Replication origins oriGNAI3 and oriB of the mammalian AMPD2 locus nested in a region of straight DNA flanked by intrinsically bent DNA sites

The aim of this work was to determine whether intrinsically bent DNA sites are present at, or close to, the mammalian replication origins oriGNAI3 and oriB in the Chinese hamster AMPD2 locus. Using an electrophoretic mobility shift assay and in silico analysis, we located four intrinsically bent DNA...

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Veröffentlicht in:BMB reports 2010, 43(11), , pp.744-749
Hauptverfasser: Balani, Valerio Americo, Universidade Estadual de Maringa, UEM, Parana, Brasil, Neto, Quirino Alves de Lima, Universidade Estadual de Maringa, UEM, Parana, Brasil, Takeda, Karen Izumi, Universidade Estadual de Maringa, UEM, Parana, Brasil, Gimenes, Fabricia, Universidade Estadual de Maringa, UEM, Parana, Brasil, Fiorini, Adriana, Universidade Estadual de Maringa, UEM, Parana, Brasil, Debatisse, Michelle, Institut Curie, UMR, Paris, France, Fernandez, Maria Aparecida, Universidade Estadual de Maringa, UEM, Parana, Brasil
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Sprache:eng
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Zusammenfassung:The aim of this work was to determine whether intrinsically bent DNA sites are present at, or close to, the mammalian replication origins oriGNAI3 and oriB in the Chinese hamster AMPD2 locus. Using an electrophoretic mobility shift assay and in silico analysis, we located four intrinsically bent DNA sites (b1 to b4) in a fragment that contains the oriGNA/3 and one site (b5) proximal to oriB. The helical parameters show that each bent DNA site is curved in a left-handed superhelical writhe. A 2D projection of 3D fragment trajectories revealed that oriGNA/3 is located in a relatively straight segment flanked by bent sites b1 and b2, which map in previously identified Scaffold/Matrix Attachment Region. Sites b3 and b4 are located approximately 2 kb downstream and force the fragment into a strong closed loop structure. The b5 site is also located in an S/MAR that is found just downstream of oriB.
ISSN:1976-6696
1976-670X
DOI:10.5483/BMBRep.2010.43.11.744