(dG-dC) and poly(dA). 2poly(dT).

The helix-helix transitions which occur in poly(dG-dC). poly(dG-dC) and in poly (dG-m(5)dC). poly(dG-m(5)dC) are commonly assumed to be changes between the right-handed A- or B-DNA double helices and the left-handed Z-DNA structure. The mechanisms for such transconformations are highly improbable, especially when they are supposed to be active in long polynucleotide chains organised in semicrystalline fibres. The present alternative possibility assumes that rather than the Z-DNA it is a right-handed double helix (S-DNA) which actually takes part in these form transitions. Two molecular models of this S form, in good agreement with X-ray measurements, are proposed. They present alternating C(2')-endo and C(3')-endo sugar puckering like the "alternating B-DNA" put forward some years ago. Dihedral angles, sets of atomic coordinates and stereo views of the two S-DNA structures are given, together with curves of calculated diffracted intensities. Furthermore, we question the possibility of obtaining semicrystalline fibres with triple helices of poly(dA). 2poly(dT) in a way which renders X-ray diffraction efficient. It is suggested that, up to now, only double helices of poly(dA). poly(dT) can actually be observed by fibre X-ray diffraction measurements.

DNA↗

PubMed1999

Fibre X-ray study of the helix-helix transitions of poly(dG-dC).poly(dG-dC).

Poly(dG-dC).poly(dG-dC) and poly(dG-m5dC).poly(dG-m5dC) present helix-helix transitions which are commonly assumed to be changes between the right-handed A- or B-DNA double helices and the left-handed Z-DNA structure. The mechanisms for such transconformations are highly improbable especially when they are supposed to be active in long polynucleotide chains organised in semicrystalline fibres. The present alternative possibility assumes that rather than the Z-DNA it is a right-handed double helix (S-DNA) which actually takes part in these form transitions. Two molecular models of this S form, in good agreement with X-ray measurements, are proposed. They present alternating C(2')-endo and C(3')-endo sugar puckering. Dihedral angles, sets of atomic co-ordinates and stereo views of the two S-DNA structures are given together with curves of calculated diffracted intensities.

Models, Molecular↗

PubMed1998

Polymorphism and disorder of poly(dA).poly(dT) in fibers.

The absence of proportionality between fiber length and interbase axial distance reveals a high degree of disorder in fibers of poly(dA).poly(dT) when the relative humidity (r.h.) varies. According to X-ray patterns, the increase of fiber length does not correspond to any conformational change. The B' structure is present alone and in a better-organized form at higher r.h. We noted a dependence of length values on the direction of variation of the r.h. An unusual minimum of fiber length is observed around 65% r.h. and explained as been due to an amorphous part of the fiber, essentially composed of single strands of poly(dA) and poly(dT). At a temperature higher than 30 degrees C, the transition B'(alpha)-B* takes place but is associated with an important decrease of fiber length in spite of constancy of the helical rise per base pair. It is shown that this behavior is also due to the amorphous part of the fiber and not to a conformational transition.

Models, Chemical↗

PubMed1997

X-ray fibre diffraction study of an elevated temperature structure of poly(dA).poly(dT).

A reversible conformational transition between two discrete double helical forms of poly(dA).poly(dT) has been put into evidence by X-ray fibre diffraction. We observed that the transition between the well known B' conformation and a new helical structure (B*) occurs at a relative humidity near 80%, when the temperature is raised above 30 degrees C. It appears that the B* conformation is not just a distorted B' form of poly(dA).poly(dT) but rather a stable (up to a least 70 degrees C) distinct double helical structure of that polynucleotide. Analysis of X-ray patterns allowed us to present the geometrical parameters of a molecular model of this new double helix. It consists of 11.4 nucleotide pairs per turn in a pitch length of about 36.7 A. The proposed high-temperature right handed helical structure of poly(dA).poly(dT) is a member of the B-DNA family since the duplex has C1'-exo furanoses in both antiparallel but geometrically identical sugar-phosphate strands. The present finding may shed light on interpretations of results obtained from premelting or nucleosome formation processes involving (dA.dT) tracts in synthetic or natural DNA polymers.

