G -rich oligodeoxyribonucleotides: Triplexes and transcription

Formation of a triple helix resulting from oligonucleotide binding to the DNA double helix offers new possibilities to control gene expression at the transcriptional level. Purine-motif triplexes can be formed under physiological pH. Nevertheless, this formation was inhibited by certain monovalent cations during the association but not during dissociation. Since triplexes are very stable, it was possible to assemble them in the absence of KCl and have them survive throughout the course of an in vitro transcription reaction. As for the design of a better triplex-forming oligonucleotide, 12 nucleotides in length afforded the highest binding affinity. G/T-rich oligonucleotides can be very polymorphic in solution. The conditions for forming purine-motif triplexes, duplexes or G-quartets were determined. Understanding these parameters will be important for the practical use of G-rich oligonucleotides in the development of DNA aptamers where the structure of the oligonucleotide is paramount in dictating its function. Finally, purine-motif triplexes were demonstrated to significantly inhibit gene transcription in vitro. The optimal effect on this process was dependent on the location of triplexes within the promoter, i.e., whether upstream or proximally downstream of the transcription start site. The mechanism for the inhibition of transcription appeared to be interference with initiation through preventing engagement by RNA polymerase. This finding is revolutionary when compared to the conventional model where triplexes inhibit transcription only by occluding binding by trans-acting proteins. Our findings broaden the utility of triplexes and support a strategy for antigene therapy by triplexes. ^

Mechanism of mRNA stability control mediated by AU -rich element: Characterization of cis-elements and trans-factors

Regulation of cytoplasmic deadenylation, the first step in mRNA turnover, has direct impact on the fate of gene expression. AU-rich elements (AREs) found in the 3′ untranslated regions of many labile mRNAs are the most common RNA-destabilizing elements known in mammalian cells. Based on their sequence features and functional properties, AREs can be divided into three classes. Class I or class III ARE directs synchronous deadenylation, whereas class II ARE directs asynchronous deadenylation with the formation of poly(A)-intermediates. Through systematic mutagenesis study, we found that a cluster of five or six copies of AUUUA motifs forming various degrees of reiteration is the key feature dictating the choice between asynchronous versus synchronous deadenylation. A 20–30 nt AU-rich sequence immediately 5 ′ to this cluster of AUUUA motifs can greatly enhance its destabilizing ability and is an integral part of the AREs. These two features are the defining characteristics of class II AREs. ^ To better understand the decay mechanism of AREs, current methods have several limitations. Taking the advantage of tetracycline-regulated promoter, we developed a new transcriptional pulse strategy, Tet-system. By controlling the time and the amount of Tet addition, a pulse of RNA could be generated. Using this new system, we showed that AREs function in both growth- and density-arrested cells. The new strategy offers for the first time an opportunity to investigate control of mRNA deadenylation and decay kinetics in mammalian cells that exhibit physiologically relevant conditions. ^ As a member of heterogeneous nuclear RNA-binding protein, hnRNP D 0/AUF1 displays specific affinities for ARE sequences in vitro . But its in vivo function in ARE-mediated mRNA decay is unclear. AUF1/hnRNP D0 is composed of at least four isoforms derived by alternative RNA splicing. Each isoform exhibits different affinity for ARE sequence in vitro. Here, we examined in vivo effect of AUF1s/hnRNP D0s on degradation of ARE-containing mRNA. Our results showed that all four isoforms exhibit various RNA stabilizing effects in NIH3T3 cells, which are positively correlated with their binding affinities for ARE sequences. Further experiments indicated that AUF1/hnRNP D0 has a general role in modulating the stability of cytoplasmic mRNAs in mammalian cells. ^

Interactions and structural analysis of the zinc -binding motif in decorin, a small leucine rich proteoglycan in extracellular matrix

