Nonlinear dynamics of a nonisothermal collisionless plasma flow

It is shown that the two-fluid electrohydrodynamic equations for a transversely homogeneous flow of cold ions and Boltzmannian electrons in the ion-acoustic region are reduced to the Boussinesq equation. Using a two-soliton solution as an example, the nonlinear mechanism of collisionless relaxation of a supersonic plasma flow toward a steady state in the form of a double space charge layer is demonstrated.     

Total synthesis of a structural gene for the human peptide hormone angiotensin II.

Seven oligonucleotide chains containing between 6 and 11 nucleotide units were synthesized. The segments were phosphorylated by T4 polynucleotide 5'-hydroxyl-kinase and joined by T4 polynucleotide synthetase (ATP) to give the double-stranded DNA consisting of 33 base pairs. The DNA sequence was deduced from the known peptide sequence according to the genetic code.     

Nucleotide sequence-dependent opening of double-stranded DNA at an electrically charged surface

It has been shown earlier that the DNA double helix is opened due to a prolonged contact of the DNA molecule with the surface of the mercury electrode. At neutral pH, the opening process is relatively slow (around 100 s), and it is limited to potentials close to -1.2 V (against SCE). The opening of the double helix has been explained by strains in the DNA molecule due to strong repulsion of the negatively charged phosphate residues from the electrode surface where the polynucleotide chain is anchored via hydrophobic bases. Interaction of the synthetic ds polynucleotides with alternating nucleotide sequences/poly(dA-dT).poly (dA-dT), poly (dA-dU).poly (dA-dU), poly (dG-dC).poly (dG-dC)/ and homopolymer pairs/poly (dA).poly (dT), poly (rA).poly (rU) and poly (dG).poly (dC)/ with the hanging mercury drop electrode has been studied. Changes in reducibility of the polynucleotides were exploited to indicate opening of the double helix. A marked difference in the behaviour was observed between polynucleotides with alternating nucleotide sequence and homopolymer pairs: opening of the double-helical structures of the former polynucleotides occurs at a very narrow potential range (less than 100 mV) (region U), while with the homopolymer pairs containing A X T or A X U pairs, the width of this region is comparable to that of natural DNA (greater than 200 mV). In contrast to natural DNA, the region U of homopolymer pairs is composed of two distinct phases. No region U was observed with poly (dG).poly (dC). In polynucleotides with alternating nucleotide sequence, the rate of opening of the double helix is strongly dependent on the electrode potential in region U, while in homopolymer pairs, this rate is less potential-dependent. It has been assumed that the difference in the behaviour between homopolymer pairs and polynucleotides with alternating nucleotide sequence is due to differences in absorbability of the two polynucleotide chains in the molecule of a homopolymer pair (resulting from different absorbability of purine and pyrimidine bases) in contrast to equal adsorbability of both chains in a polynucleotide molecule with alternating nucleotide sequence. It has been shown that the mercury electrode is a good model of biological surfaces (e.g. membranes), and that the nucleotide sequence-dependent opening (unwinding) of the DNA double helix at electrically charged surfaces may play an important role in many biological processes.     

Counterion distribution around DNA: variation with conformation and sequence.

The three-dimensional Poisson-Boltzmann equation for the distribution of counterion charge density around double helical DNA has been solved by an iterative procedure. These computations have been performed for 0.01M monovalent salt solutions. A systematic study of the ten possible sequences found among adjacent nucleotide base pairs is presented for the A, B, and C conformations of DNA. In addition, calculations of the electrostatic stabilities of these conformations of DNA allows for comparison of the charge accumulation around each of the three conformers.     

A spectroscopic and surface plasmon resonance study of oleic acid/DNA complexes

The interaction of synthetic polynucleotide double strands with a natural lipid, oleic acid, was examined in diluted aqueous solutions by circular dichroism spectra, UV-absorption measurements, and surface plasmon resonance biosensor investigations. The investigations were performed with defined double and triple stranded oligo- and polydeoxyribonucleotides. Whereas duplexes are influenced by oleic acid ligandation, which could not be removed by ethanol dialysis procedure, no binding occurs to triple stranded DNA. The spectroscopic results indicate that oleic acid shows molecular recognition to AT b.p. motifs by groove binding. GC tracts - in particular alternating d[G-C] motifs - are strongly influenced by ligand interaction up to a ratio of one molecule per two base pairs. Likewise, the spectroscopic and morphologic changes in the supramolecular association of the complexes after treatment occur even after dialysis procedure. This was monitored with scanning force microscopy (SFM) as well. Additionally, monolayers of biotinylated DNA duplexes were immobilized on a streptavidin sensor-layer for surface plasmon resonance (SPR) observations. Small portions of the ligand were injected in continuous flow. Loosely bound molecules were removed by washing procedure. Injections of sodium hydroxide denature the DNA, releasing the tightly bound effectors. The amount of tightly bound oleic acid molecules was determined at one molecule per 2-3 base pairs. As consequence, a new mechanism of regulation of gene expression at nuclear membrane or by lipids inside DNA double helix has to be discussed.     

