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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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B–A, B–X and A–X transitions of poly[d(AT)]. From the left to the right: CD spectrum of the B-form measured in 1 mM sodium phosphate, 0.25 mM EDTA, pH 7 (black); ethanol-induced B–A transition measured at 10°C and monitored by Δε at 262 nm (96% ethanol was added to the poly[d(AT)] sample). CD spectrum of the A-form in the presence of 0.2 mM sodium phosphate and 0.05 mM EDTA and 80% ethanol (blue); ethanol induced B–X transition measured in the presence of 1.3 mM CsCl at 4°C and monitored by Δε at 278 nm (1.3 mM CsCl was also present in ethanol). CD spectrum of the X-form in 0.15 mM sodium phosphate, 0.04 mM EDTA, 1.3 mM CsCl and 82% ethanol (violet). CD spectra reflecting the A–X transition induced by addition of CsCl (0, 0.53, 0.59 and 1.3 mM) to the A-form at 4°C and the course of the transition monitored by Δε at 278 nm. This figure was adapted from Vorlickova M. et al. (J. Biomol. Struct. Dyn. 1991, 9, 571–578) with permission.
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Figure 6: B–A, B–X and A–X transitions of poly[d(AT)]. From the left to the right: CD spectrum of the B-form measured in 1 mM sodium phosphate, 0.25 mM EDTA, pH 7 (black); ethanol-induced B–A transition measured at 10°C and monitored by Δε at 262 nm (96% ethanol was added to the poly[d(AT)] sample). CD spectrum of the A-form in the presence of 0.2 mM sodium phosphate and 0.05 mM EDTA and 80% ethanol (blue); ethanol induced B–X transition measured in the presence of 1.3 mM CsCl at 4°C and monitored by Δε at 278 nm (1.3 mM CsCl was also present in ethanol). CD spectrum of the X-form in 0.15 mM sodium phosphate, 0.04 mM EDTA, 1.3 mM CsCl and 82% ethanol (violet). CD spectra reflecting the A–X transition induced by addition of CsCl (0, 0.53, 0.59 and 1.3 mM) to the A-form at 4°C and the course of the transition monitored by Δε at 278 nm. This figure was adapted from Vorlickova M. et al. (J. Biomol. Struct. Dyn. 1991, 9, 571–578) with permission.

Mentions: Poly[d(AT)] and e.g. d(TA)4 provide a remarkable CD spectrum at high concentrations of CsF (63) or in aqueous ethanol (64,65). In the presence of millimolar NaCl concentrations, poly[d(AT)] isomerizes into the A-form at high ethanol concentrations (27) (Figure 6). Replacement of NaCl by the same amount of CsCl results in the appearance of a spectrum with a large negative band at 280 nm and a positive one at 210 nm (Figure 6). All the spectral changes proceed with a fast kinetics. The structure in the presence of CsCl in ethanol or in CsF in aqueous solution was called X-DNA. It provides two well-separated signals in the 31P NMR spectrum like the Z-form (63). But X-DNA is not Z-DNA as the 31P signal assignments for the purine–pyrimidine and pyrimidine–purine are opposite for the two structures (63). Cooperativity of the B–X and A–X transitions (Figure 6) also excludes the possibility that X-DNA is a member of the B- or A-DNA conformational families. A structure has recently been crystallized (66) that may correspond to the anomalous X-DNA CD spectrum. It contains Hoogsteen base pairs.Figure 6.


Circular dichroism and conformational polymorphism of DNA.

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

B–A, B–X and A–X transitions of poly[d(AT)]. From the left to the right: CD spectrum of the B-form measured in 1 mM sodium phosphate, 0.25 mM EDTA, pH 7 (black); ethanol-induced B–A transition measured at 10°C and monitored by Δε at 262 nm (96% ethanol was added to the poly[d(AT)] sample). CD spectrum of the A-form in the presence of 0.2 mM sodium phosphate and 0.05 mM EDTA and 80% ethanol (blue); ethanol induced B–X transition measured in the presence of 1.3 mM CsCl at 4°C and monitored by Δε at 278 nm (1.3 mM CsCl was also present in ethanol). CD spectrum of the X-form in 0.15 mM sodium phosphate, 0.04 mM EDTA, 1.3 mM CsCl and 82% ethanol (violet). CD spectra reflecting the A–X transition induced by addition of CsCl (0, 0.53, 0.59 and 1.3 mM) to the A-form at 4°C and the course of the transition monitored by Δε at 278 nm. This figure was adapted from Vorlickova M. et al. (J. Biomol. Struct. Dyn. 1991, 9, 571–578) with permission.
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Related In: Results  -  Collection

License
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Figure 6: B–A, B–X and A–X transitions of poly[d(AT)]. From the left to the right: CD spectrum of the B-form measured in 1 mM sodium phosphate, 0.25 mM EDTA, pH 7 (black); ethanol-induced B–A transition measured at 10°C and monitored by Δε at 262 nm (96% ethanol was added to the poly[d(AT)] sample). CD spectrum of the A-form in the presence of 0.2 mM sodium phosphate and 0.05 mM EDTA and 80% ethanol (blue); ethanol induced B–X transition measured in the presence of 1.3 mM CsCl at 4°C and monitored by Δε at 278 nm (1.3 mM CsCl was also present in ethanol). CD spectrum of the X-form in 0.15 mM sodium phosphate, 0.04 mM EDTA, 1.3 mM CsCl and 82% ethanol (violet). CD spectra reflecting the A–X transition induced by addition of CsCl (0, 0.53, 0.59 and 1.3 mM) to the A-form at 4°C and the course of the transition monitored by Δε at 278 nm. This figure was adapted from Vorlickova M. et al. (J. Biomol. Struct. Dyn. 1991, 9, 571–578) with permission.
Mentions: Poly[d(AT)] and e.g. d(TA)4 provide a remarkable CD spectrum at high concentrations of CsF (63) or in aqueous ethanol (64,65). In the presence of millimolar NaCl concentrations, poly[d(AT)] isomerizes into the A-form at high ethanol concentrations (27) (Figure 6). Replacement of NaCl by the same amount of CsCl results in the appearance of a spectrum with a large negative band at 280 nm and a positive one at 210 nm (Figure 6). All the spectral changes proceed with a fast kinetics. The structure in the presence of CsCl in ethanol or in CsF in aqueous solution was called X-DNA. It provides two well-separated signals in the 31P NMR spectrum like the Z-form (63). But X-DNA is not Z-DNA as the 31P signal assignments for the purine–pyrimidine and pyrimidine–purine are opposite for the two structures (63). Cooperativity of the B–X and A–X transitions (Figure 6) also excludes the possibility that X-DNA is a member of the B- or A-DNA conformational families. A structure has recently been crystallized (66) that may correspond to the anomalous X-DNA CD spectrum. It contains Hoogsteen base pairs.Figure 6.

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