Alternative solution of the simplest model of enzymatic synthesis of nucleic acids by homotopy perturbation method

Development of methods for obtaining approximate analytical solutions of nonlinear differential equations and their systems is a rapidly developing field of mathematical physics. Earlier, an approximate solution of the simplest system of kinetic enzymatic equations for calculating dynamics of complementary strands of nucleic acids was obtained. In this study, we consider an alternative approach to selecting the basic linear approximation of the used method, which makes it possible to obtain more accurate analytical solutions of the set problem.     

A predictive model of enzymatic cleavage of nucleic acids

A new static model of enzymatic cleavage of polymeric substrates such as nucleic acids has been derived. The model is compared to that elaborated by Tanford and to experimental data. In predicting the fragment distribution for a restriction enzyme digestion of a circular substrate, the model is superior to that of Tanford.     

System of kinetic equations describing large-scale processes in collisionless space plasma

A system of kinetic equations describing relatively slow large-scale processes in collisionless magnetoplasma structures with a spatial resolution of about the characteristic gyroradius is derived. Plasma is assumed to be quasineutral, while the magnetic and electric fields are determined by the instantaneous distributions of the particle and current densities and the stress tensor of all plasma components in the longrange instantaneous interaction approximation. A special version of equations is derived for the case of magnetized electrons described by the Vlasov equation in the drift approximation. The obtained system of equations can be used to develop a global numerical kinetic model of the Earth’s magnetosphere with a spatial resolution of about 100 km, as well as local models of certain regions of the Earth’s magnetosphere with a higher resolution.     

Novel nucleoside triphosphate analogs for the enzymatic labeling of nucleic acids

We have evaluated several novel nucleotide analogs suitable for enzymatic labeling of nucleic acid targets for a variety of array-based assays. Two new reagents in particular, a C4-labeled 1-(2',3'-dideoxy-beta-D-ribofuranosyl) imidazole-4-carboxamide 5'-triphosphate 5 and an N1-labeled 5-(beta-D-ribofuranosyl)-2,4(1H,3H)-pyrimidinedione 5'-triphosphate 3, were found to be excellent substrates for labeling with terminal deoxynucleotidyl transferase and T7 RNA polymerase, respectively.     

Solid-phase synthesis of pseudo-complementary peptide nucleic acids

Pseudo-complementary peptide nucleic acid (pcPNA) is a DNA analog in which modified DNA bases 2,6-diaminopurine (D) and 2-thiouracil (U(s)) 'decorate' a poly[N-(2-aminoethyl)glycine] backbone, together with guanine (G) and cytosine (C). One of the most significant characteristics of pcPNA is its ability to effect double-duplex invasion of predetermined DNA sites inducing various changes in the biological and the physicochemical properties of the DNA. This protocol describes solid-phase synthesis of pcPNA. The monomers for G and C are commercially available, but the monomers for D and U(s) need to be synthesized (or can be ordered to custom synthesis companies). Otherwise, the procedure is the same as that employed for Boc-strategy synthesis of conventional PNA. This protocol, if the synthesis of D and U(s) monomers is not factored in, takes approximately 7 d to complete.     

Design and synthesis of chiral peptidic nucleic acids

Due to the increasing interest in the use ofoligonucleotide analogues as antisense and antigenedrugs, we designed a chiral analogue constituted of apeptidic frame bearing nucleobases in suitablepositions (C-PNA). We recently reported the synthesisof four nonnatural -amino acids with the DNAbases in the lateral chain. In this paper we presentan improved synthesis of the Fmoc monomers and theirpolymerisation to polypeptidic oligonucleotideanalogues using a modification of the standardprotocol for solid phase peptide synthesis.     

Existence of a limiting pattern for a system of nonlinear equations describing interpopulation competition

A system of arbitrarily many nonlinear ordinary differential equations which can be interpreted as describing competition between populations is studied here. It is found that limits exist for the system given specified constraints on the “signal function” which describes input-output relations at the level of single populations. Existence of limits is shown by means of a function which records which variable in the system is growing fastest at a given time i.e. who is winning the competition. Generalizations are discussed to sigmoid signal functions which appear in models of pattern discrimination by neuron populations.     

Solution of the equations describing the flow of Na in a semi-infinite composite system containing a membrane

Solutions to the flow equations in a semi-infinite composite system consisting of protein solution and a phospholipid sol with a membrane at the interface are described in this paper. The composite system was contained in a length of precision bore capillary tubing and the flow rate in the system was followed by using labelled NaCl and a continuous monitoring apparatus.