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Nucleic Acids Research Pages 1001-1005  

Energetic and binding properties of DNA upon interaction with dodecyl trimethylammonium bromide
Introduction
Materials And Methods
   Materials
   Methods
Results And Discussion
Acknowledgements
References

Energetic and binding properties of DNA upon interaction with dodecyl trimethylammonium bromide

Energetic and binding properties of DNA upon interaction with dodecyl trimethylammonium bromide

S. Z. Bathaie, A. A. Moosavi-Movahedi* and A. A. Saboury

Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran

Received October 26, 1998; Revised December 17, 1998; Accepted January 6, 1999

ABSTRACT

The interaction of dodecyl trimethylammonium bromide (DTAB), a cationic surfactant, with calf thymus DNA has been studied by various methods, including potentiometric technique using DTAB-selective plastic membrane electrode at 27 and 37°C, isothermal titration microcalorimetry and UV spectrophotometry at 27°C using 0.05 M Tris buffer and 0.01 M NaCl at pH 7.4. The free energy is calculated from binding isotherms on the basis of Wyman binding potential theory and the enthalpy of binding according to van’t Hoff relation. The enthalpy of unfolding has been determined by subtraction of the enthalpy of binding from the microcalorimetric enthalpy. The results show that, after the interaction of first DTAB molecule to DNA (base molarity) through the electrostatic interaction, the second DTAB molecule also binds to DNA through electrostatic interaction. At this stage, the predom-inant DNA conformational change occurs. Afterwards up to 20 DTAB molecules, below the critical micelle concentration of DTAB, bind through hydrophobic interactions.

INTRODUCTION

One of the most important aims of modern biology is to understand the cell function in terms of the structure and interactions of its constituents, namely molecules of life, e.g. DNA, proteins and lipids. The use of modern techniques for structural elucidation has very much increased our understanding about cell function in molecular terms during recent years.

All forms of DNA have negative charges on their surfaces, so that they interact readily with positive charged molecules such as proteins (histones) (1), peptides (2), polyamines (3,4), metals (5), cationic lipids and liposomes (6-9) and monovalent cationic surfactants (10-13).

In gene-therapy, DNA-cationic surfactant complexes are very useful. Due to the polyanionic nature of DNA, its diffusion through the eukaryotic cell is difficult. Binding of DNA to the cell surface (generally rich in negative charge and zwitterionic lipids) is also not favorable. To remove such difficulties, various synthetic gene transfer vectors, e.g. cationic lipids and related surfactants, have been recently developed (6-9).

The cationic surfactants are useful in purification of DNA by precipitation (14,15), crystallization of DNA (13), study of stability (16), conformational alteration of DNA structure (6) and also for immunoadjuvant properties (17). A change in the conformation of the DNA could regulate biological processes such as replication, transcription and transfection. Cationic lipids or surfactants can induce a structural change in DNA, so that the structure of DNA can be controlled by selection of lipids or surfactants and temperature (6). One of the important attributes of transfection methods is that cationic peptides or liposomes generate the condensed DNA. Condensation of DNA has been suggested by Bloomfield and co-workers (18,19) and has been defined as an energetically favorable reaction that occurs spontaneously when the DNA phosphate charge is 90% neutralized. On the other hand, it is reported that cationic lipid binding does not lead to DNA condensation (8). Finally, the electrostatic interaction plays a major role in these complex formations, but the role of hydrophobic interactions should also be considered (8-11,20).

In spite of extensive studies on protein-surfactant complexes (21,22) and structural elucidation of protein denaturation by surfactants (23-26), less attention has been paid to the physico-chemical nature of DNA-surfactant interactions (7,8,10,11) and the DNA structural transitions with temperature in the presence of surfactants (16,20). Also, little is known about the factors that control these interactions, as well as the mechanism of energetic and binding properties of DNA-surfactant complexes.

