TY - JOUR
T1 - Atomic force microscopy reveals kinks in the p53 response element DNA
AU - Balagurumoorthy, P.
AU - Lindsay, Stuart
AU - Harrington, Rodney E.
N1 - Funding Information:
The authors gratefully acknowledge useful discussions, particularly with Dr Victor Zhurkin, Dr Ettore Appella and Dr Carol Prives. The authors thank Dr X.Z. Feng for help in MacMode AFM imaging and Dr Ilga Winicov and Dr Luda Shlyakhtenko for much useful information and support. Thanks are extended to Dr Ralph Bash and Mr Ken Eagan for useful discussions. Financial support is gratefully acknowledged from NIH grants GM53517 and CA70274 (REH).
PY - 2002/12/10
Y1 - 2002/12/10
N2 - p53 is a 53 kDa nuclear phosphoprotein. Its function as a tumor suppressor critically lies in its ability to recognize its target DNA response elements as a tetramer. Here, we report the structural theme intrinsic to the response element DNA that governs this recognition phenomenon. The intrinsic flexibility or dynamic bending between two distinctly different, but naturally occurring p53 response elements has been compared by ring closure. Results show that DNA binding sites containing helically phased d(CATG.CATG) tetra-nucleotide sequences at the centers of quasi-dyad symmetry in each half-response site are more intrinsically flexible (i.e. preferentially bent under axial stress) than their d(CTTG.CTTG) counterparts. Intriguingly, p53 binding sites containing these more flexible d(CATG.CATG) sequence elements also exhibit a stronger tendency for tetrameric binding of the p53 DNA binding domain peptide. Examination of the shapes of DNA microcircles obtained by circularization of oligomers constructed from such flexible p53 target DNA sequences in tandem using MacMode atomic force microscopy directly revealed sequence-specific kinks in solution. The tetra-nucleotide sequence d(CATG.CATG) is highly conserved in most functional p53 response elements. Consequently, we propose that the sequence-specific kinks originating from d(CATG.CATG) sequences could be a common structural theme in p53 response elements and as evident from the results reported here, could be a determinant of binding site recognition by the p53 protein and the subsequent stability of the p53-DNA complex.
AB - p53 is a 53 kDa nuclear phosphoprotein. Its function as a tumor suppressor critically lies in its ability to recognize its target DNA response elements as a tetramer. Here, we report the structural theme intrinsic to the response element DNA that governs this recognition phenomenon. The intrinsic flexibility or dynamic bending between two distinctly different, but naturally occurring p53 response elements has been compared by ring closure. Results show that DNA binding sites containing helically phased d(CATG.CATG) tetra-nucleotide sequences at the centers of quasi-dyad symmetry in each half-response site are more intrinsically flexible (i.e. preferentially bent under axial stress) than their d(CTTG.CTTG) counterparts. Intriguingly, p53 binding sites containing these more flexible d(CATG.CATG) sequence elements also exhibit a stronger tendency for tetrameric binding of the p53 DNA binding domain peptide. Examination of the shapes of DNA microcircles obtained by circularization of oligomers constructed from such flexible p53 target DNA sequences in tandem using MacMode atomic force microscopy directly revealed sequence-specific kinks in solution. The tetra-nucleotide sequence d(CATG.CATG) is highly conserved in most functional p53 response elements. Consequently, we propose that the sequence-specific kinks originating from d(CATG.CATG) sequences could be a common structural theme in p53 response elements and as evident from the results reported here, could be a determinant of binding site recognition by the p53 protein and the subsequent stability of the p53-DNA complex.
KW - Contour length
KW - DNA flexibility
KW - Kink
KW - MacMode atomic force microscopy
KW - p21 response element
KW - p53
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U2 - 10.1016/S0301-4622(02)00169-2
DO - 10.1016/S0301-4622(02)00169-2
M3 - Article
C2 - 12488030
AN - SCOPUS:17644442704
SN - 0301-4622
VL - 101-102
SP - 611
EP - 623
JO - Biophysical Chemistry
JF - Biophysical Chemistry
ER -