Relaxation studies of the proflavine-DNA complex: The kinetics of an intercalation reaction

Li, Hsueh Jei; Crothers, Donald M.

doi:10.1016/0022-2836(69)90138-7

Cited by 283 publications

(102 citation statements)

References 16 publications

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“…The study of the kinetics ofintercalation in native DNA has led Li and Crothers [29] to propose a two-step mechanism in which a so-called "outside" binding precedes insertion in the double helix. The absorption spectra of the and "inside" bound molecules have been found to be very similar [29]. This similarity might suggest that the species we have referred to as complex I1 in the binding to single stranded polymers could correspond to the "outside" bound form of Li and Crothers [29].…”

Section: Discussionmentioning

confidence: 89%

A Quantitative Analysis of Proflavine Binding to Polyadenylic Acid, Polyuridylic Acid, and Transfer RNA

Dourlent

Hélène

1971

European Journal of Biochemistry

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Absorbance measurements show that the binding of proflavine to poly(A) and poly(U) can be quantitatively resolved (within & 10 relative error) by the consideration of two bound species whose spectral properties and mechanisms of interaction are similar to those found in the DNA * proflavine systems: cooperative binding along the phosphate backbone (process I) and interaction between the aromatic rings of base and dye resulting presumably from some kind of intercalation of the ligand between consecutive bases (process 11). The comparison with a simple theoretical model shows that process I and process I1 are not independent but coupled.The spectrophotometric method is able to resolve the binding of proflavine to a tRNA species with the same accuracy as that obtained for poly(A) and poly(U). Accordingly, it is proposed that the mode of interaction between proflavine and all classes of polynucleotides (DNA, RNA, synthetic polymers) is similar in nature. From the differences observed in the distribution of the bound dye between the two complexes, the existence of a close correlation between the secondary structure of the polymer and its ability for binding the dye in complex I1 is proposed.Numerous and extensive studies have been reported on the interactions between acridine dyes and nucleic acids (mainly DNA). It is generally agreed that two kinds of complexes are formed between DNA and the dye in its cationic form [l]. At low ionic strength and small polymer to dye ratios (P/D < 1, where P is the total concentration of polymer expressed in nucleotide equivalents per liter, and D the total concentration of dye), the marked hypochromism and blue shift observed in the visible absorption spectrum of the dye suggest that most bound molecules are stacked along the phosphate backbone outside the double helix [a]. This All the quantitative studies report that the amount of bound ligand in complex I1 never exceeds one molecule per two base pairs. The model usually hypothesized for the interpretation of the results assumes a priori the independence of the binding sites. Accordingly, the number of type11 binding sites is found to be limited (a typical value of 0.2 binding sites per phosphate is generally reported). A recent study of Armstrong et al. shows that the experimental results can also be accounted for by assuming that every slot between two successive base pair plates is a potential binding site and that the binding of a dye molecule prevents further binding to the two adjacent sites [el. This second model is fundamentally opposite to the first one because it rests upon the existence of drastic interactions between nearest neighbors. I n several respects [el, the understanding of the phenomena is clarified by the model of Armstrong et al. However, it is quite possible that the exact behavior does not imply so strong interactions between adjacent sites, and therefore it might be better rationalized by an anticooperative binding process model with one binding site per base pair [7,8]. (In this report, "cooperativ...

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Section: Discussionmentioning

confidence: 89%

A Quantitative Analysis of Proflavine Binding to Polyadenylic Acid, Polyuridylic Acid, and Transfer RNA

Dourlent

Hélène

1971

European Journal of Biochemistry

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“…Absorbance spectra of the D-DNA system were recorded during titrations, and showed that the absorbance first decreases (phase 1, which corresponds to binding mode 1) and then increases (phase 2, which corresponds to binding mode 2) and displays a bathochromic shift (Supporting Information, Figure (Figure 6c) in that the positive band appears at longer wavelengths with respect to the negative one. [35] The shifts of spectra a) and b), with respect to c), along the wavelength axis depends on the position of the absorption band of proflavine, which is less energetic than the absorption bands of [31] 0.20 -2.0 [32] 0.24 -4.3 [33] (283 K) . Similarly, the higher amplitude of the proflavine band can be ascribed to the higher absorptivity of this dye.…”

