Effect of dC → d(m⁵C) Substitutions on the Folding of Intramolecular Triplexes with Mixed TAT and C⁺GC Base Triplets

Abstract

Oligonucleotide-directed triple helix formation has been recognized as a potential tool for targeting genes with high specificity. Cystosine methylation in the 5′ position is both ubiquitous and a stable regulatory modification, which could potentially stabilize triple helix formation. In this work, we have used a combination of calorimetric and spectroscopic techniques to study the intramolecular unfolding of four triplexes and two duplexes. We used the following triplex control sequence, named Control Tri, d(AGAGAC₅TCTCTC₅TCTCT), where C₅ are loops of five cytosines. From this sequence, we studied three other sequences with dC → d(m⁵C) substitutions on the Hoogsteen strand (2MeH), Crick strand (2MeC) and both strands (4MeHC). Calorimetric studies determined that methylation does increase the thermal and enthalpic stability, leading to an overall favorable free energy, and that this increased stability is cumulative, i.e. methylation on both the Hoogsteen and Crick strands yields the largest favorable free energy. The differential uptake of protons, counterions and water was determined. It was found that methylation increases cytosine protonation by shifting the apparent pK_a value to a higher pH; this increase in proton uptake coincides with a release of counterions during folding of the triplex, likely due to repulsion from the increased positive charge from the protonated cytosines. The immobilization of water was not affected for triplexes with methylated cytosines on their Hoogsteen or Crick strands, but was seen for the triplex where both strands are methylated. This may be due to the alignment in the major groove of the methyl groups on the cytosines with the methyl groups on the thymines which causes an increase in structural water along the spine of the triplex.

1. Introduction

Triple stranded DNA, or triplexes, are a regulatory structure found within chromosomal DNA.[1, 2] Because triplexes are inherently unstable, a feature which implicates the involvement of triplexes in cancer and neurodegenerative disorders,[3–9] they can be hard to detect and verify. Because of triplex instability, they have a high rate of generating repeat sequences such as in the case of Freidrich’s ataxia, which become progressively worse in successive generations.[8, 10–12] Despite their perceived instability, triplexes have been associated with a variety of roles related to genomic regulation; this role is supported by the fact that most identified intramolecular DNA triplex forming sequences occur only once in the genome, which imparts specificity to triplexes as a regulatory binding element.[3, 13] Triplexes have been shown to be involved in genomic regulation by acting as pause sites during replication,[6, 14–18] posttranslational processing through mRNA splicing,[19, 20] and chromatin organization by triplex formation through distant sequences.[21–23] In addition, it has been shown that triplexes promote methyltransferase recruitment and methylation of downstream cystosines,[11, 24–26] which alters gene expression and is important for gene imprinting and cell differentiation.[27–33] Recent work has suggested that the solution conditions of the cell, not often replicated in vitro, significantly stabilize Hoogsteen hydrogen bonds, leading to stable formation of triplexes.[34] This research, coupled with the identification of over a thousand sites for triplex formation by long noncoding RNAs (lncRNAs),[35, 36] suggests that triplexes may be a more widespread regulatory mechanism than originally hypothesized. In addition, significant synthetic work has been done to generate a triplex forming third strand with greater stability and pH independence for use as an antigene therapy.[37–40]

Epigenetic affects due to cytosine methylation have long been known to be a critical factor in vertebrates,[28, 33, 41, 42] and are associated with key biological processes such as genomic imprinting,[32, 33, 43, 44] X-chromosome inactivation,[45–48] silencing of transposons[33, 49–51] and cell differentiation.[45, 52, 53] These methylation-dependent processes typically occur during early development and exclusively occur at CpG dinucleotides. However, current research has shown that dynamic methylation occurs during other times and in other cell types, with a preference for CpA dinucleotides.[54, 55] This has shown to be especially prevalent in repeat sequences and transposons of fungi, which display little CpG methylation but an abundance of CpA and CpT methylation.[56, 57] The methylation of the repeat sequences is thought to silence transposons and prevent the repeat sequences from being extended. CpA methylation is also seen in methylation studies of Drosophilia, which was previously believed to not utilize methylation for gene regulation.[58] Specifically, significant CpH methylation has been found in mature human and mouse brains cells, but not in infant brain cells.[54, 59, 60] These studies revealed that non CpG methylation accumulates appreciably through human brain development.[54] Embryonic stem cells, pluripotent stem cells and oocytes have shown significant levels of non-CpG methylation which is then lost after cell differentiation, suggesting a dynamic role in gene regulation for non-CpG methylation rather than the static role of CpG methylation.[54, 55, 61–64] Because triplexes have been linked with chromatin organization and enhanced methylation of downstream cystosines,[4, 24, 65, 66] and studies have shown dynamic methylation at non-CpG sites, we decided to investigate the thermodynamic stability of methylated pyrimidine triplexes, with specific focus on determining the differential binding of protons, counterions, and water. The immobilization of these molecules is important for determining DNA stability and for their ability to interfere with polymerase binding; they also have implications in antigene strategies that seek to generate a methylated triplex that could hinder polymerase binding, or disrupt a triplex by forming two duplexes.