The aim of the present study is to clarify the nature of the DNA-surfactant interactions. It has also been attempted to elucidate the electrostatic and hydrophobic contributions, as well as energetic conformational change of DNA by dodecyl trimethyl-ammonium bromide (DTAB), a cationic surfactant.

MATERIALS AND METHODS

Materials

DTAB was obtained from Sigma Chemical Co. NaCl and Tris were from Merck Co. All of the other materials used were of analytical grade.

The experiments were carried out at pH 7.4, using 0.05 M Tris buffer containing 0.01 M NaCl.

Methods

DNA purification. High molecular weight DNA was purified from calf thymus according to the modified methods of Sambrook et al. (27) and McGuire and Dela Graza (28), as follows. An appropriate amount of calf thymus was minced at 4°C. It was homogenized in NET buffer (0.15 M NaCl, 10 mM EDTA and 10 mM Tris-HCl, pH 7.5-8) at a ratio of 1:8 (w/v) using a Blender Model SM 2460 PG. Boiled RNase, 50 µg/ml (final concentration) was added and retained at 37°C for 1 h. Sodium dodecyl sulfate (SDS) with 0.2% (w/v) final concentration and proteinase K (50 µg/ml final concentration) was added and incubated overnight at 60°C. To obtain DNA, the crude extract was treated with an equal volume of phenol, phenol-chloroform-isoamylalcohol at 25:24:1 ratio, chloroform-isoamylalcohol at a ratio of 1:1, respectively. The aqueous phase was separated by centrifugation and finally DNA was extracted by precipitation with sodium acetate (0.3 M final concentration) and 3 vol of absolute ethanol. The DNA was pooled and washed with 70% ethanol followed by transfer of DNA using sterile forceps to 10:1 of TE buffer (1 mM EDTA and 10 mM Tris, pH 7.5-8) at 4°C until use. The DNA absorbance ratio at 260 and 280 nm was ~1.85 and the molecular weight was confirmed by agarose (0.7%) gel electrophoresis (29). The DNA concentrations were determined using an extinction coefficient of 6600 M-1cm-1 at 260 nm and expressed in terms of base molarity (30).

Potentiometry. Free DTAB concentration was determined by means of a DTAB-selective plastic membrane electrode which has been reported to have an excellent DTAB selectivity and a Nernstian response (31). The reference electrode was Ag-AgCl (Corning electrode).

A titration method was used for surfactant addition to the cell containing 20 ml of DNA solution, the DNA concentration was 1.098 × 10-4 and 1.05 × 10-4 base molarity (bM) at 27 and 37°C, respectively. After addition of 10-50 µl of 0.5 M DTAB and stirring the mixture (the changes in DNA concentration were considered), the electromotive force (emf) was measured potentiometrically.

Isothermal titration microcalorimetry. Enthalpy measurements were made at 27°C using an LKB microcalorimeter (2277 Thermal Activity Monitor, Boromma, Sweden). The microcalorimeter was interfaced with an IBM PS/2 Model 40486 computer; thermometric Digital 3 was the software program used. The enthalpy of interaction between DTAB and DNA was measured by transferring of 20 µl of 20 mM DTAB (in each injection) to the 2 ml of DNA solution (7.95 × 10-5 bM). The enthalpy of demicellization of DTAB due to injection was corrected by measuring the enthalpy change after injection of DTAB solution into buffer solution, using identical procedures and experimental conditions. The heat released by DNA dilution is negligible.

Ultraviolet specrophotometery. All spectrophotometric measurements were made with a Shimadzu Model 3100 Double-beam Spectrophotometer.

