Abstract:
:We have determined the three-dimensional structure of a non-self-complementary oligodeoxynucleotide duplex that contains a model abasic site. The duplex contains six GC base pairs plus the abasic site at the center of one strand and corresponds to an abasic frameshift. Two-dimensional NMR studies on the nonexchangeable protons show that the guanine bases on either side of the abasic site are stacked over each other and that the abasic site is rotated out of the helix. Close proton-proton interactions are observed between the H4' proton of the abasic site and sugar protons of the guanosine in the 5' direction, which allows the position of the free sugar to be well-defined. NOE buildup curves from NOESY spectra recorded at very short mixing times were used to calculate a set of interproton distances. This data set was incorporated into the refinement of the oligonucleotide structure by molecular mechanics calculations. Two conformations that differ in the sugar conformation of the guanosine next to the abasic site in the 3' direction were necessary to fit all the NMR data. One of these two conformations could only be stabilized by addition of counterions at specific sites.
journal_name
Biochemistryjournal_title
Biochemistryauthors
Cuniasse P,Sowers LC,Eritja R,Kaplan B,Goodman MF,Cognet JA,Le Bret M,Guschlbauer W,Fazakerley GVdoi
10.1021/bi00431a009subject
Has Abstractpub_date
1989-03-07 00:00:00pages
2018-26issue
5eissn
0006-2960issn
1520-4995journal_volume
28pub_type
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