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Circular dichroism and conformational polymorphism of DNA.

Kypr J, Kejnovská I, Renciuk D, Vorlícková M - Nucleic Acids Res. (2009)

Bottom Line: This fast and simple method can be used at low- as well as high-DNA concentrations and with short- as well as long-DNA molecules.The course of detected CD spectral changes makes possible to distinguish between gradual changes within a single DNA conformation and cooperative isomerizations between discrete structural states.It enables measuring kinetics of the appearance of particular conformers and determination of their thermodynamic parameters.

View Article: PubMed Central - PubMed

Affiliation: Institute of Biophysics, vvi Academy of Sciences of the Czech Republic, Brno, Czech Republic. kypr@ibp.cz

ABSTRACT
Here we review studies that provided important information about conformational properties of DNA using circular dichroic (CD) spectroscopy. The conformational properties include the B-family of structures, A-form, Z-form, guanine quadruplexes, cytosine quadruplexes, triplexes and other less characterized structures. CD spectroscopy is extremely sensitive and relatively inexpensive. This fast and simple method can be used at low- as well as high-DNA concentrations and with short- as well as long-DNA molecules. The samples can easily be titrated with various agents to cause conformational isomerizations of DNA. The course of detected CD spectral changes makes possible to distinguish between gradual changes within a single DNA conformation and cooperative isomerizations between discrete structural states. It enables measuring kinetics of the appearance of particular conformers and determination of their thermodynamic parameters. In careful hands, CD spectroscopy is a valuable tool for mapping conformational properties of particular DNA molecules. Due to its numerous advantages, CD spectroscopy significantly participated in all basic conformational findings on DNA.

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MgCl2-induced B–Z and B–X transitions of poly[d(Gmethyl5C)] and poly[d(amino2AT)], respectively. Both polynucleotides were dissolved in 0.6 mM potassium phosphate buffer and 0.03 mM EDTA, pH 6.8. Left panel: the B–Z transition of poly[d(Gmethyl5C)] in 0.03 mM MgCl2 (thin line); spectra measured 1, 4, 17 and 88 min after increasing MgCl2 concentration to 0.05 mM (from dashed to full red line). Right panel: the B–X transition of poly[d(amino2AT)] in 0, 0.028, 0.056, 0.070 and 0.190 mM MgCl2 (from thin to the full violet line). Insert: the transitions of poly[d(Gmethyl5C)] (circles, Δε295) and poly[d(amino2AT)] (squares, Δε280). The left panel shows the MgCl2-induced B–Z and B–X transitions; on the right is the NaCl-induced reversion of the transitions and re-entry of the Z- and X-forms at high NaCl concentrations. It was necessary to wait hours to attain an equilibrium in the case of poly[d(Gmethyl5C)], whereas the equilibrium spectra of poly[d(amino2AT)] could be measured immediately after changing the solvent conditions. The sketch in the middle bottom indicates the difference in chemical structures of the two base pairs.
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Figure 7: MgCl2-induced B–Z and B–X transitions of poly[d(Gmethyl5C)] and poly[d(amino2AT)], respectively. Both polynucleotides were dissolved in 0.6 mM potassium phosphate buffer and 0.03 mM EDTA, pH 6.8. Left panel: the B–Z transition of poly[d(Gmethyl5C)] in 0.03 mM MgCl2 (thin line); spectra measured 1, 4, 17 and 88 min after increasing MgCl2 concentration to 0.05 mM (from dashed to full red line). Right panel: the B–X transition of poly[d(amino2AT)] in 0, 0.028, 0.056, 0.070 and 0.190 mM MgCl2 (from thin to the full violet line). Insert: the transitions of poly[d(Gmethyl5C)] (circles, Δε295) and poly[d(amino2AT)] (squares, Δε280). The left panel shows the MgCl2-induced B–Z and B–X transitions; on the right is the NaCl-induced reversion of the transitions and re-entry of the Z- and X-forms at high NaCl concentrations. It was necessary to wait hours to attain an equilibrium in the case of poly[d(Gmethyl5C)], whereas the equilibrium spectra of poly[d(amino2AT)] could be measured immediately after changing the solvent conditions. The sketch in the middle bottom indicates the difference in chemical structures of the two base pairs.

Mentions: Poly[d(AT)] can also adopt the left-handed Z-form (67,68). Interestingly, despite different chromophores, its CD spectrum is very similar to the CD spectrum of the Z-form of poly[d(GC)] (69). Methylation of cytosine at position 5 in poly[d(GC)] shifts the B–Z transition to low salt concentrations (70). As shown in Figure 7, poly[d(amino2AT)] also undergoes a salt-induced conformational transition at low salt concentrations (71). The resulting conformer has X-form characteristics and exhibits some features of A-form (72,73). Poly[d(Gmethyl5C)] and poly[d(amino2AT)] differ in the placement of the amino and keto groups in the major groove (Figure 7, bottom insert). This difference causes the two polydeoxynucleotides to undergo distinct conformational transitions under identical conditions (Figure 7, upper insert): the first polynucleotide transforms highly cooperatively to Z-form and the second, in a less cooperative manner, to X-form.Figure 7.