RESULTS AND DISCUSSION

The changes in the emf of the buffer solution in the presence and absence of DNA upon the addition of DTAB solution, at 27 and 37°C have been shown in Figure 1. The calibration curve clearly shows the excellent performance of the DTAB-specific membrane electrode. The deviation from the calibration curve in the presence of DNA (that is shown with arrows in the figures) allows us to calculate the amount of bound surfactants to DNA. According to the Nernst’s equation the following equation can be derived (31):

1

where E and E° are the electrode potential and standard electrode potential, respectively, T is the absolute temperature, R is the gas constant, F is the Faraday constant and [alpha]DTAB is the activity of DTAB. The latter term is nearly equal to the concentration of free DTAB ([DTAB]f) in solution (31). With calculation of [DTAB]f by equation 1 and subtracting it from the total concentration of DTAB ([DTAB]t), the concentration of bound DTAB ([DTAB]b) was calculated.


Figure 1. Plot of emf versus log[DTAB]t, for total concentration of DTAB in the presence and absence of DNA in Tris buffer 0.05 M, pH 7.4 and 0.01 M of NaCl at 27°C (upper) and 37°C (lower). The calibration curve shows: DTAB-DNA complexes (open square), 27°C (open triangle) and 37°C (stippled circle). CMC = 10 mM of DTAB (shown with arrows on the axis), and the arrows on the curves show the deviation from standard. The DNA concentration was 1.098 × 10-4 bM and 1.05 × 10-4 bM at 27 and 37°C, respectively.

The binding isotherms (Fig. 2a) have been plotted as the average number of bound surfactant per nucleotide of DNA, , versus logarithm of free concentration of DTAB (log[DTAB]f), at 27 and 37°C.


Figure 2. (a) Binding isotherms for DNA-DTAB interaction at 27°C (open triangle) and 37°C (stippled circle), where = [DTAB]b/[DNA] and [DTAB]b = [DTAB]t - [DTAB]f. The inset (b) is a plot of the [Delta]G versus at 27°C (open triangle) and 37°C (stippled circle).

[thetas] is a binding capacity, as discussed elsewhere (26):

2

where is the average number of DTAB bound per nucleotide of DNA, µ is the chemical potential of the ligand and [DTAB]f is the concentration of free DTAB in solution. By calculating the slope of the binding isotherms at any point, the values of [thetas] at any can be determined. The higher resolution factor, b, compared to [thetas] that subtly shows the number of sets for binding sites was calculated using equation 3 as follows (26):

3

where the R, T and are the same as described before and [thetas] was calculated according to equation 2.

Figure 3a shows the plot of b versus log[DTAB]f for thebinding of DTAB to DNA at 27°C below the critical micelle concentration (CMC). The figure shows the binding sets of DNA-DTAB complexes, which is similar to the nature of the protein-surfactant system. It was previously reported that two binding sets exist in protein-surfactant complexes, the first binding set involves an electrostatic interaction and the second one has a hydrophobic nature (24-26). Due to the nature of DNA (that is very similar to protein) with negatively charged surface and hydrophobic interior, it was also suggested that the first interaction of monovalent cationic surfactant to DNA was electrostatic (8,12). The first step in Figure 3a belongs to the electrostatic portion that ends at 2, and the other step belongs to the hydrophobic contribution.


Figure 3. (a) The variation of b respect to log[DTAB]f that is obtained by equation 3. For calculation of [thetas] and b according to equations 2 and 3, the data of the binding isotherm curve was fitted to the polynomial mathematical function with eight order (best correlation for this data). The inset (b) is the absorbance change of DNA (8.727 × 10 -5 bM) in the presence of different concentrations of DTAB at 260 nm.

The absorption change of DNA solution at 260 nm in the presence of different concentrations of DTAB (total) is also shown in Figure 3b (inset). The values of were calculated from a plot of versus [DTAB]t at DNA concentration used for the potentiometric experiments, with reference to the binding data and equation 4 (26):

4

Figure 3b shows the predominant denaturation, which occurs in the concentration range of the electrostatic interaction. This might be due to the fact that the electrostatic interaction causes the main destruction of DNA structure. This curve also shows the coincidence of [D]1/2 (concentration of DTAB that is brought half of the DNA denaturation) at 2, as the mid-point or transition point for denaturation profile. At this point the free energy change, is equal to zero (33); therefore 2 seems to be a saturation point for electrostatic interaction. Such a model has been shown previously for protein denaturation by surfactants through the two-state mechanism (34).

