Porphyrins conjugated to DNA as CD reporters of the salt-induced B to Z-DNA transition,

Baláž, Milan; Li, Benjamin C.; Steinkruger, Jay D.; Ellestad, George A.; Nakanishi, Koji; Berova, Nina

doi:10.1039/b603409h

Cited by 43 publications

(31 citation statements)

References 27 publications

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“…35 The UV-ECD spectrum also change its shape substantially, and had a negative couplet, with a maximum at 262(þ), and two minima at 270(À) and 247(À) nm, typical of the B to Z form transition. 11,34 The UV-ECD results correlate with the results on induced CD in the Soret region: both signals reverse the sign of their pattern. This supports our conclusions based on the Soret region ECD study.…”

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confidence: 56%

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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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confidence: 56%

“…9 Both UV and Soret regions were used in the ECD studies of bound porphyrin-oligonucleotide conjugates. [10][11][12][13][14] It has been shown that the CD signal of the porphyrin part of the conjugate can serve as a probe of the oligonucleotide conformation and its variation, e.g. the B-Z transitions.…”

Section: Introductionmentioning

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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“…One interesting consequence of the chiral structure of DNA is the induction of chiral effects, such as induced circular dichroism, in achiral molecules interacting with it, a property than can be profitably exploited for the study of small molecule-DNA interactions or to selectively probe DNA conformations, as in the case of the interaction of porphyrins, [21][22][23] acridine, 24 or cyanine dyes with dsDNA or its analogs. 25 The full description of these effects is beyond the scope of this review, which focuses on the chirality of the species interacting with DNA.…”

Section: Chirality and Handedness In The Structure Of Nucleic Acidsmentioning

confidence: 99%

Chirality as a tool in nucleic acid recognition: Principles and relevance in biotechnology and in medicinal chemistry

et al. 2007

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The understanding of the interaction of chiral species with DNA or RNA is very important for the development of new tools in biology and of new drugs. Several cases in which chirality is a crucial point in determining the DNA binding mode are reviewed and discussed, with the aim of illustrating how chirality can be considered as a tool for improving the understanding of mechanisms and the effectiveness of nucleic acid recognition. The review is divided into two parts: the former describes examples of chiral species interacting with DNA: intercalators, metal complexes, and groove binders; the latter part is dedicated to chirality in DNA analogs, with discussion of phosphate stereochemistry and chirality of ribose substitutes, in particular of peptide nucleic acids (PNAs) for which a number of works have been published recently dealing with the effect of chirality in DNA recognition. The discussion is intended to show how enantiomeric recognition originates at the molecular level, by exploiting the enormous progresses recently achieved in the field of structural characterization of complexes formed by nucleic acid with their ligands by crystallographic and spectroscopic methods. Examples of application of the DNA binding molecules described and the role of chirality in DNA recognition relevant for biotechnology or medicinal chemistry are reported.

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“…3). 22 The attachment of this achiral chromophore to DNA places it into a chiral environment, and allows excitonic coupling between porphyrin moieties giving rise to characteristic CD spectra. These are very sensitive to the porphyrin environment, 23 thus allowing, for example, detection of the change from B to Z form of DNA.…”

Section: Introductionmentioning

confidence: 99%

“…These are very sensitive to the porphyrin environment, 23 thus allowing, for example, detection of the change from B to Z form of DNA. 22 It should be noted that in addition to UV-Vis spectroscopy, CD spectroscopy is a major tool for analysis as it provides very useful information about the DNA's global structure.…”

Section: Introductionmentioning

confidence: 99%

DNA as supramolecular scaffold for functional molecules: progress in DNA nanotechnology

et al. 2011

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Oligonucleotides have recently gained increased attraction as a supramolecular scaffold for the design and synthesis of functional molecules on the nanometre scale. This tutorial review focuses on the recent progress in this highly active field of research with an emphasis on covalent modifications of DNA; non-covalent interactions of DNA with molecules such as groove binders or intercalators are not part of this review. Both terminal and internal modifications are covered, and the various points of attachment (nucleobase, sugar moiety or phosphodiester backbone) are compared. Using selected examples of the recent literature, the diversity of the functionalities that have been incorporated into DNA strands is discussed.

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Porphyrins conjugated to DNA as CD reporters of the salt-induced B to Z-DNA transition,

Cited by 43 publications

References 27 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

Chirality as a tool in nucleic acid recognition: Principles and relevance in biotechnology and in medicinal chemistry

DNA as supramolecular scaffold for functional molecules: progress in DNA nanotechnology

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Porphyrins conjugated to DNA as CD reporters of the salt-induced B to Z-DNA transition,

Cited by 43 publications

References 27 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

Chirality as a tool in nucleic acid recognition: Principles and relevance in biotechnology and in medicinal chemistry

DNA as supramolecular scaffold for functional molecules: progress in DNA nanotechnology

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Product

Resources

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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