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1.
Biophys J ; 120(13): 2623-2630, 2021 07 06.
Artículo en Inglés | MEDLINE | ID: mdl-33964275

RESUMEN

Many kinds of peritrichous bacteria that repeat runs and tumbles by using multiple flagella exhibit chemotaxis by sensing a difference in the concentration of the attractant or repellent between two adjacent time points. If a cell senses that the concentration of an attractant has increased, their flagellar motors decrease the switching frequency from counterclockwise to clockwise direction of rotation, which causes a longer run in swimming up the concentration gradient than swimming down. We investigated the turn angle in tumbles of peritrichous bacteria swimming across the concentration gradient of a chemoattractant because the change in the switching frequency in the rotational direction may affect the way tumbles. We tracked several hundreds of runs and tumbles of single cells of Salmonella enterica serovar Typhimurium in the concentration gradient of L-serine and found that the turn angle depends on the concentration gradient that the cell senses just before the tumble. The turn angle is biased toward a smaller value when the cells swim up the concentration gradient, whereas the distribution of the angle is almost uniform (random direction) when the cells swim down the gradient. The effect of the observed bias in the turn angle on the degree of chemotaxis was investigated by random walk simulation. In the concentration field where attractants diffuse concentrically from the point source, we found that this angular distribution clearly affects the reduction of the mean-square displacement of the cell that has started at the attractant source, that is, the bias in the turn angle distribution contributes to chemotaxis in peritrichous bacteria.


Asunto(s)
Quimiotaxis , Salmonella typhimurium , Simulación por Computador , Flagelos , Modelos Biológicos , Serogrupo
2.
PLoS One ; 8(1): e53572, 2013.
Artículo en Inglés | MEDLINE | ID: mdl-23341952

RESUMEN

It remains difficult to obtain high-resolution atomic force microscopy images of HIV-1 integrase bound to DNA in a dimeric or tetrameric fashion. We therefore constructed specific target DNAs to assess HIV-1 integrase binding and purified the complex by dialysis prior to analysis. Our resulting atomic force microscopy analyses indicated precise size of binding human immunodeficiency virus type 1 (HIV-1) recombinant integrase in a tetrameric manner, inducing formation of a loop-like or figure-eight-like secondary structure in the target DNA. Our findings regarding the target DNA secondary structure provide new insights into the intermediate states of retroviral integration.


Asunto(s)
ADN Viral/química , ADN Viral/aislamiento & purificación , Integrasa de VIH/aislamiento & purificación , Microscopía de Fuerza Atómica/métodos , Conformación de Ácido Nucleico , Multimerización de Proteína , Proteínas Recombinantes/metabolismo , ADN Circular/metabolismo , ADN Viral/metabolismo , Diálisis , Electroforesis , Integrasa de VIH/metabolismo , Humanos , Peso Molecular , Unión Proteica , Secuencias Repetitivas de Ácidos Nucleicos
3.
PLoS One ; 5(11): e13841, 2010 Nov 04.
Artículo en Inglés | MEDLINE | ID: mdl-21079805

RESUMEN

Although there have been a few reports that the HIV-1 genome can be selectively integrated into the genomic DNA of cultured host cell, the biochemistry of integration selectivity has not been fully understood. We modified the in vitro integration reaction protocol and developed a reaction system with higher efficiency. We used a substrate repeat, 5'-(GTCCCTTCCCAGT)(n)(ACTGGGAAGGGAC)(n)-3', and a modified sequence DNA ligated into a circular plasmid. CAGT and ACTG (shown in italics in the above sequence) in the repeat units originated from the HIV-1 proviral genome ends. Following the incubation of the HIV-1 genome end cDNA and recombinant integrase for the formation of the pre-integration (PI) complex, substrate DNA was reacted with this complex. It was confirmed that the integration selectively occurred in the middle segment of the repeat sequence. In addition, integration frequency and selectivity were positively correlated with repeat number n. On the other hand, both frequency and selectivity decreased markedly when using sequences with deletion of CAGT in the middle position of the original target sequence. Moreover, on incubation with the deleted DNAs and original sequence, the integration efficiency and selectivity for the original target sequence were significantly reduced, which indicated interference effects by the deleted sequence DNAs. Efficiency and selectivity were also found to vary discontinuously with changes in manganese dichloride concentration in the reaction buffer, probably due to its influence on the secondary structure of substrate DNA. Finally, integrase was found to form oligomers on the binding site and substrate DNA formed a loop-like structure. In conclusion, there is a considerable selectivity in HIV-integration into the specified sequence; however, similar DNA sequences can interfere with the integration process, and it is therefore difficult for in vivo integration to occur selectively in the actual host genome DNA.