Triplexes consist of three strands, with two of these strands forming canonical Watson-Crick base-pairs with each other, and a third strand binding to the Watson strand through Hoogsteen or reverse-Hoogsteen hydrogen bonds. There are two types of intramolecular DNA triplexes, a pyrimidine or parallel triplex, and a purine or anti-parallel triplex. The pyrimidine triplex has a pyrimidine-rich Hoogsteen strand, which runs parallel to the Watson strand and binds to it through Hoogsteen base-pairing. If this third strand contains cytosines, then only one hydrogen bond is possible without protonation at its N3 position, and thus these triplexes are stabilized by low pH to facilitate protonation.[38, 67] A pyrimidine triplex may also contain only thymines and these triplexes are stabilized by mono and divalent cations. If the third strand is rich in purines then it will run anti-parallel to the Watson strand and bind using reverse-Hoogsteen hydrogen bonds; purine rich triplexes are stabilized by mono and divalent cations.[39, 68] The triplexes studied below and shown in Figure 1 are examples of pyrimidine, or parallel, triplexes, with the third strand binding to the Watson strand with Hoogsteen hydrogen bonds.

Figure 1.

Hypothesized structures of triplexes and duplexes. • indicates Watson-Crick base-pairing, * indicates Hoogsteen base-pairing, and ^mC⁺ represents methylated cytosines.

Ions and water molecules are critical for the native function of DNA, regardless of structure, but are often overlooked. As a biopolymer, DNA is negatively charged and the repulsive forces from these charges play a role in dictating the structure of DNA. Structures such as intramolecular junctions, which have a high charge density around the junction, have a strong structural requirement for cations to neutralize the negative charge repulsion.[69, 70] The same is true for triplexes, which have a third strand inserted into the major groove and bound to the Watson strand.[71–73] While triplexes may have a higher counterion uptake, the cytosine protonation necessary for pyrimidine triplex formation would exclude counterions and may have an impact on the overall stability. In addition to influencing triplex stability, any ions bound to the surface of the DNA would need to be displaced, an entropically favourable process, in order to interact with a complementary strand, such as in an antigene therapy, or for a protein to bind.

Water also plays a fundamental role in determining the secondary and tertiary structure of oligonucleotides,[74] as previous research has indicated that nucleic acids are heavily hydrated.[75, 76] The overall hydration of an oligonucleotide is dependent on its conformation, nucleic acid composition, and sequence.[77–80] The precise details and determinants of hydration have yet to be fully elucidated, especially when taking into account the different types of water bound to the surface of nucleic acids; hydrophobic or structural water, associated with polar and non-polar groups, and electrostricted water, which are immobilized by charged groups.[81, 82] These two types of water are difficult to differentiate and the results are further confused when considering the hydration sphere of the ions bound to oligonucleotides. In a similar manner to ions, water must be displaced in order for another molecule to bind to the surface of DNA. Cation and water release have a major effect on the binding of proteins to nucleic acids due to the contribution to a favourable binding entropy.

Our lab is focused on understanding the unfolding thermodynamics of DNA structures, the physical factors that control which structures they form and the free energy of these forms. In addition, we seek to complete these thermodynamic profiles by measuring the uptake of water, protons and counterions, which are sequence and structure dependent. In this study, we used a combination of spectroscopic and calorimetric techniques to investigate the unfolding behaviour of a pyrimidine triplex (Control Tri) at pH 5.2 and 6.2, and compared its behaviour with that of a triplex containing 5-methylcytosines on the Hoogsteen strand (2MeH), the Crick strand (2MeC), and both strands (4MeHC). Our results suggest that methylation increases the thermal stability and free energy of formation of the duplex domain, but not the triplex. Methylation increases the pH range at which the cytosines become protonated; a higher amount of protonation causes a greater exclusion of counterions due to the positively charged cystosines. Methylation did not appear to increase water immobilization to any significant extent, with 2MeH and 2MeC showing the same amount of immobilization as Control Tri. However, 4MeHC did have higher water immobilization, although the reason for this is unclear.

