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.

• MeSH
• DNA, A-Form chemistry   MeSH
• Circular Dichroism * MeSH
• Nucleic Acid Denaturation MeSH
• DNA chemistry   MeSH
• G-Quadruplexes MeSH
• Nucleic Acid Conformation MeSH
• DNA, Z-Form chemistry   MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Review MeSH
• Names of Substances
• DNA, A-Form MeSH
• DNA MeSH
• triplex DNA MeSH Browser
• DNA, Z-Form MeSH

Conformational transitions of poly(dA-dC).poly(dG-dT), poly(dA-dT).poly(dA-dT), and other alternating purine-pyrimidine DNAs were studied in aqueous ethanol solutions containing molar concentrations of sodium perchlorate, which is a novel solvent stabilizing non-B duplexes of DNA. Using CD and UV absorption spectroscopies, we show that this solvent unstacks bases and unwinds the B-forms of the DNAs to transform them into the A-form or Z-form. In the absence of divalent cations poly(dA-dC).poly(dG-dT) can adopt both of these conformations. Its transition into the Z-form is induced at higher salt and lower ethanol concentrations, and at higher temperatures than the transition into the A-form. Submillimolar concentrations of NiCl2 induce a highly cooperative and slow A-Z transition or Z-Z' transition, which is fast and displays low cooperativity. Poly(dA-dT).poly(dA-dT) easily isomerizes into the A-form in perchlorate-ethanol solutions, whereas high perchlorate concentrations denature the polynucleotide, which then cannot adopt the Z-form. At low temperatures, however, NiCl2 also cooperatively induces the Z'-form in poly(dA-dT).poly(dA-dT). Poly(dI-dC).poly(dI-dC) is known to adopt an unusual B-form in low-salt aqueous solution, which is transformed into a standard B-form by the combination of perchlorate and ethanol. NiCl2 then transforms poly(dI-dC).poly(dI-dC) into the Z'-form, which is also adopted by poly(dI-br5dC).poly(dI-br5dC).

• MeSH
• Biophysics MeSH
• Biophysical Phenomena MeSH
• Circular Dichroism MeSH
• Nucleic Acid Denaturation MeSH
• DNA chemistry   MeSH
• Ethanol MeSH
• Nucleic Acid Conformation * MeSH
• Perchlorates MeSH
• Poly dA-dT chemistry   MeSH
• Polydeoxyribonucleotides chemistry   MeSH
• Solutions MeSH
• Base Sequence MeSH
• Sodium Compounds MeSH
• Spectrophotometry, Ultraviolet MeSH
• In Vitro Techniques MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Names of Substances
• DNA MeSH
• Ethanol MeSH
• Perchlorates MeSH
• Poly dA-dT MeSH
• poly(d(G-T).d(C-A)) MeSH Browser
• Polydeoxyribonucleotides MeSH
• Solutions MeSH
• Sodium Compounds MeSH
• sodium perchlorate MeSH Browser

It is shown, using circular dichroism spectroscopy, that poly(dI-dC) is capable to isomerize into both Z-DNA and A-DNA in concentrated NaCl + NiCl2 and trifluoroethanol solutions, respectively. This polynucleotide also undergoes a cooperative, two-state transition in ethanol into a structure which most probably is a canonical B-DNA. This implies that the conformation of poly(dI-dC) is unusual in low-salt aqueous solution. The canonical B-DNA is also adopted by poly(dI-methyl5dC) in trifluoroethanol while this polynucleotide adopts Z-DNA not only in NaCl + NiCl2 but also in the presence of MgCl2. Poly(dI-methyl5dC) partially adopts X-DNA in concentrated CsF and mainly ethanolic solutions. Poly(dI-bromo5dC) isomerizes into Z-DNA not only in concentrated NaCl even in the absence of NiCl2 but also in concentrated MgCl2. This polynucleotide transforms between two distinct variants of Z-DNA in ethanol or trifluoroethanol solutions.

• MeSH
• Magnesium Chloride MeSH
• Sodium Chloride MeSH
• Circular Dichroism MeSH
• DNA chemistry   MeSH
• Isomerism MeSH
• Nucleic Acid Conformation MeSH
• Polydeoxyribonucleotides chemistry   MeSH
• Solutions MeSH
• Publication type
• Journal Article MeSH
• Names of Substances
• Magnesium Chloride MeSH
• Sodium Chloride MeSH
• DNA MeSH
• poly d(I-C) MeSH Browser
• polydeoxyinosinic-polydeoxy-(5-bromocytidylic)acid MeSH Browser
• polydeoxyinosinic-polydeoxy-(5-methylcytidylic)acid MeSH Browser
• Polydeoxyribonucleotides MeSH
• Solutions MeSH