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

Recently we have shown that wild-type human p53 protein binds preferentially to supercoiled (sc) DNA in vitro in both the presence and absence of the p53 consensus sequence (p53CON). This binding produces a ladder of retarded bands on an agarose gel. Using immunoblotting with the antibody DO-1, we show that the bands obtained correspond to ethidium-stained DNA, suggesting that each band of the ladder contains a DNA-p53 complex. The intensity and the number of these hands are decreased by physiological concentrations of zinc ions. At higher zinc concentrations, binding of p53 to scDNA is completely inhibited. The binding of additional zinc ions to p53 appears much weaker than the binding of the intrinsic zinc ion in the DNA binding site of the core domain. In contrast to previously published data suggesting that 100 microM zinc ions do not influence p53 binding to p53CON in a DNA oligonucleotide, we show that 5-20 microM zinc efficiently inhibits binding of p53 to p53CON in DNA fragments. We also show that relatively low concentrations of dithiothreitol but not of 2-mercaptoethanol decrease the concentration of free zinc ions, thereby preventing their inhibitory effect on binding of p53 to DNA. Nickel and cobalt ions inhibit binding of p53 to scDNA and to its consensus sequence in linear DNA fragments less efficiently than zinc; cobalt ions are least efficient, requiring >100 microM Co2+ for full inhibition of p53 binding. Modulation of binding of p53 to DNA by physiological concentrations of zinc might represent a novel pathway that regulates p53 activity in vivo.

• MeSH
• chybné párování bází MeSH
• dithiothreitol farmakologie   MeSH
• DNA genetika   metabolismus   MeSH
• EDTA farmakologie   MeSH
• kationty dvojmocné antagonisté a inhibitory   farmakologie   MeSH
• kobalt farmakologie   MeSH
• kompetitivní vazba MeSH
• konsenzuální sekvence genetika   MeSH
• lidé MeSH
• merkaptoethanol farmakologie   MeSH
• nádorový supresorový protein p53 metabolismus   MeSH
• nikl farmakologie   MeSH
• protilátky MeSH
• responzivní elementy genetika   MeSH
• sekvence nukleotidů MeSH
• superhelikální DNA genetika   metabolismus   MeSH
• vazba proteinů účinky léků   MeSH
• vztah mezi dávkou a účinkem léčiva MeSH
• western blotting MeSH
• zinek antagonisté a inhibitory   farmakologie   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• dithiothreitol MeSH
• DNA MeSH
• EDTA MeSH
• kationty dvojmocné MeSH
• kobalt MeSH
• merkaptoethanol MeSH
• nádorový supresorový protein p53 MeSH
• nikl MeSH
• protilátky MeSH
• superhelikální DNA MeSH
• zinek MeSH

CD spectroscopy and PAGE were used to cooperatively analyze melting conformers of DNA strands containing GA and TA dinucleotide repeats. The 20mer (GA)10 formed a homoduplex in neutral solutions containing physiological concentrations of salts and this homoduplex was not destabilized even in the terminal (GA)3 hexamers of (GA)3(TA)4(GA)3, although the central (TA)4 portion of this oligonucleotide preserved the conformation adopted by (TA)10. This observation demonstrates that homoduplexes of alternating GA and TA sequences can co-exist in a single DNA molecule. Another 20mer, (GATA)5, adopted as a whole either the AT duplex, like (TA)10, or the GA duplex, like (GA)10, and switched between them reversibly. The concentration of salt controlled the conformational switching. Hence, guanine and thymine share significant properties regarding complementarity to adenine, while the TA and GA sequences can stack in at least two mutually compatible ways within the DNA duplexes analyzed here. These properties extend our knowledge of non-canonical structures of DNA.

• MeSH
• cirkulární dichroismus MeSH
• dinukleotidové repetice * MeSH
• DNA chemie   genetika   MeSH
• elektroforéza v polyakrylamidovém gelu MeSH
• heteroduplexy nukleové kyseliny chemie   genetika   MeSH
• konformace nukleové kyseliny * MeSH
• sekvence nukleotidů MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• DNA MeSH
• heteroduplexy nukleové kyseliny MeSH