2. Materials and Methods

2.1 Materials

All oligomers were synthesized and HPLC purified by the Core Synthetic Facility of the Eppley Research Institute at the University of Nebraska Medical Center. The oligomers were further desalted by gel permeation chromatography using a G-10 Sephadex column. The concentration of each oligomer shown in Figure 1 was measured at 260 nm at 80°C using the molar extinction coefficients reported below. Oligomer sequences, their designations, and extinction coefficients (in mM⁻¹cm⁻¹ of strands): d(AGAGAC₅TCTCTC₅TCTCT), Control Tri, 210; d(AGAGAC₅TCTCTC₅T^mCT^mCT), 2MeH, 210; d(AGAGAC₅T^mCT^mCTC₅TCTCT), 2MeC, 213; d(AGAGAC₅T^mCT^mCTC₅T^mCT^mCT), 4MeHC, 213; d(AGAGAC₅TCTCTCC), Control Du, 150; d(AGAGAC₅T^mCT^mCTCC), 2MeC-Du, 150. All values were calculated by extrapolating the tabulated values of the monomers and dimers from 25 °C to high temperatures, using procedures reported earlier.[83, 84] The buffer solutions consisted of 10 mM sodium cacodylate or 10 mM sodium phosphate, adjusted to different pH, salt, and water activity with HCl, NaCl and ethylene glycol, respectively. All chemicals used in this study were reagent grade and used without further purification.

2.2 Temperature-Dependent UV Spectroscopy

Absorbance versus temperature profiles for all oligonucleotides were obtained with a thermoelectrically controlled Aviv 14-DS Spectrophotometer (Lakewood, NJ). The absorbance of the oligonucleotides was recorded continuously at 260 nm, while the temperature was increased from 0 to 100°C at a heating rate of 0.6 °C min⁻¹. UV melting curves allow measurement of the midpoint of the order-disorder transition, or T_M, and the shape of the melting curves allows determination of the model dependent van’t Hoff enthalpy, ΔH_vH. The transition temperatures, T_Ms, were determined by using the Lorentz model in Origin to fit the first derivative of the melting curves; the peak maxima obtained was reported as the mid-point temperature of the triplex-duplex and duplex-coil transitions. Melting curves were done as a function of total strand concentration in order to determine the molecularity of the transition(s) of each oligonucleotide. If the T_M is constant across all concentrations then the transition is intramolecular or monomolecular. A T_M dependence on strand concentration is indicative of higher order molecularities. Additional UV melting curves were obtained to measure the model-independent release/uptake of protons, Δn_H+, counterions, Δn_Na+, and water molecules, Δn_W.

2.3 Circular Dichroism (CD)

An Aviv stopped flow circular dichroism spectrometer model 202SF (Lakewood, NJ) was used to evaluate the overall conformation of the DNA triplexes and control duplexes. The spectra were recorded from 200 to 320 nm at 20 °C in 1 nm increments in a 1 cm pathlength quartz cell using solutions with an absorbance of 1.0. Each spectrum was recorded after 20 minutes of pre-equilibration time and the spectra shown correspond to an average of at least two scans.

2.4 Differential Scanning Calorimetry (DSC)

The calorimetric measurements were performed with a VP-DSC from Malvern MicroCal (Northampton, MA). This calorimeter consists of two cells; a sample cell, containing an oligomer solution (0.6 mL) and the reference cell filled with the same volume of buffer. Both cells were equilibrated at 1 °C for 10 minutes before being heated adiabatically from 1 to 100 °C at a heating rate of 0.75 °C min⁻¹. The heat capacity, ΔC_p, was measured as a function of temperature during the unfolding process of each oligonucleotide. The corresponding buffer-buffer baselines were subtracted from the ΔC_p versus temperature curves and the resultant melting curves were deconvoluted using a non two-state zero ΔC_p model and analyzed to obtain the thermal midpoint, T_M, calorimetric enthalpy, ΔH_cal, calorimetric entropy, ΔS_cal, and van’t Hoff enthalpy, ΔH_vH. The ΔH_cal and ΔS_cal were determined by integrating the normalized area under a transition peak, (ΔH_cal = ∫ΔC_pdT; ΔS_cal = ∫(ΔC_p/T)dT), while the ΔH_vH is determined by the shape of the transition peak.[85] The folding free energy at 5 °C, ΔG° ₍₅₎, is calculated from the Gibbs equation, ΔG°₍₅₎ = ΔH_cal − TΔS_cal.

