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

Circular dichroism (CD) is remarkably sensitive to the conformational states of nucleic acids; therefore, CD spectroscopy has been used to study most features of DNA and RNA structures. Quadruplexes are among the significant noncanonical nucleic acids architectures that have received special attentions recently. This article presents examples on the contribution of CD spectroscopy to our knowledge of quadruplex structures and their polymorphism. The examples were selected to demonstrate the potential of this simple method in the quadruplex field. As CD spectroscopy detects only the global feature of a macromolecule, it should preferably be used in combination with other techniques. On the other hand, CD spectroscopy, often as a pioneering approach, can reveal the formation of particular structural arrangements, to search for the conditions stabilizing the structures, to follow the transitions between various structural states, to explore kinetics of their appearance, to determine thermodynamic parameters and also detect formation of higher order structures. This article aims to show that CD spectroscopy is an important complementary technique to NMR spectroscopy and X-ray diffraction in quadruplex studies.

• MeSH
• cirkulární dichroismus metody   MeSH
• difrakce rentgenového záření MeSH
• DNA chemie   MeSH
• G-kvadruplexy * MeSH
• guanin chemie   MeSH
• kinetika MeSH
• konformace nukleové kyseliny * MeSH
• oligonukleotidy chemie   MeSH
• termodynamika MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• přehledy MeSH
• Názvy látek
• DNA MeSH
• guanin MeSH
• oligonukleotidy MeSH

(Guanine+adenine) strands of DNA are known to associate into guanine tetraplexes, homodimerize into parallel or antiparallel duplexes, and fold into a cooperatively melting single strand resembling the protein alpha helix. Using CD spectroscopy and other methods, we studied how this conformational polymorphism depended on the primary structure of DNA. The study showed that d(GGGA)(5) and d(GGA)(7) associated into homoduplexes at low salt or in the presence of LiCl but were prone to guanine tetraplex formation, especially in the presence of KCl. In addition, they yielded essentially the same CD spectrum in the presence of ethanol as observed with the ordered single strand of d(GA)(10). Strands of d(GA)(10), d(GGAA)(5), d(GAA)(7), and d(GAAA)(5) associated into homoduplexes in both LiCl and KCl solutions, but not into guanine tetraplexes. d(GAAA)(5) and d(GAA)(7) further failed to form the single-stranded conformer in aqueous ethanol. Adenine protonation, however, stabilized the single-stranded conformer even in these adenine-rich fragments. The ordered single strands, homoduplexes as well as the guanine tetraplexes, all provided strikingly similar CD spectra, indicating that all of the conformers shared similar base stacking geometries. The increasing adenine content only decreased the conformer thermostability.

• MeSH
• adenin chemie   MeSH
• cirkulární dichroismus MeSH
• DNA chemie   MeSH
• guanin chemie   MeSH
• repetitivní sekvence nukleových kyselin * MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• adenin MeSH
• DNA MeSH
• guanin MeSH

We have used CD spectroscopy, polyacrylamide gel electrophoresis, and UV absorption spectroscopy to study conformational properties of DNA fragments containing (CCA)n and (TGG)n repeats, which are the most length-polymorphic microsatellite sequences of the human genome. The (CCA)n fragments are random single strands at neutral and alkaline pH but they fold into intramolecular intercalated cytosine tetraplexes at mildly acid pH values. More acid values stabilize intermolecular tetraplex formation. The behavior of (TGG)n repeats is more complex. They form hairpins or antiparallel homoduplexes in low salt solutions which, however, are transformed into parallel-stranded guanine tetraplexes at physiological KCl concentrations. Their molecularity depends on the repeat number: (TGG)4 associates into an octameric complex, (TGG)8 forms tetramolecular complexes. (TGG)n with odd repeat numbers (5, 7, and 9) generate bimolecular and tetramolecular tetraplexes. The only (TGG)7 folds into an intramolecular tetraplex at low KCl concentrations, which is antiparallel-stranded. Moreover, the (TGG)(n) fragments provide various mutually slipped conformers whose population increases with salt concentration and with the increasing repeat number. However, the self-structures of both strands disappear in the presence of the complementary strand because both (TGG)n and (CCA)n prefer to associate into the classical heteroduplex. We suppose that the extreme conformational variability of the DNA strands stands behind the length polymorphism which the (CCA)n/(TGG)n repeats exhibit in the human genome.