Base Composition↗

PubMed1997

Temperature effects on the structure of poly(dA).poly(dT): an X-ray fiber diffraction study.

X-ray fiber diffraction of poly(dA).poly(dT) subjected to variation in the relative humidity, has allowed us to demonstrate the effects of temperature on the conformation of the polynucleotide. When the temperature of the poly(dA).poly(dT) is greater than 30 degrees C and the relative humidity near 80%, a new diffraction pattern is obtained. We observe a transition between the classical alpha B' form of poly(dA).poly(dT) and a double helical structure, B*, which remains stable at a temperature up to 70 degrees C. This new conformation of poly(dA).poly(dT) is a right-handed double helix with 11.4 nucleotide pairs per turn and a pitch of 36.7 A.

Humidity↗

PubMed1995

Temperature effects on hydration and form transitions of DNA.

The effects of temperature on the A-B transition of DNA in fibers are determined by fiber X-ray diffraction and measurement of variations of the fiber length with the relative humidity (r.h.). It is observed that the transition from the A to the B helical form occurs at higher r.h. when the temperature is raised. At 7 degrees C, this transition is complete for a r.h. of 88% while the A form remains stable at that same r.h. and is even maintained for r.h. values up to 92% when the temperature is 37 degrees C. The interpretation of the present experimental results is given in terms of hydration effects in which the entropic contribution of the solvent molecules is dominant.

Animals↗

PubMed1992

Effect of a mechanical tension on the hydration of DNA in fibres.

Fiber X-ray diffraction and measurement of fibre dimensions yield information about the effects of a mechanical tension on hydration of DNA in fibres. At a given relative humidity, the mechanical tension changes the DNA conformation but does not modify the number of water molecules associated to a nucleotide. The number of water molecules per nucleotide necessary to maintain B form decreases for increasing tensions applied to the DNA fibre. Form transitions can be opposed by mechanical tensions; an energy of 1 Kcal per mole of nucleotide pairs is sufficient to prevent the B to A transition.

DNA↗

PubMed1992

B-Z conformational transition and hydration of poly (dC-dG).poly (dC-dG) in fibres.

The B-Z transition of poly(dC-dG).poly(dC-dG) has been studied by fibre X-ray diffraction and measurement of fibre dimensions. The polymorphism of the Z form is well observed as a function of variations of the r.h. (relative humidity). The Z to B transition is obtained at very high r.h. values. The cooperative transition from B to Z is associated with a disorganization of the fibre. Details about the hydration of the polynucleotide during conformational transitions are presented and it is shown that a nucleotide in Z form can be associated with up to 16 water molecules and up to 22 when in the B form.

Chemical Phenomena↗

PubMed1992

[Experimental method for the definition of intercalation of compounds in DNA].

Intercalation of aromatic compounds into DNA can be appreciated by using, in a complementary way, fibre X-ray diffraction and measurement of variations of the fibre dimensions. The different behaviours resulting from an actual intercalation or an association of small molecules into the DNA grooves can be distinguished by this experimental method which provides significant results for proflavine, ethidium bromide, a platinum compound, 9-aminoacridine and ellipticine.

DNA↗

PubMed1991

Conformational transitions and hydration of poly d(A-T).poly d(A-T) in fibers.

Conformational transitions of poly d(A-T).poly d(A-T) have been studied by fiber X-ray diffraction and measurement of fiber dimensions. Results obtained for the D-A-B and D-B transitions are presented and analyzed. For all these form transitions, cooperativity effects are observed for the variation of the rise per nucleotide versus the relative humidity. Detailed information about hydration of the polynucleotide during form transitions and the numbers of water molecules per nucleotide necessary to stabilize the different helical conformations are presented.

Humidity↗

PubMed1990

Changes of hydration during conformational transitions of DNA.

