Generation Of Secondary Structures Research Articles

Cyclic heterotetrameric and low-dimensional hydrogen-bonded polymeric structures in the morpholinium salts of ring-substituted benzoic acid analogues.

The morpholinium (tetrahydro-2H-1,4-oxazin-4-ium) cation has been used as a counter-ion in both inorganic and organic salt formation and particularly in metal complex stabilization. To examine the influence of interactive substituent groups in the aromatic rings of benzoic acids upon secondary structure generation, the anhydrous salts of morpholine with salicylic acid, C4H10NO(+)·C7H5O3(-), (I), 3,5-dinitrosalicylic acid, C4H10NO(+)·C7H3N2O7(-), (II), 3,5-dinitrobenzoic acid, C4H10NO(+)·C7H3N2O6(-), (III), and 4-nitroanthranilic acid, C4H10NO(+)·C7H5N2O4(-), (IV), have been prepared and their hydrogen-bonded crystal structures are described. In the crystal structures of (I), (III) and (IV), the cations and anions are linked by moderately strong N-H...Ocarboxyl hydrogen bonds, but the secondary structure propagation differs among the three, viz. one-dimensional chains extending along [010] in (I), a discrete cyclic heterotetramer in (III), and in (IV), a heterotetramer with amine N-H...O hydrogen-bond extensions along b, giving a two-layered ribbon structure. With the heterotetramers in both (III) and (IV), the ion pairs are linked though inversion-related N-H...Ocarboxylate hydrogen bonds, giving cyclic R4(4)(12) motifs. With (II), in which the anion is a phenolate rather than a carboxylate, the stronger assocation is through a symmetric lateral three-centre cyclic R1(2)(6) N-H...(O,O') hydrogen-bonding linkage involving the phenolate and nitro O-atom acceptors of the anion, with extension through a weaker O-H...Ocarboxyl hydrogen bond. This results in a one-dimensional chain structure extending along [100]. In the structures of two of the salts [i.e. (II) and (IV)], there are also π-π ring interactions, with ring-centroid separations of 3.5516 (9) and 3.7700 (9) Å in (II), and 3.7340 (9) Å in (IV).

Secondary structures in time-dependent rotating flows

The problems related with the development of secondary structures in time-dependent rotating flows are considered. The experimental results on the generation of these structures (inhomogeneities placed in series in a gas) which occur outside (inside) a cylindrical tube, when it starts (ends) suddenly to rotate, are presented. The qualitative explanation of these results is given on the basis of the ideas on the development of time-dependent viscous boundary layers, the condition of the stability of axisymmetric rotating flows obtained in the inviscid approximation, and the condition for the Gortler vortex generation. To obtain a more complete idea of the effect of secondary structure generation in time-dependent rotating flows two flows are numerically modeled on the basis of the complete Navier-Stokes equations. The first problem is that of rotating gas (air) flow in a round cylindrical tube of finite length with closed ends when it starts or ends suddenly to rotate. The second situation concerns with the generation of inside or outside (with respect to the tube surface) time-dependent vortex structures, when a tube with one closed end starts or ends suddenly to rotate; a gas flows into the tube from an external finite volume through the central region of its second open end and flows out of the tube into the volume along the periphery of this section. The flow parameters are analyzed both qualitatively and quantitatively.

Real-time PCR Analysis of RNA Extracted From Formalin-fixed and Paraffin-embeded Tissues: Effects of the Fixation on Outcome Reliability