• MeSH
• chlorid draselný farmakologie   MeSH
• cirkulární dichroismus MeSH
• cytosin chemie   MeSH
• denaturace nukleových kyselin MeSH
• DNA chemie   MeSH
• EDTA chemie   MeSH
• elektroforéza v polyakrylamidovém gelu MeSH
• genom lidský MeSH
• koncentrace vodíkových iontů MeSH
• konformace nukleové kyseliny MeSH
• konformace proteinů MeSH
• lidé MeSH
• mikrosatelitní repetice MeSH
• oligonukleotidy MeSH
• polymorfismus genetický MeSH
• soli farmakologie   MeSH
• spektrofotometrie MeSH
• teplota MeSH
• trinukleotidové repetice MeSH
• ultrafialové záření MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• chlorid draselný MeSH
• cytosin MeSH
• DNA MeSH
• EDTA MeSH
• oligonukleotidy MeSH
• soli 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

We probed conformational polymorphism of a synthetic DNA poly(dA-dT) by introducing various small amounts of bulky spherical hydrophobic isopropyl groups into the polynucleotide primary structure. For this purpose, three mixed copolymers of poly(dA-dT,ip5dU) were synthesized in which 2.6%, 8.6% or 14.2% of the polynucleotide pyrimidine bases had the isopropyl group in position 5. The isopropyls made the formation of both A-form and X-form incomplete, and this effect increased with the increasing isopropyl amount in the polynucleotide. However, the polynucleotide isomerization into the A-form was hindered by the isopropyls while the isomerization into the X-form was rather promoted. This observation indicates that, unlike the A-form, the X-form has the base pairs shifted towards the double helix major groove. Z-form was also promoted by the lowest concentration of the isopropyl groups while the most isopropylated poly(dA-dT) aggregated under the Z-form inducing conditions.

• MeSH
• cirkulární dichroismus MeSH
• DNA chemie   MeSH
• konformace nukleové kyseliny * MeSH
• poly dA-dT chemie   MeSH
• thymin chemie   MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• DNA MeSH
• poly dA-dT MeSH
• thymin MeSH

In this paper, the d(GCGAAGC) heptamer and the closely related d(GCGAGC) hexamer are examined via electrochemical (cyclic voltammetry) and spectroscopic (circular dichroism) methods. Dramatic changes in the CD spectroscopic and CV electrochemical properties, induced by the loss of only one single nucleotide (A), are detected. The CD spectra and native polyacrylamide gel electrophoresis (PAGE) confirmed structural changes taking place in the relevant chain-like oligodeoxynucleotide assemblies. Dedicated studies suggest that the heptamer (Hp) possesses a hairpin structure, whereas the hexamer (Hx) appears to be rather a duplex. Both of the structures exhibited completely different adsorption behavior at the hanging mercury drop electrode, and this factor was readily confirmed by means of elimination voltammetry with linear scan (EVLS). We established that the Hp hairpin (~-1300 mV), compared to the Hx duplex (~-1360 mV), is the thermodynamically favored electron acceptor. The adsorption isotherms were constructed based on the voltammetric peak height values, reflecting the reduction of the adenine (A) and cytosine (C) moieties as well as the oxidation of the 7,8-dihydroguanine (7,8-DHG) moieties. Finally, as revealed by the spectroscopic and electrochemical results, Hx forms a bimolecular antiparallel homo-duplex carrying both Watson-Crick base pairs (CG or GC) and mismatched edge-to-edge base pairs (GA or AG).

• Klíčová slova
• CD spectra, Duplex, GA mismatches, Hairpin, Oligodeoxynucleotide structure, Voltammetry,
• MeSH
• cirkulární dichroismus MeSH
• DNA chemie   genetika   metabolismus   MeSH
• elektrochemie MeSH
• guanin analogy a deriváty   metabolismus   MeSH
• jednonukleotidový polymorfismus * MeSH
• molekulární konformace MeSH
• molekulární modely MeSH
• sekvence nukleotidů MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• 7,8-dihydro-8-oxoguanine MeSH Prohlížeč
• DNA MeSH
• guanin MeSH

Genomic sequences susceptible to form G-quadruplexes (G4s) are always flanked by other nucleotides, but G4 formation in vitro is generally studied with short synthetic DNA or RNA oligonucleotides, for which bases adjacent to the G4 core are often omitted. Herein, we systematically studied the effects of flanking nucleotides on structural polymorphism of 371 different oligodeoxynucleotides that adopt intramolecular G4 structures. We found out that the addition of nucleotides favors the formation of a parallel fold, defined as the 'flanking effect' in this work. This 'flanking effect' was more pronounced when nucleotides were added at the 5'-end, and depended on loop arrangement. NMR experiments and molecular dynamics simulations revealed that flanking sequences at the 5'-end abolish a strong syn-specific hydrogen bond commonly found in non-parallel conformations, thus favoring a parallel topology. These analyses pave a new way for more accurate prediction of DNA G4 folding in a physiological context.

• MeSH
• cirkulární dichroismus MeSH
• DNA genetika   ultrastruktura   MeSH
• G-kvadruplexy * MeSH
• konformace nukleové kyseliny MeSH
• nukleotidy chemie   genetika   MeSH
• oligonukleotidy chemie   genetika   MeSH
• polymorfismus genetický genetika   MeSH
• RNA genetika   ultrastruktura   MeSH
• simulace molekulární dynamiky MeSH
• vodíková vazba MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• DNA MeSH
• nukleotidy MeSH
• oligonukleotidy MeSH
• RNA MeSH