Each experiment is composed of at least three scans with a pre-equilibration time of 20 to 40 minutes for successive scans. In each experiment at pH 5.2, we observed that the scans of the modified triplexes with 5-methylcytosines were not superimposable due to oligonucleotide degradation from a combination of low pH and high temperature. However, the first scans of the experiments performed each time with purified oligomers are superimposable. The data reported at this pH are the average of at least three first scans of three individual experiments. At pH 6.2 or 7.0, all scans of each experiment are superimposable and the data reported are the average of at least three scans.

2.5 Differential Binding of Protons, Sodium Ions and Water Molecules

The following equations were used to measure the thermodynamic uptake of protons, Δn_H+, counterions, Δn_Na+, and water molecules, Δn_W, upon folding of each triplex and control duplexes: [86, 87]

$$\mathrm{\Delta }{n}_{\mathrm{H}}+=0.434\left[\mathrm{\Delta }{H}_{\text{cal}}/\mathrm{R}{T_{\mathrm{M}}}^2\right]\left(\partial T_{\mathrm{M}}/\partial \text{pH}\right)$$ (1)

$$\mathrm{\Delta }{n}_{\text{Na}}+=-1.11\left[\mathrm{\Delta }{H}_{\text{cal}}/\mathrm{R}{T_{\mathrm{M}}}^2\right]\left(\partial T_{\mathrm{M}}/\partial \text{ln}\left[{\text{Na}}^{+}\right]\right)$$ (2)

$$\mathrm{\Delta }{n}_{\mathrm{W}}=-\left[\mathrm{\Delta }{H}_{\text{cal}}/\mathrm{R}{T_{\mathrm{M}}}^2\right]\left(\partial T_{\mathrm{M}}/\partial \text{ln}\left[{\mathrm{a}}_{\mathrm{W}}\right]\right)$$ (3)

where 0.434 and 1.11 are correction factors that correspond to conversion of decimal logarithms into natural logarithms and concentrations into ionic activities, respectively. The [ΔH_cal/RT_M²] term is a constant that is determined from DSC experiments where the enthalpy is model independent and R is the gas constant. The values in parenthesis are determined from UV melting curves by measuring the T_M dependencies on the concentration of protons (by varying the pH), counterions (by varying the salt concentration), and water (by varying the osmolyte, ethylene glycol, concentration).

In determining Δn_Na+, the UV experiments were carried out with a [NaCl] from 10 mM to 200 mM at pH 5.2. For Δn_H+, the UV melting curves were obtained from a pH range of 5.2 to 7.0 with a concentration of 10 mM NaCl. For Δn_W the UV melting curves were carried out at pH 5.2 in 10 mM NaCl. The activity of water was varied by increasing the concentration of ethylene glycol, an osmolyte that does not interact with DNA, from 0.5 – 2.5 M.[88] The osmolality of the ethylene glycol solutions was measured with a Model 830 UIC vapor pressure osmometer which was calibrated with standardized NaCl solutions. The osmolalities were converted into water activity using the equation lna_W = −Osm/M_W,[89] where Osm is the measured solution osmolality and M_W is the molality of pure water. Measurement of the differential binding of water using the osmotic stress method yields only the immobilization of structural, not electrostricted, water.

3. Results and Discussion

3.1 Experimental Design

All oligonucleotides studied were designed to form an intramolecular triplex with a common triple helical domain consisting of three TAT and two C⁺GC base triplets (Figure 1). The cytosines in both the Crick and/or Hoogsteen strand were methylated, as cytosines are the most abundant methylated nucleic acid, with nearly all organism utilizing cytosine methylation as a regulatory mechanism. In naming these molecules, Control Tri refers to the triplex with no modifications, 2MeH refers to the replacement of two cytosines with methylated cytosines on the Hoogsteen strand, and 2MeC refers to replacement of two cytosines with methylated cytosines on the Crick strand. 4MeHC refers to replacement of four cytosines with methylated cytosines on both the Hoogsteen and Crick strands. Two hairpin controls were studied, one without methylation (Control Dup) and one with methylation on what would be the Crick strand in a triplex (2MeC-Dup). All methylated triplexes will be compared to the non-methylated control molecule in order to understand the effects of methylation on the thermodynamic properties of triplexes.

