2hpx: Difference between revisions

Newer edit →

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 4: / Line 4: @@
 ==Overview==
-A 4'-oxidized abasic site (X) has been synthesized in a defined duplex DNA, sequence, 5'-d(CCAAAGXACCGGG)-3'/3'-d(GGTTTCATGGCCC)-5' (1). Its structure, has been determined by two-dimensional NMR methods, molecular modeling, and molecular dynamics simulations. 1 is globally B-form with the base (A), opposite X intrahelical and well-stacked. Only the alpha anomer of X is, observed, and the abasic site deoxyribose is largely intrahelical. These, results are compared with a normal abasic site (Y) in the same sequence, context (2). Y is composed of a 60:40 mixture of alpha and beta anomers, (2alpha and 2beta). In both 2alpha and 2beta, the base (A) opposite Y is, intrahelical and well-stacked and the abasic site deoxyribose is, predominantly extrahelical, consistent with the reported structures of the, normal abasic site in a similar sequence context [Hoehn, S. T., Turner, C., J., and Stubbe, J. (2001) Nucleic Acids Res. 29, 3413-3423]. Molecular, dynamics simulations reveal that the normal abasic site appears to be, conformationally more flexible than the 4'-oxidized abasic site. The, importance of the structure and flexibility of the abasic site in the, recognition by the DNA repair enzyme Ape1 is discussed.
+A 4'-oxidized abasic site (X) has been synthesized in a defined duplex DNA sequence, 5'-d(CCAAAGXACCGGG)-3'/3'-d(GGTTTCATGGCCC)-5' (1). Its structure has been determined by two-dimensional NMR methods, molecular modeling, and molecular dynamics simulations. 1 is globally B-form with the base (A) opposite X intrahelical and well-stacked. Only the alpha anomer of X is observed, and the abasic site deoxyribose is largely intrahelical. These results are compared with a normal abasic site (Y) in the same sequence context (2). Y is composed of a 60:40 mixture of alpha and beta anomers (2alpha and 2beta). In both 2alpha and 2beta, the base (A) opposite Y is intrahelical and well-stacked and the abasic site deoxyribose is predominantly extrahelical, consistent with the reported structures of the normal abasic site in a similar sequence context [Hoehn, S. T., Turner, C. J., and Stubbe, J. (2001) Nucleic Acids Res. 29, 3413-3423]. Molecular dynamics simulations reveal that the normal abasic site appears to be conformationally more flexible than the 4'-oxidized abasic site. The importance of the structure and flexibility of the abasic site in the recognition by the DNA repair enzyme Ape1 is discussed.
 ==About this Structure==
@@ Line 12: / Line 12: @@
 Nuclear magnetic resonance structural studies and molecular modeling of duplex DNA containing normal and 4'-oxidized abasic sites., Chen J, Dupradeau FY, Case DA, Turner CJ, Stubbe J, Biochemistry. 2007 Mar 20;46(11):3096-107. Epub 2007 Feb 27. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17323932 17323932]
 [[Category: Protein complex]]
-[[Category: Case, D.A.]]
+[[Category: Case, D A.]]
 [[Category: Chen, J.]]
-[[Category: Dupradeau, F.Y.]]
+[[Category: Dupradeau, F Y.]]
 [[Category: Stubbe, J.]]
-[[Category: Turner, C.J.]]
+[[Category: Turner, C J.]]
 [[Category: abasic site]]
 [[Category: bleomycin]]
@@ Line 23: / Line 23: @@
 [[Category: nmr]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 23 15:06:35 2008''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 17:44:23 2008''