Circular dichroism and conformational polymorphism of DNA.

Kypr J, Kejnovská I, Renciuk D, Vorlícková M - Nucleic Acids Res. (2009)

MgCl2-induced B–Z and B–X transitions of poly[d(Gmethyl5C)] and poly[d(amino2AT)], respectively. Both polynucleotides were dissolved in 0.6 mM potassium phosphate buffer and 0.03 mM EDTA, pH 6.8. Left panel: the B–Z transition of poly[d(Gmethyl5C)] in 0.03 mM MgCl2 (thin line); spectra measured 1, 4, 17 and 88 min after increasing MgCl2 concentration to 0.05 mM (from dashed to full red line). Right panel: the B–X transition of poly[d(amino2AT)] in 0, 0.028, 0.056, 0.070 and 0.190 mM MgCl2 (from thin to the full violet line). Insert: the transitions of poly[d(Gmethyl5C)] (circles, Δε295) and poly[d(amino2AT)] (squares, Δε280). The left panel shows the MgCl2-induced B–Z and B–X transitions; on the right is the NaCl-induced reversion of the transitions and re-entry of the Z- and X-forms at high NaCl concentrations. It was necessary to wait hours to attain an equilibrium in the case of poly[d(Gmethyl5C)], whereas the equilibrium spectra of poly[d(amino2AT)] could be measured immediately after changing the solvent conditions. The sketch in the middle bottom indicates the difference in chemical structures of the two base pairs.
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Figure 7: MgCl2-induced B–Z and B–X transitions of poly[d(Gmethyl5C)] and poly[d(amino2AT)], respectively. Both polynucleotides were dissolved in 0.6 mM potassium phosphate buffer and 0.03 mM EDTA, pH 6.8. Left panel: the B–Z transition of poly[d(Gmethyl5C)] in 0.03 mM MgCl2 (thin line); spectra measured 1, 4, 17 and 88 min after increasing MgCl2 concentration to 0.05 mM (from dashed to full red line). Right panel: the B–X transition of poly[d(amino2AT)] in 0, 0.028, 0.056, 0.070 and 0.190 mM MgCl2 (from thin to the full violet line). Insert: the transitions of poly[d(Gmethyl5C)] (circles, Δε295) and poly[d(amino2AT)] (squares, Δε280). The left panel shows the MgCl2-induced B–Z and B–X transitions; on the right is the NaCl-induced reversion of the transitions and re-entry of the Z- and X-forms at high NaCl concentrations. It was necessary to wait hours to attain an equilibrium in the case of poly[d(Gmethyl5C)], whereas the equilibrium spectra of poly[d(amino2AT)] could be measured immediately after changing the solvent conditions. The sketch in the middle bottom indicates the difference in chemical structures of the two base pairs.
Mentions: Poly[d(AT)] can also adopt the left-handed Z-form (67,68). Interestingly, despite different chromophores, its CD spectrum is very similar to the CD spectrum of the Z-form of poly[d(GC)] (69). Methylation of cytosine at position 5 in poly[d(GC)] shifts the B–Z transition to low salt concentrations (70). As shown in Figure 7, poly[d(amino2AT)] also undergoes a salt-induced conformational transition at low salt concentrations (71). The resulting conformer has X-form characteristics and exhibits some features of A-form (72,73). Poly[d(Gmethyl5C)] and poly[d(amino2AT)] differ in the placement of the amino and keto groups in the major groove (Figure 7, bottom insert). This difference causes the two polydeoxynucleotides to undergo distinct conformational transitions under identical conditions (Figure 7, upper insert): the first polynucleotide transforms highly cooperatively to Z-form and the second, in a less cooperative manner, to X-form.Figure 7.

Bottom Line: This fast and simple method can be used at low- as well as high-DNA concentrations and with short- as well as long-DNA molecules.The course of detected CD spectral changes makes possible to distinguish between gradual changes within a single DNA conformation and cooperative isomerizations between discrete structural states.It enables measuring kinetics of the appearance of particular conformers and determination of their thermodynamic parameters.

View Article: PubMed Central - PubMed

Affiliation: Institute of Biophysics, vvi Academy of Sciences of the Czech Republic, Brno, Czech Republic. kypr@ibp.cz

ABSTRACT
Here we review studies that provided important information about conformational properties of DNA using circular dichroic (CD) spectroscopy. The conformational properties include the B-family of structures, A-form, Z-form, guanine quadruplexes, cytosine quadruplexes, triplexes and other less characterized structures. CD spectroscopy is extremely sensitive and relatively inexpensive. This fast and simple method can be used at low- as well as high-DNA concentrations and with short- as well as long-DNA molecules. The samples can easily be titrated with various agents to cause conformational isomerizations of DNA. The course of detected CD spectral changes makes possible to distinguish between gradual changes within a single DNA conformation and cooperative isomerizations between discrete structural states. It enables measuring kinetics of the appearance of particular conformers and determination of their thermodynamic parameters. In careful hands, CD spectroscopy is a valuable tool for mapping conformational properties of particular DNA molecules. Due to its numerous advantages, CD spectroscopy significantly participated in all basic conformational findings on DNA.

Show MeSH