All the triplexes contain cytosine in their third strand which must be protonated at the N3 position in order to enhance triplex formation, and so are stabilized by low pH. Therefore, most triplex experiments are conducted at pH 6.2 and 5.2. However, the duplexes are not stabilized by low pH and experiments pertaining to the control duplexes are run at pH 7.0.

3.2 All triplexes and duplexes fold intramolecularly

Figure S1 shows typical UV melting curves for all the triplexes in 10 mM sodium cacodylate at pH 6.2. Figure S2 shows UV melting curves for the control duplexes in 10 mM sodium cacodylate at pH 7.0. The UV melts were obtained over a total strand concentration range of 2–100 μM in order to determine the transition molecularities of each molecule; the corresponding dependencies on T_M are shown in Figure S1 and S2 (Right). The T_Ms remain constant over a 50-fold range in strand concentration, indicating that all molecules are forming intramolecular complexes. The curves of the unmethylated control molecules (Control Tri and Control Dup) are monophasic, while those of the methylated molecules are biphasic, indicating that methylation, even in the case of the duplexes, causes a significant change to the melting behavior of the oligonucleotides.

3.3 All oligonucleotides adopt a triplex structure and are in a mixture of the A- and B-conformation

The CD spectra of each triplex was recorded in 10 mM sodium cacodylate at pH 5.2 and are shown in Figure 2; the spectra of the control duplexes in 10 mM sodium cacodylate at pH 7.0 are shown in Figure S3. All oligonucleotides deviate from the typical B-form DNA spectrum, which consists of two peaks at ~250 and 280 nm that are approximately equivalent in magnitude. Instead, the oligonucleotides have an intense positive peak at ~280 nm and a weak negative peak at ~260 and 210 nm, except for the duplexes which lack the band at 210 nm, features which resembles A-form DNA.[90] However, true A-form DNA has a large positive peak at ~270 nm and negative peaks at ~240 and 210 nm. These differences are likely due to spectroscopic influences from the loop cytosines. This is consistent with what has been previously observed with triplexes of mixed TAT and C⁺GC base triplets.[72, 73] Because this is consistent across all molecules it can be assumed that both triplex formation and methylation are not responsible for this non-canonical DNA form, but rather the sequence of the DNA itself. However, it should be noted that the negative peak at 210 nm is also considered characteristic of triplexes[91], although it is much weaker than expected, and would explain why the duplexes lack this peak. The lack of this peak in the duplexes indicates that it is due to triplex formation.

Figure 2.

CD spectra at 20 °C in 10 mM sodium cacodylate at pH 5.2 of Control Tri (solid line), 2MeH (dashed line), 2MeC (dotted line) and 4MeHC (short dashed line).

3.4 Methylation increases the stability of the duplex

The DSC thermograms of the triplexes at pH 5.2 and 6.2 are shown in Figure 3 while the thermograms of the duplex controls are shown in Figure S4. Because the triplexes studied contain cytosines in the Hoogsteen strand they should be stabilized at low pH; this can be seen in Table 1, which list the thermodynamic parameters obtained at pH 5.2 and 6.2 for all oligonucleotides studied. The change in the thermodynamic parameters of the methylated triplexes compared to Control Tri is shown in Table 2. In all cases the triplexes are significantly thermally destabilized at pH 6.2 compared to pH 5.2.

Figure 3.

DSC thermograms of Control Tri (solid line), 2MeH (dashed line), 2MeC (dotted line) and 4MeHC (short dashed line) in (Top) 10 mM sodium cacodylate at pH 5.2 and (Bottom) 10 mM sodium cacodylate at pH 6.2.

Table 1.

Thermodynamic Profiles for the Unfolding of Triplexes and Duplexes.

pH	Transition	TM (°C)	ΔHCal (kcal/mol)	ΔG°(5) (kcal/mol)	TΔScal (kcal/mol)
Control Tri
5.2		56.7	93.9	14.7	79.2
6.2		38.5	87.6	9.4	78.2
2MeH
5.2		61.6	91.4	15.5	75.9
6.2	1st	35.2	50.4	4.9	45.5
	2nd	49.1	45.2	6.2	39.0
Total			95.6	11.1	84.5
2MeC
5.2	1st	57.1	57.8	9.1	48.7
	2nd	66.7	42.2	7.7	34.5
Total			100.0	16.8	83.2
6.2	1st	37.9	46.4	4.9	41.5
	2nd	53.5	56.0	8.3	47.7
Total			102.4	13.2	89.2
4MeHC
5.2	1st	55.3	51.5	7.9	43.6
	2nd	70.2	55.7	10.6	45.1
Total			107.2	18.5	88.7
6.2	1st	35.6	46.4	4.6	41.8
	2nd	57.9	64.6	10.3	54.3
Total			111.0	14.9	96.1
Control Dup
7.0		31.9	29.2	2.6	26.6
2MeC-Dup
7.0	1st	13.7	4.3	0.1	4.2
	2nd	36.9	42.3	4.4	37.9
Total			46.6	4.5	42.1

