Effects of Minor and Major Groove‐Binding Drugs and Intercalators on the DNA Association of Minor Groove‐Binding Proteins RecA and Deoxyribonuclease I Detected by Flow Linear Dichroism

Tuite, Eimer; Sehlstedt, Ulrica; Hagmar, Per; Nordén, Bengt; Takahashi, Masayuki

doi:10.1111/j.1432-1033.1997.0482a.x

Cited by 40 publications

(33 citation statements)

References 77 publications

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“…Our results clearly indicated that SC-dots could influence the interactions between DNA and MG, a proven DNA major groove binder (29,45,46). Figure 4B showed CD spectral changes in the presence of SC-dots.…”

Section: Resultsmentioning

confidence: 51%

Lighting up left-handed Z-DNA: photoluminescent carbon dots induce DNA B to Z transition and perform DNA logic operations

Feng

Zhao

Ren

et al. 2013

Nucleic Acids Research

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Left-handed Z-DNA has been identified as a transient structure occurred during transcription. DNA B-Z transition has attracted much attention because of not only Z-DNA biological importance but also their relation to disease and DNA nanotechnology. Recently, photoluminescent carbon dots, especially highly luminescent nitrogen-doped carbon dots, have attracted much attention on their applications to bioimaging and gene/drug delivery because of carbon dots with low toxicity, highly stable photoluminescence and controllable surface function. However, it is still unknown whether carbon dots can influence DNA conformation or structural transition, such as B-Z transition. Herein, based on our previous series work on DNA interactions with carbon nanotubes, we report the first example that photoluminescent carbon dots can induce right-handed B-DNA to left-handed Z-DNA under physiological salt conditions with sequence and conformation selectivity. Further studies indicate that carbon dots would bind to DNA major groove with GC preference. Inspired by carbon dots lighting up Z-DNA and DNA nanotechnology, several types of DNA logic gates have been designed and constructed based on fluorescence resonance energy transfer between photoluminescent carbon dots and DNA intercalators.

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Section: Resultsmentioning

confidence: 51%

Lighting up left-handed Z-DNA: photoluminescent carbon dots induce DNA B to Z transition and perform DNA logic operations

Feng

Zhao

Ren

et al. 2013

Nucleic Acids Research

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“…The further digestion and subsequent shortening of the DNA resulted in a decrease in the magnitude of the LD (20). A decrease in the magnitude of the LD reflecting the shortening of the DNA due to double strand cleavage by deoxyribonuclease I has also been reported (22). In this case, the decrease in the magnitude of the LD was able to be modeled as a single exponential decay.…”

Section: Introductionmentioning

confidence: 79%

Real-time detection of Fe{middle dot}EDTA/H2O2-induced DNA cleavage by linear dichroism

Wang

Lee

Jang

et al. 2008

Nucleic Acids Research

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The conditions for the measurement of linear dichroism (LD) can be adjusted so as to solely reflect the length and the flexibility of DNA. The real-time detection of the EDTA·Fe2+-induced oxidative cleavage of double-stranded native and synthetic DNAs was performed using LD. The decrease in the magnitude of the LD at 260 nm, which reflects an increase in the flexibility and a decrease in the length of the DNA, can be described by the sum of two or three exponential curves in relation to the EDTA·Fe2+ concentration. The fast component was assigned to the cleavage of one of the double strands, inducing an increase in the flexibility, while the other slower component was assigned to the cleavage of the double strand, resulting in the shortening of DNA. The decrease in the magnitude of the LD of poly[d(A-T)2] was similar to that of poly[d(I-C)2], while that of poly[d(G-C)2] was found to be the slowest, indicating that the resistance of poly[d(G-C)2] against the Fenton-type reagent was the strongest. This observation suggests that the amine group in the minor groove of the double helix may play an important role in slowing the EDTA·Fe2+-induced oxidative cleavage.

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“…Thus, methyl green, a DNA major groove binder [25], [26] was used as a major groove binding competitor for this competitive experiment. As shown in Figure 6A, in the presence of methyl green, no distinct effect on DNA band shifting could be observed on the agarose gel.…”

Section: Resultsmentioning

confidence: 99%

Binding to the Minor Groove of the Double-Strand, Tau Protein Prevents DNA from Damage by Peroxidation

et al. 2008

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Tau, an important microtubule associated protein, has been found to bind to DNA, and to be localized in the nuclei of both neurons and some non-neuronal cells. Here, using electrophoretic mobility shifting assay (EMSA) in the presence of DNA with different chain-lengths, we observed that tau protein favored binding to a 13 bp or a longer polynucleotide. The results from atomic force microscopy also showed that tau protein preferred a 13 bp polynucleotide to a 12 bp or shorter polynucleotide. In a competitive assay, a minor groove binder distamycin A was able to replace the bound tau from the DNA double helix, indicating that tau protein binds to the minor groove. Tau protein was able to protect the double-strand from digestion in the presence of DNase I that was bound to the minor groove. On the other hand, a major groove binder methyl green as a negative competitor exhibited little effect on the retardation of tau-DNA complex in EMSA. This further indicates the DNA minor groove as the binding site for tau protein. EMSA with truncated tau proteins showed that both the proline-rich domain (PRD) and the microtubule-binding domain (MTBD) contributed to the interaction with DNA; that is to say, both PRD and MTBD bound to the minor groove of DNA and bent the double-strand, as observed by electron microscopy. To investigate whether tau protein is able to prevent DNA from the impairment by hydroxyl free radical, the chemiluminescence emitted by the phen-Cu/H2O2/ascorbate was measured. The emission intensity of the luminescence was markedly decreased when tau protein was present, suggesting a significant protection of DNA from the damage in the presence of hydroxyl free radical.

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Effects of Minor and Major Groove‐Binding Drugs and Intercalators on the DNA Association of Minor Groove‐Binding Proteins RecA and Deoxyribonuclease I Detected by Flow Linear Dichroism

Cited by 40 publications

References 77 publications

Lighting up left-handed Z-DNA: photoluminescent carbon dots induce DNA B to Z transition and perform DNA logic operations

Lighting up left-handed Z-DNA: photoluminescent carbon dots induce DNA B to Z transition and perform DNA logic operations

Real-time detection of Fe{middle dot}EDTA/H2O2-induced DNA cleavage by linear dichroism

Binding to the Minor Groove of the Double-Strand, Tau Protein Prevents DNA from Damage by Peroxidation

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