Characterization of DNA structures by infrared spectroscopy: double helical forms of poly(dG-dC)•poly(dG-dC), poly(dD⁸G-dC)•poly(dD⁸G-dC), and poly(dG-dm⁵C)•poly(dG-dm⁵C)

Abstract

Infrared spectroscopy in the 1750-700 cm-.' region is used to characterize the right-and left-handed helices of poly (dG-dC) .poly(dG-dC) with sodium counterions. The use of polymers selectively deuterated on the C8 of guanincs and methylated on the C5 of cytosines allows us to propose explanations for several spectroscopic modifications which occur under thc B + Z transition. Similar substitutions on nucleosides and nucleotides are used so as to assign base absorptions in poly(dGdC).poly(dG-dC). A set of ir bands characteristic of DNA conformations, which can be used in studies of interactions with this polynucleotide and to identify the left handed Z conformation in more complex systems, is proposed. J . A. TABOURY, J. LIQUIER, et E. TAILLANDIER. Can. J. Chem. 63, 1904Chem. 63, (1985. La spectroscopie infrarouge dans la region 1750-700 cm-' permet de caracttriser la forme droite et la forme gauche de la double hClice de poly(dG-dC) -poly(dG-dC). L'Ctude de dCrivCs du poly(dG-dC).poly(dG-dC) deutCrits sklectivement sur le C8 de la guanine ou mCthylCs sur le C5 de la cytosine permet d'expliquer diffkrentes modifications du spectre de ce polynuclCotide au cours de la transition B + Z. Des modifications similaires sur des nuclCotides ou nucltosides apportent Cgalement des informations pour I'attribution des bandes d'absorption des bases du poly(dG-dC).poly(dG-dC).Nous proposons un ensemble de bandes d'absorption caractkristiques des conformations de I'ADN. qui pourra 2tre utilisC pour 1'Ctude d'interactions avec ce polynuclCotide ou pour la mise en evidence de la conformation en double hklice gauche dans des systkmes plus complexes. IntroductionThe DNA molecule, which for a long time had been considered a rather rigid entity, is now known to be extremely flexible and capable of adopting a great variety of secondary structures. The study of purine-pyrimidine alternating copolymers has, moreover, shown that classical right-handed A and B helices can be turned into left-handed forms belonging to the so-called Z family. These novel structures were first characterized in the case of poly(dG-dC)-poly(dG-dC) by the modification of the uv absorbance spectrum and by the inversion of the cd (circular dichroism) signal (1). Their existence has been definitively proved by X-ray diffraction studies on d(C-G)3 crystals (2). Nuclear magnetic resonance (nmr) (3, 4) and Raman spectroscopy (5-9) have also been used to investigate Z DNA. Thamann et al. (6) showed that the Raman spectrum of the Z DNA d(C-G), crystal is essentially identical to the high salt

Characterization of parallel and antiparallel G-tetraplex structures by vibrational spectroscopy

“…In the present case, the degree of co-planarity between dG residues in each G tetrad is greater in the parallel structures than in the antiparallel ones. The perturbation of each G tetrad directly affects the stacking energy of the neighboring G tetrad [43]. This is reflected on the FTIR spectra by the shift of the guanine C6=O6 carbonyl band.…”

Surface enhanced IR absorption of nucleic acids from tumor cells: FTIR reflectance study

“…17 Their spectral band positions are 890, 878, 860, and 805 cm Ϫ1 for the C 3Ј endo/anti (A-form helix) conformation and 890 and 835 cm Ϫ1 for the C 2Ј endo/anti (B-form helix) conformation. 21 In the left-handed helix DNA (Z form) the positions of the IR bands are 925-929, 868, 835-840, and 802-805 cm Ϫ1 in the C 3Ј endo/syn and C 2Ј endo/anti sugar-base geometries. 14,21 It is known that DNA conformations in the film and their IR spectra (especially the symmetrical phosphate band) strongly depend on the humidity of the film.…”

“…21 In the left-handed helix DNA (Z form) the positions of the IR bands are 925-929, 868, 835-840, and 802-805 cm Ϫ1 in the C 3Ј endo/syn and C 2Ј endo/anti sugar-base geometries. 14,21 It is known that DNA conformations in the film and their IR spectra (especially the symmetrical phosphate band) strongly depend on the humidity of the film.…”

Specific Applications of Vibrational Spectroscopy in Biomedical Engineering

“…Vibrational spectroscopy is one of the main methods used to determine the secondary structures of A, B, C, D and Z-DNA forms (Banyay et al, 2003;Pohle & Fritzsche, 1980;Rauch et al, 2005;Taboury et al, 1985;Taillandier et al, 1989). IR spectroscopy can also be used successfully to study conformational changes during B→A and B→Z transitions (Adam et al, 1986;Pilet & Brahms, 1973;Taboury et al, 1985;Taillandier et al, 1989;Taillandier & Liquier, 1992) and DNA denaturation (Banyay et al, 2003;Lee et al, 2004).…”

“…IR spectroscopy can also be used successfully to study conformational changes during B→A and B→Z transitions (Adam et al, 1986;Pilet & Brahms, 1973;Taboury et al, 1985;Taillandier et al, 1989;Taillandier & Liquier, 1992) and DNA denaturation (Banyay et al, 2003;Lee et al, 2004). The IR spectra of DNA show many characteristic bands, which are sensitive to denaturation, dehydration and conformational transition.…”