All experiments are done in 10 mM sodium cacodylate buffer. Experimental errors are as follows: T_M (±0.5 °C), ΔH_cal (±5 %), TΔS (±5 %), ΔG° ₍₅₎ (±7 %).

Table 2.

Thermodynamic Contributions of the Methylated Triplexes.

pH	Transition	δTM (°C)	ΔΔHcal (kcal/mol)	ΔΔG°(5) (kcal/mol)	Δ(TΔScal) (kcal/mol)
2MeH – Control Tri
5.2		+4.9	+2.5	−0.8	+3.3
6.2	1st	−3.3
	2nd	+10.6
Total			−8.0	−1.7	−6.3
2MeC – Control Tri
5.2	1st	−0.4
	2nd	+10.0
Total			−6.1	−2.1	−4.0
6.2	1st	−0.6
	2nd	+15.0
Total			−14.8	−3.8	−11
4MeHC – Control Tri
5.2	1st	−1.4
	2nd	+13.5
Total			−13.3	−3.8	−9.5
6.2	1st	−2.9
	2nd	+19.4
Total			−23.4	−5.5	−17.9
2MeC-Dup – Control Dup
7.0		+5.0	−13.1	−1.8	−11.3

Values calculated relative to the control triplex and duplex.

Control Tri is monophasic at both pHs and gains significant thermal and enthalpic stability as the pH is decreased. At pH 6.2 Control Tri has a T_M of 38.5 °C and a ΔH_cal of 87.6 kcal/mol. While this is greater than the predicted nearest-neighbor enthalpy of the duplex (40.4 kcal/mol), indicating that the triplex is forming, it is less than what would be expected for the addition of a third strand (100.5 kcal/mol),[72] indicating poor base-triplet stacking or lack of base-triplet stacks. At pH 5.2 Control Tri has a T_M of 56.7 °C and a ΔH_cal of 93.7, indicating improved triplex formation although it is still below the expect value for complete formation of the triplex. This is an increase of 18.2 °C and −6.3 kcal/mol due to protonation of the cytosines in the Hoogsteen strand.

In 2MeH the two cytosines on the Hoogsteen strand are methylated and, similar to Control Tri, it gains significant thermal stability when lowering the pH. At pH 6.2, 2MeH has two transitions at 35.2 and 49.1 °C with ΔH_cals of 50.4 and 45.2 kcal/mol, respectively. The increased thermal stability suggests significant effects of methylation on the unfolding of triplexes, consistent with previous literature on methylated triplexes.[40, 92–94] However, in previous studies intermolecular triplexes with a methylated Hoogsteen strand were studied and only the triplex was stabilized. For intramolecular triplexes, methylation uncouples the simultaneous unfolding of the triplex and duplex seen in Control Tri with the duplex domain of 2MeH unfolding at a significantly higher temperature (ΔT_M of 10.6 °C) than that of Control Tri, and with a higher enthalpy, suggesting that methylation of the Hoogsteen strand affects the stability of the unmethylated duplex; this increase in stability is not seen in the unfolding of the triplex. The total enthalpy (95.6 kcal/mol) is higher than Control Tri at pH 6.2, indicating that methylation facilitates base-triplet stacking or that the methyl groups engage in enthalpically favorable interactions with the surrounding nucleotides, as previously described.[93, 95, 96] At pH 5.2 2MeH is monophasic, with a T_M of 61.6 °C and a ΔH_cal of 91.4 kcal/mol. While the total enthalpy is not increased (ΔΔH_cal −2.5 kcal/mol, well within experimental error), the thermal stability of the duplex and triplex is increased (ΔT_M of 4.9 °C). This suggests that at physiological pH, without partial protonation of the cytosines, methylation of the Hoogsteen strand stabilizes duplex formation, but at low pH when the cytosines are protonated methylation stabilizes both duplex and triplex formation.

