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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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CD spectra reflecting the temperature-controlled psi-type condensation of poly[d(AT)] in ethanol-NaClO4 solutions. Solution A was 34% ethanol, 0.6 M NaClO4; solution B was 30% ethanol, 2.0 M NaClO4.
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Figure 8: CD spectra reflecting the temperature-controlled psi-type condensation of poly[d(AT)] in ethanol-NaClO4 solutions. Solution A was 34% ethanol, 0.6 M NaClO4; solution B was 30% ethanol, 2.0 M NaClO4.

Mentions: DNA containing natural bases does not absorb light above 300 nm. Detection of a signal above 300 nm indicates that the DNA is condensed into particles that scatter light. This region of the spectrum must be monitored, as when this type of signal is observed, the CD changes can no longer be interpreted in terms of changes in DNA secondary structure. However, species of regularly packed, condensed DNA can be studied by CD (74,75). Infrared CD spectroscopy in combination with atomic force microscopy has proven very powerful for these analyses (76). The associates are called psi-forms or DNA wires (77,78). The psi-forms are chromosome analogues with a regular tertiary folding. These forms are characterized by either positive or negative CD signals with extremely large amplitudes (Figure 8) that are caused by chiral condensates possessing large-scale helicity. The condensation can be caused by a number of factors like high ionic strength polyethylene glycol (PEG) or other alcohols or basic proteins. These factors induce formation of short non-B (depending on nucleotide sequence) DNA segments that propagate as a perturbation along the DNA double helix and result in cooperative condensation. Condensation and decondensation processes may take place in vivo due to DNA-binding proteins such as histones and protamines, which control and modulate ionic strength and hydrophobic environment in the close vicinity of DNA molecules.Figure 8.


Circular dichroism and conformational polymorphism of DNA.

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

CD spectra reflecting the temperature-controlled psi-type condensation of poly[d(AT)] in ethanol-NaClO4 solutions. Solution A was 34% ethanol, 0.6 M NaClO4; solution B was 30% ethanol, 2.0 M NaClO4.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2665218&req=5

Figure 8: CD spectra reflecting the temperature-controlled psi-type condensation of poly[d(AT)] in ethanol-NaClO4 solutions. Solution A was 34% ethanol, 0.6 M NaClO4; solution B was 30% ethanol, 2.0 M NaClO4.
Mentions: DNA containing natural bases does not absorb light above 300 nm. Detection of a signal above 300 nm indicates that the DNA is condensed into particles that scatter light. This region of the spectrum must be monitored, as when this type of signal is observed, the CD changes can no longer be interpreted in terms of changes in DNA secondary structure. However, species of regularly packed, condensed DNA can be studied by CD (74,75). Infrared CD spectroscopy in combination with atomic force microscopy has proven very powerful for these analyses (76). The associates are called psi-forms or DNA wires (77,78). The psi-forms are chromosome analogues with a regular tertiary folding. These forms are characterized by either positive or negative CD signals with extremely large amplitudes (Figure 8) that are caused by chiral condensates possessing large-scale helicity. The condensation can be caused by a number of factors like high ionic strength polyethylene glycol (PEG) or other alcohols or basic proteins. These factors induce formation of short non-B (depending on nucleotide sequence) DNA segments that propagate as a perturbation along the DNA double helix and result in cooperative condensation. Condensation and decondensation processes may take place in vivo due to DNA-binding proteins such as histones and protamines, which control and modulate ionic strength and hydrophobic environment in the close vicinity of DNA molecules.Figure 8.

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
Related in: MedlinePlus