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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 of d(GA)20. (A) Spectra reflecting formation of the zinc-specific anti-parallel homoduplex. The spectra were measured in Tris–HCl buffer, pH 8.3. The yellow line corresponds to 0.7 mM ZnCl2. (B) CD spectra reflecting the NaCl-induced transition of d(GA)10 into the parallel homoduplex. To increase the salt concentration, 5 M NaCl was added to the oligonucleotide dissolved in 10 mM sodium phosphate, pH 7. (C) CD spectra of an ordered single-stranded conformer containing protonated adenine. The pH value was changed directly in the CD cell by addition of dilute HCl to the oligonucleotide in 1 mM sodium phosphate.
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Figure 5: CD spectra of d(GA)20. (A) Spectra reflecting formation of the zinc-specific anti-parallel homoduplex. The spectra were measured in Tris–HCl buffer, pH 8.3. The yellow line corresponds to 0.7 mM ZnCl2. (B) CD spectra reflecting the NaCl-induced transition of d(GA)10 into the parallel homoduplex. To increase the salt concentration, 5 M NaCl was added to the oligonucleotide dissolved in 10 mM sodium phosphate, pH 7. (C) CD spectra of an ordered single-stranded conformer containing protonated adenine. The pH value was changed directly in the CD cell by addition of dilute HCl to the oligonucleotide in 1 mM sodium phosphate.

Mentions: DNA fragments rich in guanine and adenine exhibit cooperatively melting conformers that differ from classical structures. Their molecular structures have not yet been solved in spite of several attempts. The first conformer is an anti-parallel homoduplex (54) containing G·A pairs. Its CD spectrum is B-like (55) (Figure 5A). This duplex is stabilized by divalent zinc cations. Low concentrations of the zinc cations induce various conformers so that the process is not of a two-state nature. This anti-parallel homoduplex is probably a part of a zinc-stabilized d(GA)n·d(GA)n·d(TC)n triplex (55).Figure 5.


Circular dichroism and conformational polymorphism of DNA.

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

CD spectra of d(GA)20. (A) Spectra reflecting formation of the zinc-specific anti-parallel homoduplex. The spectra were measured in Tris–HCl buffer, pH 8.3. The yellow line corresponds to 0.7 mM ZnCl2. (B) CD spectra reflecting the NaCl-induced transition of d(GA)10 into the parallel homoduplex. To increase the salt concentration, 5 M NaCl was added to the oligonucleotide dissolved in 10 mM sodium phosphate, pH 7. (C) CD spectra of an ordered single-stranded conformer containing protonated adenine. The pH value was changed directly in the CD cell by addition of dilute HCl to the oligonucleotide in 1 mM sodium phosphate.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 5: CD spectra of d(GA)20. (A) Spectra reflecting formation of the zinc-specific anti-parallel homoduplex. The spectra were measured in Tris–HCl buffer, pH 8.3. The yellow line corresponds to 0.7 mM ZnCl2. (B) CD spectra reflecting the NaCl-induced transition of d(GA)10 into the parallel homoduplex. To increase the salt concentration, 5 M NaCl was added to the oligonucleotide dissolved in 10 mM sodium phosphate, pH 7. (C) CD spectra of an ordered single-stranded conformer containing protonated adenine. The pH value was changed directly in the CD cell by addition of dilute HCl to the oligonucleotide in 1 mM sodium phosphate.
Mentions: DNA fragments rich in guanine and adenine exhibit cooperatively melting conformers that differ from classical structures. Their molecular structures have not yet been solved in spite of several attempts. The first conformer is an anti-parallel homoduplex (54) containing G·A pairs. Its CD spectrum is B-like (55) (Figure 5A). This duplex is stabilized by divalent zinc cations. Low concentrations of the zinc cations induce various conformers so that the process is not of a two-state nature. This anti-parallel homoduplex is probably a part of a zinc-stabilized d(GA)n·d(GA)n·d(TC)n triplex (55).Figure 5.

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