Figure 2a shows that an increase in the temperature caused a shift in the binding isotherm to the high concentration of free DTAB, which suggests exothermicity for the enthalpy of the interaction. Calculation of the apparent binding constant, Kapp, can be applied to the entire binding isotherm. This is based on the Wyman binding potential energy (35). The binding potential, [pi], is calculated from the area under the binding isotherm according to equation 5:

5

and is related to the apparent binding constant, Kapp, as follows (36):

6

Values of Kapp as a function of were determined by application of equations 5 and 6, and values were determined by equation 7:

7

shows the free energy changes of binding of 1 mol of DTAB to 1 mol of DNA (bM) at corresponding value. The electrostatic interaction is principally stronger than the hydrophobic ones (37). Figure 2b depicts the first two DTAB binding in higher negative free energy (-), related to electrostatic interactions. The limiting value of , at high values of , corresponds predominately to hydrophobic contribution (23,36-38). It is clear that the dominant contribution to is a large and positive T[Delta] (entropy) term consistent with hydrophobic interaction.

The enthalpy of the binding ([Delta]Hb) of DTAB with DNA was obtained from the temperature dependency of the binding constant (Kapp) using the van’t Hoff relation using equation 8 (39):

8

The [Delta]Hb is an approximate value of [Delta]Hb per each ([Delta]Hb = [Delta]Hb/). The plot of [Delta]Hb as a function of is shown in Figure 4. This plot shows two processes. The initial binding process is exothermic, which belongs to the electrostatic interaction up to 2. Over this range ( > 2), the endothermic process (reduction of exothermicity) occurs by hydrophobic bonding (37,40-42). The enthalpy of transfer of non-polar groups from the biomolecule (protein and DNA) interior into water is endothermic over 25°C (39-41). Therefore, the increase in the enthalpy after this point ( 2) is related to the unfolding process of DNA at the end of the exothermic electrostatic interactions.


Figure 4. The enthalpy of binding of 1 mol of DTAB to 1 mol of DNA (bM) against , calculated by van’t Hoff equation for binding between 27 and 37°C.

The enthalpy ([Delta]Hcal) was also measured using isothermal titration microcalorimetry (ITC) at 27°C, for DTAB-DNA interaction. The calorimetric enthalpy per each , [Delta]Hcal([Delta]Hcal = [Delta]Hcal/ ) versus , is shown in Figure 5. It depicts a minimum at = 1 and a maximum at = 2. This shows that the first ligand molecule binds through the electrostatic interaction and such as shown in Figure 4, the second ligand also binds through the electrostatic interaction. Because of the neutralization of the surface charges of the DNA molecule, the latter is mostly accompanied by the conformational changes. The other surfactant molecules can bind to DNA through hydrophobic interaction at lower values of energy changes.


Figure 5. The calorimetric enthalpy for binding of 1 mol of DTAB to 1 mol of DNA (7.95 × 10-5 bM ) at 27°C. The changes of [Delta]Hcal, against over 3.5 is negligible.

The calorimetric enthalpy (determined by ITC) consists of the enthalpy of binding ([Delta]Hb) and enthalpy of DNA unfolding ([Delta]Hu) as follows (24,34):

9

The enthalpy of unfolding ([Delta]Hu) curve (Fig. 6) shows that most of the unfolding occurred at 2, which is corresponding mostly to electrostatic interaction in DNA-DTAB complexes. The enthalpy of unfolding for the first interaction is ~35 kJ mol-1, whereas the unfolding enthalpy for the second one is ~105 kJ mol-1. The overall enthalpy of unfolding for electrostatic portion (up to 2) of DNA-DTAB complexes is ~140 kJ mol-1, which is consistent to ~67% of the energy for DNA destruction and is ~70 kJ mol-1 for hydrophobic contributions, leading to complete unfolding. This indicates that, after neutralization of surface charges of DNA, which were induced by the electrostatic interactions, the dominant conformational changes occurred. Subsequently, overall conformational changes take place by hydrophobic moiety.