Section: Dye Displacement Assaymentioning

confidence: 99%

“…The values of the related binding constant, K 2 , are close to the value that was measured for the DNA-proflavine system (Table 2), which is known to bind doublestranded nucleic acids by intercalation. [31][32][33] 2 + ]), respectively, the slopes of log K versus Àlog A C H T U N G T R E N N U N G [Na + ] plots could be much higher (ffi3 and ffi2). The lower values that were obtained suggest that not the entire molecule, but only the proflavine residue takes part in binding mode 2.…”

Section: Full Papermentioning

confidence: 99%

DNA Binding by a New Metallointercalator that Contains a Proflavine Group Bearing a Hanging Chelating Unit

Bazzicalupi

Bencini

Bianchi

et al. 2007

Chemistry A European J

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The new bifunctional molecule 3,6‐diamine‐9‐[6,6‐bis(2‐aminoethyl)‐1,6‐diaminohexyl]acridine (D), which is characterised by both an aromatic moiety and a separate metal‐complexing polyamine centre, has been synthesised. The characteristics of D and its ZnII complex ([ZnD]) (protonation and metal‐complexing constants, optical properties and self‐aggregation phenomena) have been analysed by means of NMR spectroscopy, potentiometric, spectrophotometric and spectrofluorimetric techniques. The equilibria and kinetics of the binding process of D and [ZnD] to calf thymus DNA have been investigated at I=0.11 M (NaCl) and 298.1 K by using spectroscopic methods and the stopped‐flow technique. Static measurements show biphasic behaviour for both D–DNA and [ZnD]–DNA systems; this reveals the occurrence of two different binding processes depending on the polymer‐to‐dye molar ratio (P/D). The binding mode that occurs at low P/D values is interpreted in terms of external binding with a notable contribution from the polyamine residue. The binding mode at high P/D values corresponds to intercalation of the proflavine residue. Stopped‐flow, circular dichroism and supercoiled‐DNA unwinding experiments corroborate the proposed mechanism. Molecular‐modelling studies support the intercalative process and evidence the influence of NH+⋅⋅⋅O interactions between the protonated acridine nitrogen atom and the oxygen atoms of the polyanion; these interactions play a key role in determining the conformation of DNA adducts.

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“…Detailed studies of the interaction of proflavine with DNA (Li & Crothers, 1969) have been made and it is believed that the interaction occurs via an intercalation mechanism. In order to obtain precise interatomic distances and angles and to determine the nature of the stacking of molecules in the crystalline state a crystal structure determination of the dihydrochloride dihydrate was done.…”

Section: Introductionmentioning

confidence: 99%

Proflavine dichloride dihydrate (3,6-diaminoacridine dihydrochloride dihydrate)

Obendorf¹,

Carrell²,

Glusker³

1974

Acta Crystallogr Sect B

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Proflavine dichloride dihydrate (3,6-diaminoacridine dihydrochloride dihydrate), Ca3NsHll. 2HC1.2H20, crystallizes in the monoclinic space group P2Ja, a=17.960 (2), b=7-156 (1), c=12-615 (1)A,, ,fly 109.47 ° (1), V= 1528-6 (3) ~3, F.W. 318.21, Z=4, Dx= 1-38, Dot, s = 1.37 gcm -3, J.(Cu Kc0= 1.541 8A, /x(Cu Ke)=37-4 cm -1. A structural determination by X-ray diffraction resulted in a final residual R=0.074 for 1170 observed reflections. The hydrogen atoms were located from a difference map and were refined isotropically. The proflavine cations are stacked with considerable molecular overlap between nearest neighbor molecules. In the cation studied here, the protons are on the nitrogen atom of the central ring and on one amino group. The ring nitrogen atom is hydrogen bonded to a chloride ion.

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Relaxation studies of the proflavine-DNA complex: The kinetics of an intercalation reaction

Cited by 283 publications

References 16 publications

A Quantitative Analysis of Proflavine Binding to Polyadenylic Acid, Polyuridylic Acid, and Transfer RNA

A Quantitative Analysis of Proflavine Binding to Polyadenylic Acid, Polyuridylic Acid, and Transfer RNA

DNA Binding by a New Metallointercalator that Contains a Proflavine Group Bearing a Hanging Chelating Unit

Proflavine dichloride dihydrate (3,6-diaminoacridine dihydrochloride dihydrate)

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