Asunto(s)
ADN Viral/genética , VIH-1/genética , Integración Viral/genética , Secuencia de Bases , Sitios de Unión/genética , Cloruros/farmacología , ADN Viral/metabolismo , Relación Dosis-Respuesta a Droga , Integrasa de VIH/genética , Integrasa de VIH/metabolismo , Duplicado del Terminal Largo de VIH/genética , Humanos , Compuestos de Manganeso/farmacología , Modelos Genéticos , Oligonucleótidos/genética , Plásmidos/genética , Integración Viral/efectos de los fármacos
4.
Ultramicroscopy ; 109(8): 868-73, 2009 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-19328628

RESUMEN

In order to reveal the roles of histone tails in the formation of higher-order chromatin structures, we employed atomic force microscopy (AFM), and an in vitro reconstitution system to examine the properties of reconstituted chromatin composed of tail-less histones and a long DNA (106-kb plasmid) template. The tail-less nucleosomes did not aggregate at high salt concentrations or with an excess amount of core histones, in contrast with the behavior of nucleosomal arrays composed of nucleosomes containing normal, N-terminal tails. Analysis of our nucleosome distributions reveals that the attractive interaction between tail-less nucleosomes is weakened. Addition of linker histone H1 into the tail-less nucleosomal array failed to promote the formation of 30nm chromatin fibers that are usually formed in the normal nucleosomal array. These results demonstrate that the attractive interaction between nucleosomes via histone tails plays a critical role in the formation of the uniform 30-nm chromatin fiber.


Asunto(s)
Histonas/metabolismo , Nucleosomas/metabolismo , Nucleosomas/ultraestructura , Sales (Química)/metabolismo , Sustancias Macromoleculares/metabolismo , Microscopía de Fuerza Atómica , Plásmidos , Unión Proteica
5.
Biomacromolecules ; 8(1): 273-8, 2007 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-17206817

RESUMEN

A large-scale conformational change in genomic DNA is an essential feature of gene activation in living cells. Considerable effort has been applied to explain the mechanism in terms of key-lock interaction between sequence-specific regulatory proteins and DNA, in addition to the modification of DNA and histones such as methylation and acetylation. However, it is still unclear whether these mechanisms can explain the ON/OFF switching of a large number of genes that accompanies differentiation, carcinogenesis, etc. In this study, using single-molecule observation of DNA molecules by fluorescence microscopy with the addition of poly-L-lysine with different numbers of monomer units (n = 3, 5, 9, and 92), we found that an ON/OFF discrete transition in the higher-order structure of long duplex DNA is induced by short poly-L-lysine, whereas a continuous gradual change is induced by long poly-L-lysine. On the other hand, polycations with a lower positive charge have less potential to induce DNA compaction. Such a drastic difference in the conformational transition of a giant DNA between short and large oligomers is discussed in relation to the mechanisms of gene regulation in a living cell.


Asunto(s)
Química Física/métodos , ADN/química , Polilisina/química , Biofisica/métodos , Iones , Cinética , Sustancias Macromoleculares , Microscopía de Fuerza Atómica , Microscopía Fluorescente , Modelos Químicos , Conformación Molecular , Conformación de Ácido Nucleico
6.
Eur J Biochem ; 270(14): 3101-6, 2003 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-12846844

RESUMEN

Ascorbic acid is often regarded as an antioxidant in vivo, where it protects against cancer by scavenging DNA-damaging reactive oxygen species. However, the detailed mechanism of the action of ascorbic acid on genetic DNA is still unclear. We examined the effect of ascorbic acid on the higher-order structure of DNA through real-time observation by fluorescence microscopy. We found that ascorbic acid generates a pearling structure in single giant DNA molecules, with elongated and compact regions coexisting along a molecular chain. Results from electron microscopy and atomic force microscopy indicate that the compact regions assume a loosely packed conformation. A possible mechanism for the induction of this conformational change is discussed in relation to the interplay between the higher-order and second-order structures of DNA.


Asunto(s)
Ácido Ascórbico/farmacología , ADN Viral/química , Conformación de Ácido Nucleico/efectos de los fármacos , Bacteriófago T4/química , Bacteriófago T4/genética , Dicroismo Circular , ADN Viral/ultraestructura , Microscopía/métodos , Modelos Moleculares
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