Interaction of Z form poly(dG-dC). poly(dG-dC) with divalent metal ions: localization of the binding sites by I.R. spectroscopy

Taboury, Jean; Bourtayre, P.; Liquier, J.; Taillandier, E.

doi:10.1093/nar/12.10.4247

Cited by 74 publications

(49 citation statements)

References 26 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In contrast, when poly(dA-dT) (which has no intercalation sites available for cationic porphyrins) is complexed with BAP or H 2 TMPyP-4, no appreciable change is detected in the spectral region of the double bond stretching vibrations of the adenines and thymines (data not shown). Figures 8e and h. Earlier studies, which bore on poly(dG-dC), revealed by C 8 -H selective deuteration that the broad band at 1498 cm -1 is a superposition of both cytosine and guanine absorption bands (94), and that the guanine component stems from the N 7 -C 8 -H deformation (95,96). Modifications of the position or of the relative intensity of this band could therefore be used as a diagnostic for interactions involving N 7 of guanine.…”

Section: Circular Dichroismmentioning

confidence: 76%

Joint Molecular Modeling and Spectroscopic Studies of DNA Complexes of a Bis(arginyl) Conjugate of a Tricationic Porphyrin Designed to Target the Major Groove

et al. 1998

View full text Add to dashboard Cite

To target selectively the major groove of double-stranded B DNA, we have designed and synthesized a bis(arginyl) conjugate of a tricationic porphyrin (BAP). Its binding energies with a series of double-stranded dodecanucleotides, having in common a central d(CpG)2 intercalation site were compared. The theoretical results indicated a significant energy preference favoring major groove over minor groove binding and a preferential binding to a sequence encompassing the palindrome GGCGCC encountered in the Primary Binding Site of the HIV-1 retrovirus. Spectroscopic studies were carried out on the complexes of BAP with poly(dG-dC) and poly(dA-dT) and a series of oligonucleotide duplexes having either a GGCGCC, CCCGGG, or TACGTA sequence. The results of UV-visible and circular dichroism spectroscopies indicated that intercalation of the porphyrin takes place in poly(dG-dC) and all the oligonucleotides. Thermal denaturation studies showed that BAP increased significantly the melting temperature of the oligonucleotides having the GGCGCC sequence, whereas it produced only a negligible stabilization of sequences having CCCGGG or TACGTA in place of GGCGCC. This indicates a preferential binding of BAP to GGCGCC, fully consistent with the theoretical predictions. IR spectroscopy on d(GGCGCC)2 indicated that the guanine absorption bands, C6=O6 and N7-C8-H, were shifted by the binding of BAP, indicative of the interactions of the arginine arms in the major groove. Thus, the de novo designed compound BAP constitutes one of the very rare intercalators which, similar to the antitumor drugs mitoxantrone and ditercalinium, binds DNA in the major groove rather than in the minor groove.

show abstract

Section: Circular Dichroismmentioning

confidence: 76%

Joint Molecular Modeling and Spectroscopic Studies of DNA Complexes of a Bis(arginyl) Conjugate of a Tricationic Porphyrin Designed to Target the Major Groove

et al. 1998

View full text Add to dashboard Cite

show abstract

“…A and B geometries and the B -, A conformational transition of DNA, alone or in the presence of polypeptides, proteins, or drugs, in highly concentrated conditions (hydrated films), have been characterized and followed by this technique (10)(11)(12). The left-handed Z structure of poly(dG-dC).poly(dG-dC) has also been investigated by ir spectroscopy (13)(14)(15)(16)(17), and we have previously shown that, in films, the reversible B -, Z transition can be induced by varying the relative humidity (18). This conforrnational transition has been identified by correlating the ir and uv absorbance spectroscopy results obtained on the same films, in the same salt and hydration conditions.…”

Section: Introductionmentioning

confidence: 99%

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)

Taboury¹,

Liquier²,

Taillandier³

1985

Can. J. Chem.

Self Cite

View full text Add to dashboard Cite

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

show abstract

“…2b). [88][89][90][91] The left-handed sequences have been found in natural DNA and are believed to play a major role in many fundamental life processes, including gene regulation and DNA replication. 92,93 One of the first spectroscopic techniques used for investigations of DNA B-Z transition was ECD.…”

Section: Illustrative Examples Dna B-z Transitionmentioning

confidence: 99%

Applications of the Cartesian coordinate tensor transfer technique in the simulations of vibrational circular dichroism spectra of oligonucleotides

Andrushchenko

Bouř

2010

Chirality

View full text Add to dashboard Cite

The application of the Cartesian coordinate tensor transfer (CCT) technique for simulations of the IR absorption and vibrational circular dichroism (VCD) spectra of relatively large nucleic acid fragments is demonstrated on several case studies. The approach is based on direct ab initio calculations of atomic tensors, determining molecular properties, for relatively small fragments, and subsequent transfer of these tensors to the larger systems in Cartesian coordinates. This procedure enables precise computations of vibrational spectra for large biomolecular systems, currently with up to several thousands of atoms. The versatile ability of the CCT methods is emphasized on the examples of VCD and IR absorption spectra calculations for B- and Z-forms of DNA, single-, double-, and triple-stranded RNA helices and DNA structures with different base content and sequences. The development and recent improvements of the methodology are followed, including utilization of the constrained normal mode optimization (NMO) strategy and combined quantum mechanics and molecular dynamics simulations. Advantages, drawbacks, and recommendations for future improvements of the CCT method as applied to nucleic acid spectra calculations are discussed.

show abstract

Interaction of Z form poly(dG-dC). poly(dG-dC) with divalent metal ions: localization of the binding sites by I.R. spectroscopy

Cited by 74 publications

References 26 publications

Joint Molecular Modeling and Spectroscopic Studies of DNA Complexes of a Bis(arginyl) Conjugate of a Tricationic Porphyrin Designed to Target the Major Groove

Joint Molecular Modeling and Spectroscopic Studies of DNA Complexes of a Bis(arginyl) Conjugate of a Tricationic Porphyrin Designed to Target the Major Groove

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)

Applications of the Cartesian coordinate tensor transfer technique in the simulations of vibrational circular dichroism spectra of oligonucleotides

Contact Info

Product

Resources

About

Interaction of Z form poly(dG-dC). poly(dG-dC) with divalent metal ions: localization of the binding sites by I.R. spectroscopy

Cited by 74 publications

References 26 publications

Joint Molecular Modeling and Spectroscopic Studies of DNA Complexes of a Bis(arginyl) Conjugate of a Tricationic Porphyrin Designed to Target the Major Groove

Joint Molecular Modeling and Spectroscopic Studies of DNA Complexes of a Bis(arginyl) Conjugate of a Tricationic Porphyrin Designed to Target the Major Groove

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)

Applications of the Cartesian coordinate tensor transfer technique in the simulations of vibrational circular dichroism spectra of oligonucleotides

Contact Info

Product

Resources

About

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)