Beilstein J. Org. Chem.2014,10, 2293–2306, doi:10.3762/bjoc.10.239
interstrand cross-linked DNA is an interesting tool to study DNA binding proteins that locally open up the DNA duplex by flipping single bases out of the DNA helix or melting whole stretches of base pairs to perform their function. The ideal DNAcross-link to study protein–DNA interactions should be specific
demonstrate that the presented cross-linked DNA with an ethylene-linked A/T base pair analog at the target position is a useful tool to determine the base-flipping equilibrium constant of a base-flipping enzyme which lies mostly on the extrahelical side for M.TaqI.
Keywords: DNA base flipping; DNAcross-link
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Graphical Abstract
Figure 1:
Covalent cross-linking of a I6S/U4S or G6S/U4S base pair within duplex ODN 1∙2 (a) by bis-alkylatio...