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KMID : 0624620100430110744
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BMB Reports
2010 Volume.43 No. 11 p.744 ~ p.749
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Replication origins oriGNAI3 and oriB of the mammalian AMPD2 locus nested in a region of straight DNA flanked by intrinsically bent DNA sites
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Balani Valerio Americo
De Lima Neto Quirino Alves
Takeda Karen Izumi
Gimenes Fabricia
Fiorini Adriana
Debatisse Michelle
Fernandez Maria Aparecida
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Abstract
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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.
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KEYWORD
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Electrophoretic mobility shift assay, In silico analysis, Intrinsically bent DNA sites, Mammalian amplified AMPD2 locus, oriGNAI3 and oriB replication origins
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