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DNA abasic lesions in a different light: solution structure of an endogenous topoisomerase II poison
S D Cline1, W R Jones, M P Stone
1Department of Biochemistry, Vanderbilt University School of Medicine, Nashville Tennessee 37232-0146, USA.
Abstract:
Topoisomerase II is the target for several anticancer drugs that "poison" the enzyme and convert it to a cellular toxin by increasing topoisomerase II-mediated DNA cleavage. In addition to these "exogenous topoisomerase II poisons," DNA lesions such as abasic sites act as "endogenous poisons" of the enzyme. Drugs and lesions are believed to stimulate DNA scission by altering the structure of the double helix within the cleavage site of the enzyme. However, the structural alterations that enhance cleavage are unknown. Since abasic sites are an intrinsic part of the genetic material, they represent an attractive model to assess DNA distortions that lead to altered topoisomerase II function. Therefore, the structure of a double-stranded dodecamer containing a tetrahydrofuran apurinic lesion at the +2 position of a topoisomerase II DNA cleavage site was determined by NMR spectroscopy. Three major features distinguished the apurinic structure ( = 0.095) from that of wild-type ( = 0.077). First, loss of base stacking at the lesion collapsed the major groove and reduced the distance between the two scissile phosphodiester bonds. Second, the apurinic lesion induced a bend that was centered about the topoisomerase II cleavage site. Third, the base immediately opposite the lesion was extrahelical and relocated to the minor groove. All of these structural alterations have the potential to influence interactions between topoisomerase II and its DNA substrate.
Insights
DNA lesions like abasic sites can poison topoisomerase II, an anticancer drug target. This study reveals how abasic sites distort DNA structure, potentially altering enzyme function and drug interactions.
Area of Science:
- Biochemistry
- Molecular Biology
- Structural Biology
Background:
- Topoisomerase II is a crucial target for anticancer drugs.
- These drugs, known as "poisons," enhance DNA cleavage by the enzyme.
- Endogenous DNA lesions, like abasic sites, can also act as topoisomerase II poisons.
Purpose of the Study:
- To investigate the structural basis by which abasic sites alter topoisomerase II function.
- To understand how DNA distortions enhance topoisomerase II-mediated DNA cleavage.
- To model endogenous topoisomerase II poisons using abasic sites.
Main Methods:
- Nuclear Magnetic Resonance (NMR) spectroscopy was used to determine the structure of a DNA dodecamer.
- The DNA dodecamer contained a tetrahydrofuran abasic lesion at a key topoisomerase II cleavage site.
- Structural parameters were compared between the abasic DNA and wild-type DNA.
Main Results:
- The abasic DNA structure showed significant differences compared to wild-type DNA.
- Loss of base stacking at the lesion collapsed the major groove and reduced scissile phosphodiester bond distance.
- The abasic lesion induced a bend in the DNA centered at the cleavage site, with the opposite base extruding into the minor groove.
Conclusions:
- Abasic sites induce distinct structural alterations in DNA at topoisomerase II cleavage sites.
- These structural changes, including major groove collapse and DNA bending, likely influence topoisomerase II interactions.
- Understanding these endogenous poison mechanisms may inform the development of novel anticancer therapies targeting topoisomerase II.