Circular dichroism spectroscopy analysis of conformational transitions of a 54 base pair DNA duplex composed of alternating CGCGCG and TATATA blocks

Experimental detection of conformational transitions between forms of DNA: problems and prospects

Under different conditions, the DNA double helix can take different geometric forms. Of the large number of its conformations, in addition to the "canonical" B form, the A, C, and Z forms are widely known, and the D, Hoogsteen, and X forms are less known. DNA locally takes the A, C, and Z forms in the cell, in complexes with proteins. We compare different methods for detecting non-canonical DNA conformations: X-ray, IR, and Raman spectroscopy, linear and circular dichroism in both the infrared and ultraviolet regions, as well as NMR (measurement of chemical shifts and their anisotropy, scalar and residual dipolar couplings and inter-proton distances from NOESY (nuclear Overhauser effect spectroscopy) data). We discuss the difficulties in applying these methods, the problems of theoretical interpretation of the experimental results, and the prospects for reliable identification of non-canonical DNA conformations.

Characterization of Z-DNA Using Circular Dichroism

The B-DNA to Z-DNA transition is a remarkable conformational change in DNA, which was originally observed in poly-GC DNA in the presence of high salt concentration. This eventually prompted the observation of the crystal structure of Z-DNA, a left-handed double-helical DNA, at atomic resolution. Despite advances in Z-DNA research, the application of circular dichroism (CD) spectroscopy as the fundamental technique to characterize this unique DNA conformation has remained constant. In this chapter, we describe a CD spectroscopic method for characterizing the B-DNA to Z-DNA transition of a CG-repeat double-stranded DNA fragment formed from a protein or chemical inducer.

Dramatic changes in the electrochemical and spectroscopic behavior of DNA fragments induced by the loss of a single nucleotide

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).

Circular dichroism spectroscopy of DNA: from duplexes to quadruplexes

Nucleic acids bear the genetic information and participate in its expression and evolution during replication, repair, recombination, transcription, and translation. These phenomena are mostly based on recognition of nucleic acids by proteins. The major factor enabling the specific recognition is structure. Circular dichroism (CD) spectroscopy is very useful to study secondary structures of nucleic acids, in general, and DNA, in particular. CD sensitively reflects isomerizations among distinct conformational states. The isomerizations may operate as molecular switches regulating various physiological or pathological processes. Here, we review CD spectra of nucleic acids, beginning with early studies on natural DNA molecules through analyses of synthetic polynucleotides to study of selected genomic fragments.

The CdCl2 effects on synthetic DNAs encaged in the nanodomains of a cationic water-in-oil microemulsion

The present work is dedicated to the study of the interactions of CdCl(2) with the synthetic polynucleotides polyAT and polyGC confined in the nanoscopic aqueous compartment of the water-in-oil microemulsion CTAB/pentanol/hexane/water, with the goal to mimic in vitro the situation met by the nucleic acids in vivo. In biological structures, in fact, very long strings of nucleic acids are segregated into very small compartments having a radius exceedingly smaller than the length of the encapsulated macromolecule. For comparison, the behaviour of polyGC was also studied in aqueous solutions of matched composition. The conformational and thermal stabilities of both polynucleotides enclosed in the inner compartment of the microemulsion are scarcely affected by the presence of CdCl(2), whereas in solution immediate and large effects were observed also at room temperature. The lack of effects of CdCl(2) on the properties of the biopolymers entrapped in the aqueous core of the microemulsion has been attributed to the peculiar characteristics of the medium (low dielectric constant, in particular) which cause a total repression of the CdCl(2) dissociation that is not complete even in water. In fact, several of the numerous effects of CdCl(2) observed on the conformational stability of polyGC in aqueous solutions have also been ascribed to the limited dissociation of the cadmium salt.