In 2MeC the two cytosines in the Crick strand are methylated. At pH 6.2 2MeC looks similar to 2MeH, with two transitions at 37.9 and 53.5 °C and ΔH_cals of 46.4 and 56.0 kcal/mol, respectively. The triplex and duplex are uncoupled, similar to 2MeH, with the duplex unfolding at a much higher temperature than in Control Tri or even 2MeC-Dup, indicating that methylation of cytosines causes stabilization of the duplex regardless of where the methylation occurs. The enthalpy of the duplex folding transition (53.5 kcal/mol) is higher than expected based on 2MeC-Dup, indicating a greater number of base-pair stacks occurring, or perhaps contributions from the methylated cytosines, consistent with previous reports of hydrophobic effects from the methyl groups that increase the enthalpy of formation.[95, 96] The total enthalpy is higher than what is seen for Control Tri at pH 6.2 (ΔΔH_cal of 14.8 kcal/mol), indicating that there is complete formation of all possible base-triplet stacks and the triplex is fully formed. At pH 5.2 2MeC is biphasic, with the first transition corresponding to the unfolding of the triplex with a T_M of 57.1 °C, identical to the unfolding of the triplex in Control Tri. 2MeC is methylated on the Crick strand and the duplex portion unfolds at 66.7 °C, 9.6 °C higher than the triplex. This is also higher than the formation of the duplex domain of 2MeH (61.6 °C), indicating increased stability of the duplex domain when the Crick strand is methylated instead of the Hoogsteen strand.

4MeHC has four methylated cytosines, two on the Hoogsteen strand and two on the Crick strand. As methylation increased the stability of both 2MeH and 2MeC, it is expected that 4MeHC will have even more stability. This is seen to be true at pH 6.2, where 4MeHC has two transitions, at 35.6 and 57.9 °C. Higher thermal stability translates to increased enthalpy, as 4MeHC has a slightly higher total enthalpy than 2MeC (−111.0 kcal/mol). At this pH, the effects of methylation on the thermodynamics of triplex unfolding are additive, in that the difference between 2MeH/2MeC and Control Tri add together to give the thermodynamic difference between 4MeHC and Control Tri. At pH 5.2 the total enthalpy remains the same and the unfolding of the triplex at 55.3 °C has gained no stability compared to the same transition in Control Tri, but the duplex domain has the highest T_M of all the oligonucleotides in this study, including 2MeC, which is also methylated on the Crick strand, indicating that stability from methylation is additive, consistent with the stability being from hydrophobic interactions of the methyl groups.[95, 96]

In summary, substitution of cytosines with methylated cytosines increases the thermal stability and improves base-triplet stacking, leading to a more favorable folding reaction. The order of thermal and enthalpic stability follow the same trend and are as follows: 4MeCH > 2MeC > 2MeH > Control Tri.

Standard thermodynamic profiles, including entropy and free energy, for the formation of each molecule are summarized in Table 1 and comparison of the methylated triplexes with Control Tri are in Table 2. The ΔG°₍₅₎ and TΔS terms are estimated at 5 °C, where all the molecules are in the helical state. Inspection of Table 1 indicates that the folding of each molecule is accompanied by a favorable free energy term, which results from the characteristic compensation of favorable enthalpy and unfavorable entropy contributions.[97] The favorable enthalpy term is caused by the formation of base-pairs and base-pair stacks, while the unfavorable entropy term is due to the order of the strands, which is minimized for intramolecular complexes, and the immobilization of water, protons and counterions. In the case of the methylated triplexes, the total free energy and entropy of folding follow the same trend as the enthalpy: 4MeCH > 2MeC > 2MeH > Control Tri. This is primarily due to the increased thermal stability, related to the entropy, with slight contributions from the higher enthalpy term, although the overall difference in enthalpy of 4MeHC, which has the highest ΔG°₍₅₎, compared to Control Tri is modest.

A comparison between the thermodynamic profiles of the methylated triplexes with Control Tri allowed us to determine the thermodynamic contribution of a single methylated ATA/CGC⁺ base-triplet stack (Table 3). Methylation on the Hoogsteen strand decreased the enthalpy and entropy but increases the free energy due to the increase in thermal stability. Methylation on the Crick and both Hoogsteen and Crick strands increases all parameters.

Table 3.

Thermodynamic Profiles for the Formation of Methylated Base-Triplet Stacks

Stack	ΔHcal (kcal/mol)	TΔScal (kcal/mol)	ΔG°(5) (kcal/mol)
TAT/CG5MeC+	−22.9	−18.3	−4.6
TAT/5MeCGC+	−23.4	−18.7	−4.7
TAT/5MeCG5Me C+	−23.8	−19.1	−4.8

Values calculated using thermodynamic parameters of base-triplet formation as described in ref [63].