Dynamics of kinks in inhomogeneous polynucleotide chains

In the present paper the dynamics of the nonlinear conformational excitations — kinks, in inhomogeneous polynucleotide DNA chains is investigated. To calculate the kink rest energy E₀ and its size d the method of dynamical interval is used. This makes it possible to take into account that all coefficients of the model dynamic equation — the sine-Gordon equation depend on the sequence of bases. It is shown that the method gives an opportunity to calculate dynamical characteristics of any artificial and real sequences that is important for implementing tasks associated with the search and analysis of functionally important DNA sites.     

Contribution of individual structural components to stabilization of the secondary structure of double-helical polynucleotides

Contributions of individual structural components of the double-helical polynucleotide to the stabilization of its secondary structure have been studied. The energy of intramolecular interactions was calculated by the method of atom-atom potentials. Sections of the energy function were constructed according to the parameters determining mutual location of base pairs with the optimal conformation of ribose-phosphate backbone in the points close to A- and B-forms of DNA. A complicated nature of the contribution of different structural components of the polynucleotide to its stabilization was revealed by means of different parameters. Relationships between the change of conformational parameters corresponding to optimal values of energy for A- and B-families of nucleic acids were found.     

On molecular mechanisms of nucleic acid synthesis fidelity aspects. 1. Contribution of base interactions

This paper is concerned with the molecular mechanisms of spontaneous replacements of base pairs in the processes of template synthesis of nucleic acids. The method of atom-atom potential functions was used to calculate the energies of interaction in non-complementary base pairs arranged in a common plane so that the mutual position of the glycosidic bonds does not differ appreciably from their position for Watson-Crick pairs in the DNA double helix. A number of local minima of this energy have been found, which could occur in template synthesis and result in insertion of incorrect bases into the double helix. The calculation results are indicative of formation of purine-purine pairs with one of the purine nucleotides in syn-conformation, which can be regarded as a typical pathway of transversion, and that of wobble-pairs TG and AC, which can be regarded as a typical pathway of transition. The contribution of intramolecular interactions of nucleic acids as well as interactions of polynucleotide chains with an enzyme to the fidelity of template synthesis of nucleic acids is discussed. The calculation results are compared with the experimental data on the frequency of spontaneous mutations and the frequency of errors in template synthesis of nucleic acids in vitro.     

Binding of recA protein to Z-form DNA studied with circular and linear dichroism spectroscopy

Binding of RecA to poly(dG-m5dC) and poly(dG-dC) under B- and Z-form conditions was studied using circular dichroism (CD) and linear dichroism (LD). LD revealed a quantitative binding of RecA to Mg2+-induced Z-form poly(dG-m5dC) with a stoichiometry of 3.1 base pairs/RecA monomer, which is slightly larger than the 2.7 base pairs observed for the B-form. The LD spectra indicate a preferentially perpendicular orientation of DNA bases and a rather parallel orientation of the tryptophan residues relative to the fiber axis in both complexes. The association rate of RecA to Z-form DNA was found to be slower than to B-form. CD measurements showed that the polynucleotide conformation is retained upon RecA binding, and CD and LD confirm that RecA binds to both forms of DNA. The Mg2+-induced Z-form is shown to be retransformed into B-form, both in free and in RecA-complexed polynucleotides by addition of NaCl, whereas the B----Z transition cannot be induced by addition of Mg2+ when the polynucleotide is complexed with RecA. From this it is inferred that RecA does not stabilize the Z-conformation of the polynucleotide but that it can kinetically "freeze" the polynucleotide in its B-conformation. On all essential points, the same conclusions were also reached in a corresponding study of unmethylated poly(dG-dC) with the Z-form induced by Mn2+.     

Dust−ion acoustic freak wave propagation in a nonthermal mesospheric dusty plasma

Nonlinear properties of dust?ion acoustic freak waves have been studied in homogeneous unmagnetized dusty plasmas consisting of ions, nonthermal fast electrons, and positive and negative dust grains. By using derivative expansion method under the assumption of strongly dispersive medium, the basic equations are reduced to nonlinear Schrödinger equation (NLSE). One of NLSE solutions in the unstable region is the rational one which is responsible for creation of the freak waves. The dependence of the freak wave profile on the dust grain charge, carrier wavenumber, and energetic nonthermal electron population is discussed.     