Figure 6. Variation of enthalpy of unfolding ([Delta]Hu) for DNA by DTAB. The arrows show the change in the slope of the curve, under the effect of different kinds of interactions.

It has been demonstrated by the work of Bloomfield and co-workers (19) that when polyvalent cations are mixed with DNA it can lead to the condensation reaction. The same consideration about the condensation of DNA after interaction with cationic lipids was proposed by Bhattacharya and Mandel (11). They have also confirmed the occurrence of hydrophobic interaction in this complex formation. On the other hand, Reimer and co-workers (8) have proposed a different model for complexes between plasmid DNA and monovalent cationic lipids. On the basis of this model, the first interaction between these two molecules is electrostatic and DNA was not condensed. Then the hydrophobic interactions occurred. Also, the formation of the electrostatic bond between one molecule of cationic surfactant and each site of DNA with cooperativity in binding was reported previously (12).

The binding mechanism of detergent to DNA is not much different with protein, because DNA, like protein, has two portions, e.g. a surface composed of charges and an interior composed of hydrophobic forces (stacking forces composed of electrostatic, hydrophobic and dispersion or van der Waals forces, the latter three of which have a hydrophobic nature). The interaction of these groups with water resemble those of their counterparts in the proteins, unless at the low temperature (42). The interaction between detergents and the globular proteins occurs by ionic binding of the charged group of the detergent to oppositely charged sites on the proteins. The protein unfolds as a consequence of the resulting change in the balance of the polar and apolar interaction. Once all the ionic sites are saturated, the hydrophobic mechanism predominates. Also in DNA after neutralization of surface charges, the destabilization of DNA occurs (6); subsequently the hydrophobic forces contribute to the binding (10-12,20,42).

In this study (with various techniques such as potentiometry, spectrophotometry and ITC and also with determination of different parameters such as: b, [Delta]G, [Delta]Hb, [Delta]Hcal and [Delta]Hu), it is shown that the first interaction between the DTAB molecule and DNA is electrostatic (backbone phosphate), and has a considerable energy content. Afterwards, the second DTAB molecule binds to DNA mostly through electrostatic interaction, which is accompanied with the conformational change (Fig. 5) and denaturation of DNA (Fig. 3b). The exact site of this interaction is not clearly known, but it seems that binding is through the nitrogen of the bases, which has the electrostatic character (43,44). Other DTAB molecules bind to DNA through the hydrophobic interactions.

Due to the hydrophobic nature of the interior of DNA (42,45), after the formation of the electrostatic interactions and unfolding of DNA, the lipophilic alkyl chains can possibly penetrate through the bases and the hydrophobic bonds are formed. The propensity of the hydrophobic chains of the surfactants to interact with the hydrophobic interior of DNA is further necessitated to form the spontaneous tendency of surfactant hydrocarbon chains to minimize water contacts. On the other hand, the large hydrophobic interactions due to base stacking are related to entropic contributions yielding from binding of DTAB tail to hydrophobic chains of double-stranded DNA interior.

In conclusion, the thermodynamic and binding parameters show that the interaction of DTAB to DNA did not cause any condensation in DNA, but it has led to DNA unfolding. The predominant force in this conformational change is the electrostatic interaction between DNA and DTAB, and the hydrophobic interaction leading to complete DNA denaturation.

ACKNOWLEDGEMENTS

We are grateful to Dr H. Gharibi for his guidance in preparing the valuable DTAB electrodes and Dr A. A. Ziaee for his careful consideration to extract DNA. The financial support for this work was provided by the Research Council of University of Tehran.

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*To whom correspondence should be addressed. Tel: +98 21 6113381; Fax: +98 21 6404680; Email: moosavi@ibb.ut.ac.ir

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