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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 and sketches of distinct quadruplex arrangements of a human telomere fragment G3(TTAG3)7. In green is the spectrum in 150 mM NaCl and the oligonucleotide adopts the antiparallel basket type quadruplex (92); in grey is the spectrum in 150 mM KCl; in blue dashes is the spectrum in 10 mM KCl, 57% ethanol measured 24 h after ethanol addition; and in blue is the spectrum of the same sample measured after denaturation and slow cooling to room temperature. The final spectrum corresponds to parallel quadruplex observed in the crystal (93).
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Figure 9: CD spectra and sketches of distinct quadruplex arrangements of a human telomere fragment G3(TTAG3)7. In green is the spectrum in 150 mM NaCl and the oligonucleotide adopts the antiparallel basket type quadruplex (92); in grey is the spectrum in 150 mM KCl; in blue dashes is the spectrum in 10 mM KCl, 57% ethanol measured 24 h after ethanol addition; and in blue is the spectrum of the same sample measured after denaturation and slow cooling to room temperature. The final spectrum corresponds to parallel quadruplex observed in the crystal (93).

Mentions: Conformations of DNA in aqueous solutions and crystals differ. CD spectroscopy contributed to the elucidation of the relationship between DNA conformations in these two environments. It was shown that the DNA structures observed in crystals are adopted in aqueous ethanol or trifluorethanol solutions (Figure 9) (30). This observation has been made for DNA duplexes and also guanine quadruplexes (44,46,80).Figure 9.


Circular dichroism and conformational polymorphism of DNA.

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

CD spectra and sketches of distinct quadruplex arrangements of a human telomere fragment G3(TTAG3)7. In green is the spectrum in 150 mM NaCl and the oligonucleotide adopts the antiparallel basket type quadruplex (92); in grey is the spectrum in 150 mM KCl; in blue dashes is the spectrum in 10 mM KCl, 57% ethanol measured 24 h after ethanol addition; and in blue is the spectrum of the same sample measured after denaturation and slow cooling to room temperature. The final spectrum corresponds to parallel quadruplex observed in the crystal (93).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 9: CD spectra and sketches of distinct quadruplex arrangements of a human telomere fragment G3(TTAG3)7. In green is the spectrum in 150 mM NaCl and the oligonucleotide adopts the antiparallel basket type quadruplex (92); in grey is the spectrum in 150 mM KCl; in blue dashes is the spectrum in 10 mM KCl, 57% ethanol measured 24 h after ethanol addition; and in blue is the spectrum of the same sample measured after denaturation and slow cooling to room temperature. The final spectrum corresponds to parallel quadruplex observed in the crystal (93).
Mentions: Conformations of DNA in aqueous solutions and crystals differ. CD spectroscopy contributed to the elucidation of the relationship between DNA conformations in these two environments. It was shown that the DNA structures observed in crystals are adopted in aqueous ethanol or trifluorethanol solutions (Figure 9) (30). This observation has been made for DNA duplexes and also guanine quadruplexes (44,46,80).Figure 9.

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