In many pathologic circumstances, quantitative mRNA expression levels are important for evaluation of possible genome mutations. The development of real-time polymerase chain reaction (RT-PCR) technology has facilitated the realization of nucleic acid quantification. Potentially, quantitative PCR offers a number of advantages over traditional methods because it permits the use of small amounts of genetic material. In the present study, we optimize a RNA purification technique on specimens that are formalin-fixed, paraffin-embedded and we examine prolonged formalin fixation effects on quantitative RT-PCR analysis. We compared RNA levels with 70 colic mucosa samples using the cyclooxygenase 2 gene as marker. The difference in amplification successes between formalin-fixed tissues and formalin-fixed, paraffin-embedded tissues was not statistically significant. Moreover, we compared the expression of formalin-fixed samples with the expression of each fresh tissue. Wilcoxon Mann-Whitney test shows that only the difference in the expression levels of 1- or 3-hour formalin-fixed samples is not statistically significant with respect to other fixation times. We found that the mRNA can be reliably extracted from formalin fixed, paraffin-embedded tissue sections but that prolonged formalin fixation produces different results in quantitative RT-PCR. It can be related to difference in RNA sequences length and the generation of secondary structures that are more susceptible to the prolonged formalin fixation. We suppose that the paraffin do not influence the RNA extraction yield because there are no statistical significant differences between amplification success of formalin-fixed tissues and paraffin-embedded tissues. Therefore, in relative expression quantization, we confirm that it is appropriate to use specimens with same protocols and time for formalin fixation.

The 11 kb FGA deletion responsible for congenital afibrinogenaemia is mediated by a short direct repeat in the fibrinogen gene cluster.

Congenital afibrinogenaemia is an autosomal recessive disorder characterised by the complete absence of detectable fibrinogen. We previously identified the first known causative mutations for this disorder in a non-consanguineous Swiss family. The four affected male individuals (two brothers and their first two cousins) were shown to have homozygous deletions of approximately 11 kb of the fibrinogen alpha chain (FGA) gene. Haplotype data suggested that the deletions occurred on three distinct ancestral chromosomes, implying that the FGA region of the fibrinogen locus is susceptible to deletion by a common mechanism, but the sequences responsible for the recombination remained to be identified. Here, we report the detailed characterisation of the deletion by nucleotide sequence analysis of all three deletion junctions and comparison with normal sequences. We found that all three deletions were identical to the base-pair and probably resulted from non-homologous (illegitimate) recombination. The centromeric and telomeric deletion junctions featured both a 7 bp direct repeat, AACTTTT, situated in FGA intron 1 and in the FGA-FGB intergenic sequence and a number of inverted repeats which could be involved in the generation of secondary structures. Analysis with closely linked flanking polymorphic markers revealed the existence of at least two haplotypes, further suggesting independent origins of the deletions in this family.

SPROUT: a program for structure generation.

SPROUT is a new computer program for constrained structure generation that is designed to generate molecules for a range of applications in molecular recognition. It uses artificial intelligence techniques to moderate the combinatorial explosion that is inherent in structure generation. The program is presented here for the design of enzyme inhibitors. Structure generation is divided into two phases: (i) primary structure generation to produce molecular graphs to fit the steric constraints; and (ii) secondary structure generation which is the process of introducing appropriate functionality to the graphs to produce molecules that satisfy the secondary constraints, e.g., electrostatics and hydrophobicity. Primary structure generation has been tested on two enzyme receptor sites; the p-amidino-phenyl-pyruvate binding site of trypsin and the acetyl pepstatin binding site of HIV-1 protease. The program successfully generates structures that resemble known substrates and, more importantly, the predictive power of the program has been demonstrated by its ability to suggest novel structures.

Energy directed folding of RNA sequences.

A modification of Nussinov's algorithm (1) for (planar) secondary structure generation is described. Our algorithm postpones decisions on matches involving destabiling loops until they prove to be energetically more favourable than more local matches. We present, moreover, an alternative way of representing secondary structures which avoids unwarranted suggestions on higher order neighbourhood, can be automated easily, allows for any amount of annotation of the sequences, makes comparison of alternate foldings easy and is pleasing to the eye. 5S RNA sequences are used to illustrate the methods.

Genetic information analysis of bacteriophage phiX 174.

The genetic information of phix 174 genome (genes and intermediate segments) is analyzed in terms of its independent (D1 index) and dependent information (D2 and D3 Markovian indexes), as well as of its ability to generate secondary structure. Genes B and E, enclosed in A and D respectively, have: 1) values of D1 and D3 indexes closer to the theoretical random distribution curves than those of (A-B) and (D-E) gene fractions, and 2) in the ability for secondary structure generation minor differences with genes A and D. F leads to G and mRNA start leads to A intermediate segments differ from randomness in their D1 and D2 indexes, but not so much in the D3 values. All these data point out the use of code degeneracy for increasing the genetic information density of the virus.