1AUL image
Deposition Date 1997-08-29
Release Date 1997-12-24
Last Version Date 2024-05-22
Entry Detail
PDB ID:
1AUL
Keywords:
Title:
SOLUTION STRUCTURE OF A HIGHLY STABLE DNA DUPLEX CONJUGATED TO A MINOR GROOVE BINDER, NMR, MINIMIZED AVERAGE STRUCTURE
Biological Source:
Source Organism:
(Taxon ID: )
Method Details:
Experimental Method:
Conformers Calculated:
6
Conformers Submitted:
1
Selection Criteria:
LEAST RESTRAINT VIOLATION
Macromolecular Entities
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(P*THXP*GP*AP*TP*TP*AP*TP*CP*TP*G)-3')
Chain IDs:A
Chain Length:10
Number of Molecules:1
Biological Source:
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*CP*AP*GP*AP*TP*AP*AP*TP*CP*A)-3')
Chain IDs:B
Chain Length:10
Number of Molecules:1
Biological Source:
Ligand Molecules
Primary Citation
Solution structure of a highly stable DNA duplex conjugated to a minor groove binder.
Nucleic Acids Res. 26 831 838 (1998)
PMID: 9443977 DOI: 10.1093/nar/26.3.831

Abstact

The tripeptide 1,2-dihydro-(3 H)-pyrrolo[3,2- e ]indole-7-carboxylate (CDPI3) binds to the minor groove of DNA with high affinity. When this minor groove binder is conjugated to the 5'-end of short oligonucleotides the conjugates form unusually stable hybrids with complementary DNA and thus may have useful diagnostic and/or therapeutic applications. In order to gain an understanding of the structural interactions between the CDPI3minor groove binding moiety and the DNA, we have determined and compared the solution structure of a duplex consisting of oligodeoxyribonucleotide 5'-TGATTATCTG-3' conjugated at the 5'-end to CDPI3 and its complementary strand to an unmodified control duplex of the same sequence using nuclear magnetic resonance techniques. Thermal denaturation studies indicated that the hybrid of this conjugate with its complementary strand had a melting temperature that was 30 degrees C higher compared with the unmodified control duplex. Following restrained molecular dynamics and relaxation matrix refinement, the solution structure of the CDPI3-conjugated DNA duplex demonstrated that the overall shape of the duplex was that of a straight B-type helix and that the CDPI3moiety was bound snugly in the minor groove, where it was stabilized by extensive van der Waal's interactions.

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