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Induced topological changes in DNA complexes: influence of DNA sequences and small molecule structures.

Hunt RA, Munde M, Kumar A, Ismail MA, Farahat AA, Arafa RK, Say M, Batista-Parra A, Tevis D, Boykin DW, Wilson WD - Nucleic Acids Res. (2011)

Bottom Line: The changes caused by binding of the compounds are sequence dependent, but generally the topological effects on AAAAA and AAATT are similar as are the effects on TTTAA and ATATA.A total of 13 compounds with a variety of structural differences were evaluated for topological changes to DNA.Similar, but generally smaller, effects are seen with TTTAA.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, Georgia State University, Atlanta, GA 30302, USA.

ABSTRACT
Heterocyclic diamidines are compounds with antiparasitic properties that target the minor groove of kinetoplast DNA. The mechanism of action of these compounds is unknown, but topological changes to DNA structures are likely to be involved. In this study, we have developed a polyacrylamide gel electrophoresis-based screening method to determine topological effects of heterocyclic diamidines on four minor groove target sequences: AAAAA, TTTAA, AAATT and ATATA. The AAAAA and AAATT sequences have the largest intrinsic bend, whereas the TTTAA and ATATA sequences are relatively straight. The changes caused by binding of the compounds are sequence dependent, but generally the topological effects on AAAAA and AAATT are similar as are the effects on TTTAA and ATATA. A total of 13 compounds with a variety of structural differences were evaluated for topological changes to DNA. All compounds decrease the mobility of the ATATA sequence that is consistent with decreased minor groove width and bending of the relatively straight DNA into the minor groove. Similar, but generally smaller, effects are seen with TTTAA. The intrinsically bent AAAAA and AAATT sequences, which have more narrow minor grooves, have smaller mobility changes on binding that are consistent with increased or decreased bending depending on compound structure.

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Compounds grouped by structural similarity.
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Figure 1: Compounds grouped by structural similarity.

Mentions: The interesting DNA topological changes observed on binding of DB75 and analogs suggested that it would be worthwhile to evaluate additional compounds as well as DNA sequences to determine the generality of the observations. Such studies will also help to establish relationships for compound structural effects on the topology of kDNA and other biologically important sequences. In order to increase the number of compounds and DNA sequences that can be evaluated per gel, a method that does not use compound in the gel is needed. Here a different PAGE method (Method 2), without compound in the gel, has been tested. Method 2 was tested with compounds of varied structure (Figure 1), and binding constants were determined to establish the limits for application of the method. The PAGE method without compound in the gel is able to qualitatively reproduce the more quantitative results with Method 1, and with Method 2 it is possible to study several compounds at different ratios to DNA sites with different DNAs on one gel.Figure 1.


Induced topological changes in DNA complexes: influence of DNA sequences and small molecule structures.

Hunt RA, Munde M, Kumar A, Ismail MA, Farahat AA, Arafa RK, Say M, Batista-Parra A, Tevis D, Boykin DW, Wilson WD - Nucleic Acids Res. (2011)

Compounds grouped by structural similarity.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3105405&req=5

Figure 1: Compounds grouped by structural similarity.
Mentions: The interesting DNA topological changes observed on binding of DB75 and analogs suggested that it would be worthwhile to evaluate additional compounds as well as DNA sequences to determine the generality of the observations. Such studies will also help to establish relationships for compound structural effects on the topology of kDNA and other biologically important sequences. In order to increase the number of compounds and DNA sequences that can be evaluated per gel, a method that does not use compound in the gel is needed. Here a different PAGE method (Method 2), without compound in the gel, has been tested. Method 2 was tested with compounds of varied structure (Figure 1), and binding constants were determined to establish the limits for application of the method. The PAGE method without compound in the gel is able to qualitatively reproduce the more quantitative results with Method 1, and with Method 2 it is possible to study several compounds at different ratios to DNA sites with different DNAs on one gel.Figure 1.

Bottom Line: The changes caused by binding of the compounds are sequence dependent, but generally the topological effects on AAAAA and AAATT are similar as are the effects on TTTAA and ATATA.A total of 13 compounds with a variety of structural differences were evaluated for topological changes to DNA.Similar, but generally smaller, effects are seen with TTTAA.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, Georgia State University, Atlanta, GA 30302, USA.

ABSTRACT
Heterocyclic diamidines are compounds with antiparasitic properties that target the minor groove of kinetoplast DNA. The mechanism of action of these compounds is unknown, but topological changes to DNA structures are likely to be involved. In this study, we have developed a polyacrylamide gel electrophoresis-based screening method to determine topological effects of heterocyclic diamidines on four minor groove target sequences: AAAAA, TTTAA, AAATT and ATATA. The AAAAA and AAATT sequences have the largest intrinsic bend, whereas the TTTAA and ATATA sequences are relatively straight. The changes caused by binding of the compounds are sequence dependent, but generally the topological effects on AAAAA and AAATT are similar as are the effects on TTTAA and ATATA. A total of 13 compounds with a variety of structural differences were evaluated for topological changes to DNA. All compounds decrease the mobility of the ATATA sequence that is consistent with decreased minor groove width and bending of the relatively straight DNA into the minor groove. Similar, but generally smaller, effects are seen with TTTAA. The intrinsically bent AAAAA and AAATT sequences, which have more narrow minor grooves, have smaller mobility changes on binding that are consistent with increased or decreased bending depending on compound structure.

Show MeSH
Related in: MedlinePlus