Circular dichroism of polynucleotides: Interactions of NiCl2 with poly(dA-dT).poly(dA-dT) and poly(dG-dC).poly(dG-dC) in a water-in-oil microemulsion

The thermal behavior of the synthetic, high molecular weight, double stranded polynucleotides poly(dA-dT).poly(dA-dT) [polyAT] and poly(dG-dC).poly(dG-dC) [polyGC] solubilized in the aqueous core of the quaternary water-in-oil cationic microemulsion CTAB|n-pentanol|n-hexane|water in the presence of increasing amounts of NiCl(2) at several constant ionic strength values (NaCl) has been studied by means of circular dichroism and electronic absorption spectroscopies. In the microemulsive medium, both polynucleotides show temperature-induced modifications that markedly vary with both Ni(II) concentration and ionic strength. An increase of temperature causes denaturation of the polyAT duplex at low nickel concentrations, while more complex CD spectral modifications are observed at higher nickel concentrations and ionic strengths. By contrast, thermal denaturation is never observed for polyGC. At low Ni(II) concentrations, the increase of temperature induces conformational transitions from B-DNA to Z-DNA form, or, more precisely, to left-handed helical structures. In some cases, at higher nickel concentrations, the CD spectra suggest the presence of Z'-type forms of the polynucleotide.

Effect of spermine conjugation on the interaction of acridine with alternating purine-pyrimidine oligodeoxyribonucleotides studied by CD, fluorescence and absorption spectroscopies

We studied by electronic spectroscopies the interaction between double-stranded oligonucleotides containing either adenine-thymine or guanine-cytosine alternating sequences and N(1)-(acridin-9-yl)-1,16-diamino-4,8,13-triazahexadecane, which is a conjugated molecule formed by the covalent binding of spermine and 9-aminoacridine moieties via a trimethylene chain. Solutions containing the oligonucleotides and the conjugate, at different molar ratios, were studied by using electronic absorption, fluorescence emission and circular dichroism. Calculated association constants and fluorescence emission spectra showed that spermine conjugation induces sequence selectivity. The orientation of the intercalated acridine rings with respect to the oligonucleotide base planes was deduced from the electronic circular dichroism spectra. Evidence of the formation of spermine-induced aggregated structures, with potential applications to DNA packaging, gene therapy and anti-tumor therapy, was also achieved. Our data demonstrates that this spermine-acridine conjugate adds several specific characteristics provided by the polyamine moiety, as sequence selectivity, to the interesting properties of acridine derivatives.

To be dinuclear or not: Z-DNA induction by nickel complexes

The left-handed Z-DNA has been identified as a gene regulating element. Therefore the generation of Z-DNA through metal complexes might be an innovative way for the regulation of gene expression. Use of the new dinuclear complex N,N,N',N'-tetrakis-[2-(3,5-dimethylpyrazol-1-yl)ethyl]-1,3-propylenediamine-bis(nickel(II) dinitrate) (2) reversibly induced Z-DNA formation. However, when a 1:1 ratio of metal/dinucleating ligand was used as a control, the midpoint of the B- to Z-DNA transition was at the same nickel concentration as in case of the dinuclear complex. The novel mononuclear analogue, N-methyl-N,N-bis-[2-(3,5-dimethylpyrazol-1-yl)ethyl]amine-nickel(II)-dinitrate (3) was inducing the Z-DNA at a similar ratio versus nucleotides as free nickel(II) itself. For the first time, proton and nickel binding constants for the bis-[2-(pyrazol-1-yl)ethyl]amine ligand system are reported and discussed. Both nickel complexes 2 and 3 were structurally characterized by single crystal analysis. Furthermore, the synthesis of the two new ligands, N,N,N',N'-tetrakis-[2-(3,5-dimethylpyrazol-1-yl)ethyl]-1,2-propylenediamine (4) and N-methyl-N,N-bis-[2-(3,5-dimethylpyrazol-1-yl)ethyl]amine (5) is described. The two major synthetic pathways leading to polypyrazoyl amines in general are critically discussed with respect to yield, reproducibility and handling of the intermediates.

Vibrational and electronic circular dichroism study of the interactions of cationic porphyrins with (dG-dC)10 and (dA-dT)10

The interactions of two different porphyrins, without axial ligands-5,10,15,20-tetrakis(1-methylpyridinium-4-yl)porphyrin-Cu(II) tetrachloride (Cu(II)TMPyP) and with bulky meso substituents-5,10,15,20-tetrakis(N,N,N-trimethylanilinium-4-yl)porphyrin tetrachloride (TMAP), with (dG-dC)10 and (dA-dT)10 were studied by combination of vibrational circular dichroism (VCD) and electronic circular dichroism (ECD) spectroscopy at different [oligonucleotide]/[porphyrin] ratios, where [oligonucleotide] and [porphyrin] are the concentrations of oligonucleotide per base-pair and porphyrin, respectively. The combination of VCD and ECD spectroscopy enables us to identify the types of interactions, and to specify the sites of interactions: The intercalative binding mode of Cu(II)TMPyP with (dG-dC)(10), which has been well described, was characterized by a new VCD "marker" and it was shown that the interaction of Cu(II)TMPyP with (dA-dT)10 via external binding to the phosphate backbone and major groove binding caused transition from the B to the non-B conformer. TMAP interacted with the major groove of (dG-dC)10, was semi-intercalated into (dA-dT)10, and caused significant variation in the structure of both oligonucleotides at the higher concentration of porphyrin. The spectroscopic techniques used in this study revealed that porphyrin binding with AT sequences caused substantial variation of the DNA structure. It was shown that VCD spectroscopy is an effective tool for the conformational studies of nucleic acid-porphyrin complexes in solution.

