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

DNA fragments crystallize in an unpredictable manner, and relationships between their crystal and solution conformations still are not known. We have studied, using circular dichroism spectroscopy, solution conformations of (G + C)-rich DNA fragments, the crystal structures of which were solved in the laboratory of one of the present authors. In aqueous trifluorethanol (TFE) solutions, all of the examined oligonucleotides adopted the same type of double helix as in the crystal. Specifically, the dodecamer d(CCCCCGCGGGGG) crystalized as A-DNA and isomerized into A-DNA at high TFE concentrations. On the other hand, the hexamer d(CCGCGG) crystallized in Z-form containing tilted base pairs, and high TFE concentrations cooperatively transformed it into the same Z-form as adopted by the RNA hexamer r(CGCGCG), although d(CCGCGG) could isomerize into Z-DNA in the NaCl + NiCl2) aqueous solution. The fragments crystallizing as B-DNA remained B-DNA, regardless of the solution conditions, unless they denatured or aggregated. Effects on the oligonucleotide conformation of 2-methyl-2,4-pentanediol and other crystallization agents were also studied. 2-Methyl-2,4-pentanediol induced the same conformational transitions as TFE but, in addition, caused an oligonucleotide condensation that was also promoted by the other crystallization agents. The present results indicate that the crystal double helices of DNA are stable in aqueous TFE rather than aqueous solution.

• MeSH
• Biophysics MeSH
• Biophysical Phenomena MeSH
• Circular Dichroism MeSH
• DNA chemistry   MeSH
• Glycols pharmacology   MeSH
• Nucleic Acid Conformation drug effects   MeSH
• Crystallization MeSH
• Oligodeoxyribonucleotides chemistry   MeSH
• Solutions MeSH
• Base Sequence MeSH
• In Vitro Techniques MeSH
• Water MeSH
• Base Composition MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Comparative Study MeSH
• Names of Substances
• DNA MeSH
• Glycols MeSH
• hexylene glycol MeSH Browser
• Oligodeoxyribonucleotides MeSH
• Solutions MeSH
• Water 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