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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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Example biosensor-SPR sensorgrams (instrument response in RU values versus time) for binding of DB262 to (A) ATATA and (B) AAATT at 25°C. The unbound compound concentrations in the flow solutions range from 0.005 µM in the lowest curve to 1 µM in the top curve. Experiments were conducted in cacodylic acid buffer with 0.1 M NaCl. (C) SPR binding plots for DB262 in the presence of ATATA (top), AAATT (middle) and TTTAA (lower). The RU values from the steady-state region of SPR sensorgrams are plotted versus the unbound compound concentration. The RUs and the concentrations of DB262 are from repeat experiments. The lines in the Figure are for one or two-site fitting (‘Methods’ section). K values for AAATT were obtained by using a one-site model and for ATATA and TTTAA with a two-site model to get K1 and K2. K2 was much lower than K1 and only K1 values were used in the comparison plot in Figure 7.
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Figure 6: Example biosensor-SPR sensorgrams (instrument response in RU values versus time) for binding of DB262 to (A) ATATA and (B) AAATT at 25°C. The unbound compound concentrations in the flow solutions range from 0.005 µM in the lowest curve to 1 µM in the top curve. Experiments were conducted in cacodylic acid buffer with 0.1 M NaCl. (C) SPR binding plots for DB262 in the presence of ATATA (top), AAATT (middle) and TTTAA (lower). The RU values from the steady-state region of SPR sensorgrams are plotted versus the unbound compound concentration. The RUs and the concentrations of DB262 are from repeat experiments. The lines in the Figure are for one or two-site fitting (‘Methods’ section). K values for AAATT were obtained by using a one-site model and for ATATA and TTTAA with a two-site model to get K1 and K2. K2 was much lower than K1 and only K1 values were used in the comparison plot in Figure 7.

Mentions: Example sensorgrams for DB262, which has similar structure and DNA binding to DB75, show that the compound has relatively fast association and dissociation kinetics for binding to ATATA and AAATT (Figure 6A and B). In this case K values can be determined by fitting the kinetic constants for association (ka) and dissociation (kd) or from the steady-state response where the rates of association and dissociation are equal (Figure 6A and B). The steady-state method is not subject to any mass transport issues at the sensor surface, and steady-state RU values for DB262 and three DNA sequences are plotted in Figure 6C. K values were determined by fitting the plots in Figure 6C to one or two site functions as described in the ‘Materials and Methods’ section. In all cases the K1 values are significantly larger than the K2 values when a two-site fit was required, for example, with the ATATA and TTTAA DNAs (Figure 6C). A simple two-site binding function can be used in these cases because the primary binding is for complex formation at the AT target sequences while the much weaker, secondary binding is generally a non-specific electrostatic interaction (34). Results for DB921, which has slower association and dissociation rates, are shown in Supplementary Figure SM15, Supplementary Data. K values for DB921 and related compounds were determined by global fitting of the sensorgrams to determine ka and kd values as a function of the compound concentration in the flow solution. DB921, DB985 and DB1055 are generally quite strong minor groove binding compounds. For visualization, primary binding constants (K1) are compared for representative compounds as a histogram in Figure 7, and the actual K values are tabulated in Supplementary Figure SM15.Figure 6.


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)

Example biosensor-SPR sensorgrams (instrument response in RU values versus time) for binding of DB262 to (A) ATATA and (B) AAATT at 25°C. The unbound compound concentrations in the flow solutions range from 0.005 µM in the lowest curve to 1 µM in the top curve. Experiments were conducted in cacodylic acid buffer with 0.1 M NaCl. (C) SPR binding plots for DB262 in the presence of ATATA (top), AAATT (middle) and TTTAA (lower). The RU values from the steady-state region of SPR sensorgrams are plotted versus the unbound compound concentration. The RUs and the concentrations of DB262 are from repeat experiments. The lines in the Figure are for one or two-site fitting (‘Methods’ section). K values for AAATT were obtained by using a one-site model and for ATATA and TTTAA with a two-site model to get K1 and K2. K2 was much lower than K1 and only K1 values were used in the comparison plot in Figure 7.
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Figure 6: Example biosensor-SPR sensorgrams (instrument response in RU values versus time) for binding of DB262 to (A) ATATA and (B) AAATT at 25°C. The unbound compound concentrations in the flow solutions range from 0.005 µM in the lowest curve to 1 µM in the top curve. Experiments were conducted in cacodylic acid buffer with 0.1 M NaCl. (C) SPR binding plots for DB262 in the presence of ATATA (top), AAATT (middle) and TTTAA (lower). The RU values from the steady-state region of SPR sensorgrams are plotted versus the unbound compound concentration. The RUs and the concentrations of DB262 are from repeat experiments. The lines in the Figure are for one or two-site fitting (‘Methods’ section). K values for AAATT were obtained by using a one-site model and for ATATA and TTTAA with a two-site model to get K1 and K2. K2 was much lower than K1 and only K1 values were used in the comparison plot in Figure 7.
Mentions: Example sensorgrams for DB262, which has similar structure and DNA binding to DB75, show that the compound has relatively fast association and dissociation kinetics for binding to ATATA and AAATT (Figure 6A and B). In this case K values can be determined by fitting the kinetic constants for association (ka) and dissociation (kd) or from the steady-state response where the rates of association and dissociation are equal (Figure 6A and B). The steady-state method is not subject to any mass transport issues at the sensor surface, and steady-state RU values for DB262 and three DNA sequences are plotted in Figure 6C. K values were determined by fitting the plots in Figure 6C to one or two site functions as described in the ‘Materials and Methods’ section. In all cases the K1 values are significantly larger than the K2 values when a two-site fit was required, for example, with the ATATA and TTTAA DNAs (Figure 6C). A simple two-site binding function can be used in these cases because the primary binding is for complex formation at the AT target sequences while the much weaker, secondary binding is generally a non-specific electrostatic interaction (34). Results for DB921, which has slower association and dissociation rates, are shown in Supplementary Figure SM15, Supplementary Data. K values for DB921 and related compounds were determined by global fitting of the sensorgrams to determine ka and kd values as a function of the compound concentration in the flow solution. DB921, DB985 and DB1055 are generally quite strong minor groove binding compounds. For visualization, primary binding constants (K1) are compared for representative compounds as a histogram in Figure 7, and the actual K values are tabulated in Supplementary Figure SM15.Figure 6.

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