Fiber X-ray diffraction and measurement of fiber dimensions yields information about the hydration of DNA in fibers. The results obtained give us the fraction of nucleotides in the B form for the A-B transition or the rate of progression for the B-C transition as functions of the number of water molecules per nucleotide. The present experimental results confirm the importance of cooperativity in the A-B transition and the progressive change of the DNA double helix conformation during the C-B transition. At least twenty additional water molecules per nucleotide are necessary to stabilize the B form for DNA molecules in fibers following the A to B transition whereas only ten are sufficient when the B conformation is obtained starting from the C form.

DNA↗

PubMed1990

A method for the experimental study of DNA conformational transitions in fibers.

The method proposed for the study of DNA conformational transitions is based on the proportionality, experimentally observed, between the length of a DNA fiber and the axial rise per nucleotide characterizing the molecular helix. Precise curves for the A-B and B-C transitions as a function of the relative humidity are obtained by using X-ray fiber data and measurements of fiber dimensions. It is thus shown that the A-B transition is a cooperative process between two different states, whereas the B-C transition can be considered as a progressive change of conformation. The present method is applied on two natural DNAs differing in base composition so that the effect of the nucleotide content on the conformational changes can be estimated.

DNA↗

PubMed1989

[Experimental method for studying conformational transitions in DNA].

An experimental method combining fiber X-ray and direct fiber dimension measurements is proposed for the study of DNA conformational transitions. Curves corresponding to the A-B and B-C transitions are obtained by using the proportionality which exists between the fiber length and the axial rise per nucleotide in the DNA helix. The A-B transition is shown to be cooperative while the B-C one is a progressive change of helical conformation.

DNA, Superhelical↗

PubMed1988

Influence of a mechanical tension on the B-A and B-C conformational transitions in DNA fibres.

In the present fibre X-ray study we attempt to quantify the effect of a mechanical tension on the conformations, and transitions between the structural forms of DNA. A simple experimental device has been realized in order to apply precise mechanical forces on DNA fibres during X-ray exposure. It is shown that, as the applied tension is increased, the B----A transition can be prevented as well as with a decrease of the sodium salt content. A kind of distorted B form is then observed the helical parameters of which change with the relative humidity. On the contrary, the mechanical tension does not prevent the B----C transition; it only slows down the form change and improves the X-ray patterns up to a relative humidity of 0%.

Animals↗

PubMed1986

DNA models for A, B, C and D conformations related to fiber X-ray, infrared and NMR measurements.

A conformational analysis of the A, B, C and D DNA forms was made in order to establish molecular models presenting a good agreement with experimental data obtained from fiber X-ray, infrared linear dichroism and 31P NMR. The proposed models have been refined and do present good stereochemistry and optimized H-bond distances between bases associated with the Watson-Crick pairing. The DNA conformations proposed are a left handed double helix for the C form and right handed helices for A, B and D. Relations to conformational transitions between these forms are discussed.

DNA↗

PubMed1985

Fibre X-ray and conformational study of the binding of metal ions on DNA.

Results obtained from X-ray diffraction as well as from conformational analysis of Ag-DNA fibres are presented. For small percentages of Ag+ bound and high humidity, the B-DNA form is maintained. As the percentage of Ag+ is increased, the helical parameters of the B-DNA are modified. These modifications are directly related to the percentage of G-C bases. The periodicity of the DNA fibres are perturbed as Ag+ is mainly bound to G-C pairs and, thus, only the equatorial diffracted intensities can be compared to values calculated from molecular models. It is shown, by this way, that the first binding site is located on N7 of G. A second site is situated between N3 and N1 of the G-C pair, at the place of a hydrogen bond. A molecular model of the Ag-DNA complex is proposed and shown to be in agreement with experimental data. Results obtained allow to get some information on the binding of other ions such as Cu2+ and Hg2+ which give very little modification of the fibre X-ray patterns.

Base Composition↗