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

Kypr, Jaroslav; Štěpán, Jiří; Chládková, Jana; Vorlı́čková, Michaela

doi:10.1002/(sici)1520-6343(1999)5:4<253::aid-bspy6>3.0.co;2-6

Cited by 15 publications

(5 citation statements)

References 46 publications

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“…These spectral patterns suggest that a conformation variation of (dA-dT) 10 from right-handed to left-handed took place, which corresponds to the B to Z transition. 33,34 According to Ref. 35 the conformational change of oligonucleotide did not occur, because of the increase of the ionic strength that accompanies the increased concentration of porphyrin, 36 but is caused by porphyrin binding on (dA-dT) 10 .…”

Section: Cu(ii)tmpyp-oligonucleotide Complexesmentioning

confidence: 99%

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

Nový

Urbanová

2006

Biopolymers

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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.

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Section: Cu(ii)tmpyp-oligonucleotide Complexesmentioning

confidence: 99%

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

Nový

Urbanová

2006

Biopolymers

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“…},31 can adopt B, A, Z, and X conformations. Thus, the secondary structure of the alternating purine-pyrimidine sequences is very flexible.…”

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Circular Dichroism Spectroscopy of DNA: From Duplexes to Quadruplexes

et al. 2012

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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.

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“…Indeed, the actual concentration of Cd 2+ ions increases on decreasing the amount of added NaCl, because the dissociation equilibrium of CdCl 2 is more and more shifted to the right and thus the transition from B-to C-to (C + Z)-DNA conformation appears reasonable. 29,49,51,69 As for the series at constant I (=0.21) and increasing CdCl 2 concentration, three effects have to be considered, i.e. the decreasing weight of the NaCl present as the CdCl 2 concentration increases, the increase of the analytical concentration of total cadmium counterbalanced by a reduced dissociation degree of CdCl 2 .…”

Section: Discussionmentioning

confidence: 99%

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

Airoldi

Gennaro

Giomini

et al. 2011

Phys. Chem. Chem. Phys.

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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.

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

Cited by 15 publications

References 46 publications

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

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

Circular Dichroism Spectroscopy of DNA: From Duplexes to Quadruplexes

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

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

Cited by 15 publications

References 46 publications

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

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

Circular Dichroism Spectroscopy of DNA: From Duplexes to Quadruplexes

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

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About

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

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