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
• A-DNA chemie   MeSH
• cirkulární dichroismus * MeSH
• denaturace nukleových kyselin MeSH
• DNA chemie   MeSH
• G-kvadruplexy MeSH
• konformace nukleové kyseliny MeSH
• Z-DNA chemie   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• přehledy MeSH
• Názvy látek
• A-DNA MeSH
• DNA MeSH
• triplex DNA MeSH Prohlížeč
• Z-DNA 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
• biofyzika MeSH
• biofyzikální jevy MeSH
• cirkulární dichroismus MeSH
• DNA chemie   MeSH
• glykoly farmakologie   MeSH
• konformace nukleové kyseliny účinky léků   MeSH
• krystalizace MeSH
• oligodeoxyribonukleotidy chemie   MeSH
• roztoky MeSH
• sekvence nukleotidů MeSH
• techniky in vitro MeSH
• voda MeSH
• zastoupení bazí MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• srovnávací studie MeSH
• Názvy látek
• DNA MeSH
• glykoly MeSH
• hexylene glycol MeSH Prohlížeč
• oligodeoxyribonukleotidy MeSH
• roztoky MeSH
• voda 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
• biofyzika MeSH
• biofyzikální jevy MeSH
• cirkulární dichroismus MeSH
• denaturace nukleových kyselin MeSH
• DNA chemie   MeSH
• ethanol MeSH
• konformace nukleové kyseliny * MeSH
• perchloráty MeSH
• poly dA-dT chemie   MeSH
• polydeoxyribonukleotidy chemie   MeSH
• roztoky MeSH
• sekvence nukleotidů MeSH
• sloučeniny sodíku MeSH
• spektrofotometrie ultrafialová MeSH
• techniky in vitro MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• DNA MeSH
• ethanol MeSH
• perchloráty MeSH
• poly dA-dT MeSH
• poly(d(G-T).d(C-A)) MeSH Prohlížeč
• polydeoxyribonukleotidy MeSH
• roztoky MeSH
• sloučeniny sodíku MeSH
• sodium perchlorate MeSH Prohlížeč

Extensive circular dichroism studies have been conducted with the title polynucleotides under various solution conditions. The studies provided the following information: (i) The halogen atoms in place of thymine methyl hinder the isomerization into X-DNA. (ii) The brominated but not iodinated polynucleotide isomerizes into Z-DNA in concentrated NaCl+NiCl2. The transition takes place at lower NiCl2 concentrations than with poly(dA-dT). (iii) The iodinated polynucleotide forms an unusual conformation in aqueous solution in which it is very stable. It isomerizes from this conformer into the usual B-type double helix in concentrated ethanol solutions. The isomerization is a two-state cooperative process. (iv) Both title polynucleotides undergo still another two-state cooperative transition in trifluorethanol solutions presumably into A-DNA showing a rather unusual circular dichroism spectrum.

• MeSH
• cirkulární dichroismus MeSH
• idoxuridin chemie   MeSH
• konformace nukleové kyseliny * MeSH
• poly A-U chemie   MeSH
• poly dA-dT chemie   MeSH
• spektrální analýza MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• idoxuridin MeSH
• poly (dA-BrdU) MeSH Prohlížeč
• poly A-U MeSH
• poly dA-dT MeSH
• poly(dA-IdU) MeSH Prohlížeč