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http://dx.doi.org/10.5483/BMBRep.2010.43.11.744

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

Balani, Valerio Americo (Departamento de Biologia Celular e Genetica, Universidade Estadual de Maringa)
De Lima Neto, Quirino Alves (Departamento de Biologia Celular e Genetica, Universidade Estadual de Maringa)
Takeda, Karen Izumi (Departamento de Biologia Celular e Genetica, Universidade Estadual de Maringa)
Gimenes, Fabricia (Departamento de Biologia Celular e Genetica, Universidade Estadual de Maringa)
Fiorini, Adriana (Departamento de Biologia Celular e Genetica, Universidade Estadual de Maringa)
Debatisse, Michelle (Institut Curie)
Fernandez, Maria Aparecida (Departamento de Biologia Celular e Genetica, Universidade Estadual de Maringa)
Publication Information
BMB Reports / v.43, no.11, 2010 , pp. 744-749 More about this Journal
Abstract
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 oriGNAI3 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 oriGNAI3 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.
Keywords
Electrophoretic mobility shift assay; In silico analysis; Intrinsically bent DNA sites; Mammalian amplified AMPD2 locus; oriGNAI3 and oriB replication origins;
Citations & Related Records
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