Restriction map of maxicircle kinetoplastic DNA of Leishmania gymnodactyli

Kinetoplast DNA (kDNA) of Leishmania gymnodactyli, as in other Trypanosoma species, is a complicated associate consisting of mini- and maxicircular molecules. Minicircular DNA are presented by the homogeneous in size and heterogeneous in base sequence population. Their size determined by the agarose electrophoretic mobility in gel is 920 pairs of nucleotides. Maxicircular molecules of DNA are homogeneous and contains about 38 thou pairs of nucleotides. The restriction map of maxicircular kDNA molecule of L. gymnodactyli has been made up on the basis of the cleavage data of the whole associate kDNA by restrictases.     

Probing Conformational Isomerizations of Double-Stranded Poly(dA-dT) by a Substitution of Minor Amounts of the Thymine Methyls with Bulky Hydrophobic Isopropyl Groups

Abstract

We probed conformational polymorphism of a synthetic DNA poly(dA-dT) by introducing various small amounts of bulky spherical hydrophobic isopropyl groups into the polynucleotide primary structure. For this purpose, three mixed copolymers of poly(dA-dT, ip⁵dU) were synthesized in which 2.6 %, 8.6 % or 14.2 % of the polynucleotide pyrimidine bases had the isopropyl group in position 5. The isopropyls made the formation of both A-form and X-form incomplete, and this effect increased with the increasing isopropyl amount in the polynucleotide. However, the polynucleotide isomerization into the A-form was hindered by the isopropyls while the isomerization into the X-form was rather promoted. This observation indicates that, unlike the A-form, the X-form has the base pairs shifted towards the double helix major groove. Z-form was also promoted by the lowest concentration of the isopropyl groups while the most isopropylated poly(dA-dT) aggregated under the Z-form inducing conditions.     

Acoustical investigation of poly(dA).poly(dT), poly[d(A-T)], poly(A).poly(U) and DNA hydration in dilute aqueous solutions.

Apparent molar adiabatic compressibilities and apparent molar volumes of poly[d(A-T)].poly[d(A-T)], poly(dA).poly(dT), DNA and poly(A).poly(U) in aqueous solutions were determined at 1 degree C. The change of concentration increment of the ultrasonic velocity upon replacing counter ion Cs+ by the Mg2+ ion was also determined for these polymers. The following conclusions have been made: (1) the hydration of the double helix of poly(dA).poly(dT) is remarkably larger than that of other polynucleotides; (2) the hydration of the AT pair in the B-form DNA is larger than that of the GC pair; (3) the substitution of Cs+ for Mg2+ ions as counter ions results in a decrease of hydration of the system polynucleotide plus Mg2+, and (4) the magnitude of this dehydration depends on the nucleotide sequence; the following rule is true: the lesser is a polynucleotide hydration, the larger dehydration upon changing Cs+ for Mg2+ ions in the ionic atmosphere of polynucleotide.     

Longitudinal displacements of base pairs in DNA and effects on the dynamics of nonlinear excitations

A model of the DNA is proposed and studied analytically and numerically. The model is an extension of a well known model and describes the double helix as two chains of pendula (each pendulum representing a base). Each base (or pendulum) can rotate and translate along the helix axis. In the continuum limit the system is described by the perturbed Sine–Gordon equation describing the twist of the bases and by a nonlinear partial differential equation (PDE) describing the longitudinal displacements of the bases. This coupled system of PDEs was studied analytically using different approaches and the corresponding results were tested through numerical simulations. It was found that if the coupling parameters satisfy a well defined relationship, then there exist bounded travelling wave solutions.     

End group labelling of RNA and double stranded DNA by phosphate exchange catalyzed by bacteriophage T4 induced polynucleotide kinase.

End group labelling of sheared double-stranded DNA, and tRNA has been effected without prior dephosphorylation, utilizing the reversal of T₄ polynucleotide kinase activity. Incubation of DNA with polynucleotide kinase in the presence and absence of a phosphate acceptor (ADP) allowed the determination of the relative ratio of 5′ hydroxyl and 5′ phosphoryl terminii in the polynucleotide. This method of analysis has demonstrated a high preference in the formation of 5′ vs 3′ phosphomonoesters during high pressure shearing of double stranded DNA.     

The effect of intrinsic curvature on conformational properties of circular DNA.