Decorin, a dermatan/chondroitin sulfate proteoglycan, is ubiquitously distributed in the extracellular matrix (ECM) of mammals. Decorin belongs to the small leucine rich proteoglycan (SLRP) family, a proteoglycan family characterized by a core protein dominated by Leucine Rich Repeat motifs. The decorin core protein appears to mediate the binding of decorin to ECM molecules, such as collagens and fibronectin. It is believed that the interactions of decorin with these ECM molecules contribute to the regulation of ECM assembly, cell adhesions, and cell proliferation. These basic biological processes play critical roles during embryonic development and wound healing and are altered in pathological conditions such as fibrosis and tumorgenesis. ^ In this dissertation, we discover that decorin core protein can bind to Zn2+ ions with high affinity. Zinc is an essential trace element in mammals. Zn2+ ions play a catalytic role in the activation of many enzymes and a structural role in the stabilization of protein conformation. By examining purified recombinant decorin and its core protein fragments for Zn2+ binding activity using Zn2+-chelating column chromatography and Zn2+-equilibrium dialysis approaches, we have located the Zn2+ binding domain to the N-terminal sequence of the decorin core protein. The decorin N-terminal domain appears to contain two Zn2+ binding sites with similar high binding affinity. The sequence of the decorin N-terminal domain does not resemble any other reported zinc-binding motifs and, therefore, represents a novel Zn 2+ binding motif. By investigating the influence of Zn2+ ions on decorin binding interactions, we found a novel Zn2+ dependent interaction with fibrinogen, the major plasma protein in blood clots. Furthermore, a recombinant peptide (MD4) consisting of a 41 amino acid sequence of mouse decorin N-terminal domain can prolong thrombin induced fibrinogen/fibrin clot formation. This suggests that in the presence of Zn2+ the decorin N-terminal domain has an anticoagulation activity. The changed Zn2+-binding activities of the truncated MD4 peptides and site-directed mutagenesis generated mutant peptides revealed that the functional MD4 peptide might contain both a structural zinc-binding site in the cysteine cluster region and a catalytic zinc site that could be created by the flanking sequences of the cysteine cluster region. A model of a loop-like structure for MD4 peptide is proposed. ^

Eficiencia de control de "orugas defoliadoras" en soja (Glycine max L.), con insecticidas neurotóxicos y reguladores del crecimiento de los insectos

Las "orugas defoliadoras" afectan la producción del cultivo de soja, sobre todo en años secos y con altas temperaturas que favorecen su desarrollo. El objetivo del presente trabajo fue evaluar la eficiencia de control de insecticidas neurotóxicos e IGRs sobre "orugas defoliadoras" en soja. Se realizaron ensayos en lotes comerciales en tres localidades de la provincia de Córdoba en las campañas agrícolas 2008/09 y 2009/10, bajo un diseño de bloques al azar, con seis tratamientos y tres repeticiones. Los tratamientos fueron: T1: Clorpirifos (384 g p.a.ha-1), T2: Cipermetrina (37,5 g p.a.ha-1), T3: Lufenuron+Profenofos (15 + 150 g p.a.ha-1), T4: Metoxifenocide (28,8 g p.a.ha-1), T5: Novaluron (10 g p.a.ha-1) y T6: Testigo. El tamaño de las parcelas fue de 12 surcos de 10 m de largo distanciados a 0,52 m. La aplicación se realizó con una mochila provista de boquillas de cono hueco (40 gotas.cm-2), cuando la plaga alcanzó el umbral de daño económico. En cada parcela se tomaron cinco muestras a los 0, 2, 7 y 14 días después de la aplicación (DDA) utilizando el paño vertical, identificando y cuantificando las orugas vivas mayores a 1,5 cm. A los 14 DDA se extrajeron 30 folíolos por parcela (estrato medio y superior de la planta) y se determinó el porcentaje de defoliación utilizando el software WinFolia Reg. 2004. Se estimó el rendimiento sobre 5 muestras de 1 m2 en cada parcela y se realizó ANOVA y test de comparación de medias LSD de Fisher. El Clorpirifos mostró el mayor poder de volteo y el Metoxifenocide la mayor eficiencia a los 7 DDA. En general los IGRs mostraron mayor poder residual.

Desarrollo y validación de una escala para evaluación de daño por orugas defoliadoras en soja (Glycine max L.), para el sur de la provincia de Córdoba

Para desarrollar y validar una escala logarítmica diagramática de evaluación de daño por orugas defoliadoras al cultivo de soja, para el centro-sur de Córdoba, se colectaron folíolos dañados a fin de obtener la máxima defoliación presente. Se calculó el porcentaje de defoliación escaneando cada folíolo, utilizando el software WinFolia. Se planteó una escala de siete clases obteniendo el valor medio de cada una con el programa DOSLOG. Posteriormente 140 folíolos, cuya defoliación real se determinó con WinFolia, fueron evaluados por seis evaluadores con y sin experiencia previa en estimaciones de defoliación, con y sin escala. La validación por precisión y exactitud se realizó por regresión lineal simple entre la defoliación real y la estimada, y la reproducibilidad por regresión entre las 140 estimaciones de los evaluadores combinados de a pares. Sin la escala la mayoría de los evaluadores sobreestimaron la defoliación, indicando desvíos positivos constantes para todos los niveles, y en 9 de 12 evaluadores ocurrieron desvíos sistemáticos. Con la escala mejoró la exactitud (-1,74 a 1,39), precisión (0,77 a 0,90) y reproducibilidad, por lo que se la considera adecuada para evaluaciones de daños causados por orugas defoliadoras al cultivo de soja, en la región centro-sur de Córdoba.