Genomic occurrence of microsatellites containing integral and non-integral repeat numbers

We calculated occurrences of all dinucleotide and trinucleotide microsatellites in the human, mouse, and yeast genomes. The microsatellites were considered separately not only according to the repeated dinucleotide or trinucleotide and the microsatellite length but also according to the starting/terminal nucleotide. The analysis showed that dramatically non-equal amounts occurred in the human genome of microsatellites that differed only by the terminal nucleotides. For example, the 23-mer (TTG)(7)TT occurs 635 times in the human genome whereas (GTT)(7)GT is present only three times in the human genome though the two 23-mers share a 22 nucleotide sequence. The dramatically non-equal occurrences of microsatellites differing only by the terminal nucleotides are observed for most dinucleotide and trinucleotide microsatellites and in all analyzed genomes. We suppose that the strikingly non-equal genomic occurrences of these closely related microsatellites originate from conformational properties of DNA.

The fragile X chromosome (GCC) repeat folds into a DNA tetraplex at neutral pH

UV absorption and CD spectroscopy, along with polyacrylamide gel electrophoresis, were used to study conformational properties of DNA fragments containing the trinucleotide repeat (GCC)(n) (n = 4, 8 or 16), whose expansion is correlated with the fragile X chromosome syndrome. We have found that the conformational spectrum of the (GCC)(n) strand is wider than has been shown so far. (GCC)(n) strands adopt the hairpin described in the literature under a wide range of salt concentrations, but only at alkaline (>7.5) pH values. However, at neutral and slightly acid pH (GCC)(4) and (GCC)(8) strands homodimerize. Our data suggest that the homodimer is a bimolecular tetraplex formed by two parallel-oriented hairpins held together by hemi-protonated intermolecular C.C(+) pairs. The (GCC)(16) strand forms the same tetraplex intramolecularly. We further show that below pH 5 (GCC)(n) strands generate intercalated cytosine tetraplexes, whose molecularity depends on DNA strand length. They are tetramolecular with (GCC)(4), bimolecular with (GCC)(8) and monomolecular with (GCC)(16). i-Tetraplex formation is a complex and slow process. The neutral tetraplex, on the other hand, arises with fast kinetics under physiological conditions. Thus it is a conformational alternative of the (GCC)(n) strand duplex with a complementary (GGC)(n) strand.

(CGA)(4): parallel, anti-parallel, right-handed and left-handed homoduplexes of a trinucleotide repeat DNA

Conformational properties of microsatellite DNA regions are the probable reason of their expansions in genomes which lead to serious genetic diseases in some cases. Using CD spectroscopy, UV absorption spectroscopy and polyacrylamide gel electrophoresis, we study in this paper conformational properties of (CGA)(4) and compare them with those of (CAG)(4) - a related repeat, connected with Huntington's disease. We show that (CGA)(4) can adopt several distinct conformations in solution. Around neutral pH it forms a parallel-stranded homoduplex containing C(+).C, G.G, and A.A base pairs. Under the same conditions (CAG)(4) forms a hairpin. At slightly alkaline pH values and low ionic strength, (CGA)(4) also folded into a hairpin which transformed into a bimolecular anti-parallel homoduplex at increasing salt concentrations. The duplex easily isomerized into left-handed Z-DNA, implying that the mismatched adenines between G.C pairs facilitate rather than hinder the B-Z transition. No similar changes took place with (CAG)(4). Thus, the conformational repertoire of (CGA)(4) includes parallel, anti-parallel, right-handed, and left-handed homoduplexes. In contrast, (CAG)(4) invariably adopts only a single conformation, namely the very stable hairpin.