Both thermal fluctuations and the intrinsic curvature of DNA contribute to conformations of the DNA axis. We looked for a way to estimate the relative contributions of these two components of the double-helix curvature for DNA with a typical sequence. We developed a model and Monte Carlo procedure to simulate the Boltzmann distribution of DNA conformations with a specific intrinsic curvature. Two steps were used to construct the equilibrium conformation of the model chain. We first specified the equilibrium DNA conformation at the base pair level of resolution, using a set of the equilibrium dinucleotide angles and DNA sequence. This conformation was then approximated by the conformation of the model chain consisting of a reduced number of longer, straight cylindrical segments. Each segment of the chain corresponded to a certain number of DNA base pairs. We simulated conformational properties of nicked circular DNA for different sets of equilibrium dinucleotide angles, different random DNA sequences, and lengths. Only random sequences of DNA generated with equal probability of appearance for all types of bases at any site of the sequence were used. The results showed that for a broad range of intrinsic curvature parameters, the radius of gyration of DNA circles should be nearly independent of DNA sequence for all DNA lengths studied. We found, however, a DNA properly that should strongly depend on DNA sequence if the double helix has essential intrinsic curvature. This property is the equilibrium distribution of the linking number for DNA circles that are 300-1000 bp in length. We found that a large fraction of the distributions corresponding to random DNA sequences should have two separate maxima. The physical nature of this unexpected effect is discussed. This finding opens new opportunities for joined experimental and theoretical studies of DNA intrinsic curvature.     

Alteration of the DNA double helix conformation upon incorporation of mispairs as revealed by energy computations and pathways of point mutations.

To explain biochemical and genetic data on spontaneous nucleotide replacements in nucleic acid biosynthesis all the 8 mispairs in normal tautomeric forms have been considered. Possible B-conformations of DNA fragments containing each of such mispairs incorporated between Watson-Crick pairs have been found using computations of the energy of non-bonded interactions via classical potential functions. These conformations have no reduced interatomic contacts. The values of each dihedral angle of the sugar-phosphate backbone fall within the limits of those of double-helical fragments of B-DNA in crystals. These values differ from those of the corresponding angles for the low-energy polynucleotide conformations consisting of canonical pairs by no more than 30 degrees (except for the fragment with the U:U pair for which the C4'-C3'-O-P angle differs by about 50 degrees). The difference in experimentally observed frequencies of various nucleotide replacements in DNA biosynthesis correlates with the difference in the energy of non-bonded interactions and with the extent of the sugar-phosphate backbone distortion for the fragments containing the mispairs which serve as intermediates for the replacements.     

Interaction of tripeptides containing arginine and tyrosine (or phenylalanine) residues with synthetic polynucleotides and DNA of various origins

Model peptides--L-Arg-Gly-L-Arg, L-Arg-L-Tyr-L-Arg and L-Arg-L-Phe-L-Arg bind to different DNAs and synthetic polynucleotides and are found in the major groove of the double helix. Polynucleotide complexes containing L-Arg-Gly-L-Arg were studied in order to consider the influence of the arginine residues on the polynucleotide melting temperature. It was shown, that L-Arg-L-Tyr-L-Arg and L-Arg-L-Phe--L-Arg lowers the melting temperature in all polynucleotides studied. The dependence of the melting temperature of polynucleotide (DNA)--L-Arg-L-Tyr(L-Phe)-L-Arg complexes upon the polynucleotide GC-content has been detected. These effects reflect the intercalation of peptide tyrosyl (or phenylalanyl) residues into the double-stranded polynucleotide.     

Configurational statistics of the DNA duplex: Extended generator matrices to treat the rotations and translations of adjacent residues

The base-to-base virtual bond treatment of nucleic acids used in statistical mechanical calculations of polynucleotide chain properties has been refined by incorporating the six parameters that relate the positions and orientations of sequential rigid bodies. The scheme allows for the sequence-dependent bending, twisting, and displacement of base pairs as well as for asymmetry in the angular and translational fluctuations of individual residues. Expressions are developed for the generator matrices required for the computation, as a function of chain length, of various parameters measuring the overall mean extension and shape of the DNA. Quantities of interest include the end-to-end vector r , the square of the end-to-end distance r², the square radius of gyration s², the center-of-gravity vector g , the second moments of inertia S ^×2, and the higher moments of r and g . The matrix expressions introduced in the 1960s by Flory and co-workers for the determination of configuration-dependent polymer chain averages are decomposed into their translational and orientational contributions so that the methods can be extended to the rigid body analysis of chemical moieties. The new expressions permit, for the first time, examination of the effects of sequence-dependent translations, such as the lateral sliding of residues in A- and B-helices and the vertical opening of base pairs in drug–DNA complexes, on the average extension and shape of the long flexible double helix. The approach is illustrated in the following paper using conformational energy estimates of the base sequence-dependent flexibility of successive B-DNA base pairs. © 1994 John Wiley & Sons, Inc.