3.5 Methylation increases the uptake of protons

The differential binding of protons was calculated using Equation 1. The dependence of T_M on pH was determined from UV melting curves and are shown in Figure S5. The ΔH_cal/RT_M² term was determined from DSC experiments at several pHs and the Δn_H+ values are shown in Table 4 and displayed in Figure 4. The folding of all triplexes is accompanied by an uptake of protons. Control Tri has the smallest uptake of protons among the studied triplexes, which suggests that methylation enhances protonation of the cytosines, whether it be in the stem or the loops. The increased uptake of protons for the methylated triplexes is attributed to enhanced protonation caused by a shift of the pK_a of the cytosines toward a more neutral pH; how methylation is achieving this is unclear. However, previous studies have shown that methylation alters the pK_a by up to at least one pH unit, allowing for protonation at a more physiological pH.[93, 94] The proton uptake of the control molecules does highlight the fact that triplex formation itself alters the amount of protonation and likely the pK_a of the cytosines, as unless the electronic properties of the cytosines are altered no additional protonation would occur compared to the duplexes. Methylation increases proton uptake although the location of the methylation does not appear to matter, since the uptake of protons for all methylated triplexes is within experimental error of each other. In addition, the proton uptake for the first transition (white bars) and second transition (black bars) are all similar, again indicating that position is unimportant regarding protonation. The large increase in protonation of the methylated triplexes compared to Control Tri is possibly due to a shift in the apparent pK_a of both the Hoogsteen and Crick strand cytosines toward a more basic pH, which would lead to ~100% protonation of the cytosines on both strands, as well as the surrounding cytosines in the loop, leading to an overall more protonated triplex. This may also explain the overall exclusion of counterions by methylated triplexes, specifically in the duplex domain which would normally not be protonated (see below).

Table 4.

Differential Binding of Protons, Counterions and Water for the Unfolding of the Triplexes.

Transition	∂TM/∂pH	ΔnH+ (mol H+/mol)	∂TM/∂ln[Na+]	ΔnNa+ (mol Na+/mol)	∂TM/∂ln(aw)	Δnw (mol H2O/mol)
			Control Tri
	−14.1	−2.9	0.197	−0.10	171.7	−75
			2MeH
1st 2nd	−21.4 −16.3	−2.7 −1.7	−0.884 0.564	0.24 −0.15	185.4	−76
			2MeC
1st 2nd	−19.3 −14.9	−2.5 −1.3	−0.662 0.417	0.20 −0.09	107.9 253.7	−29 −47
			4MeHC
1st 2nd	−19.7 −14.8	−2.3 −1.7	−0.475 0.091	0.13 −0.02	142.8 258.2	−26 −61
			Control Dup
	−4.4	−0.3	1.300	−0.22	95.7	−15
			2MeC-Dup
	−5.2	−0.6	1.414	−0.35	252.2	−23

Experimental errors are as follows: Δn_H+ (± 12%), Δn_Na+ (± 12%), Δn_W (± 12%).

Figure 4.

Uptake of protons for all triplexes in 10 mM sodium cacodylate.

3.6 Methylation leads to an overall exclusion of sodium ions upon formation of the triplex

The differential binding of sodium ions was calculated using Equation 2. The T_M dependence on salt concentration obtained from UV melting curves is shown in Fig S6. The ΔH_cal/RT_M² term was obtained from DSC thermograms at several salt concentrations at pH 5.2. The resultant Δn_Na⁺ values are summarized in Table 4 and Figure 5. Typically, the unfolding of an oligonucleotide is associated with an uptake of counterions; this can be seen for the control molecules at pH 7.0 in Table 3, where both Control Dup and 2MeC-Dup have an associated uptake of counterions during unfolding. At pH 5.2, Control Tri also has an overall uptake of counterions during folding. However, the uptake is very small compared to duplex DNA[87, 98] and triplexes consisting of TAT base-triplets[72, 73] but is consistent with the values from triplexes containing C⁺GC base-triplets.[73, 99] This is attributed to the presence of protonated cytosines, which excludes counterions from the phosphate backbone. For all methylated triplexes at pH 5.2 as the salt concentration increases (Table S1) there are two transitions, the first corresponding to the folding of the triplex and the second the folding of the duplex. 2MeH has only one peak at pH 5.2 in the absence of salt; in the presence of salt the two transitions are stabilized to different amounts, leading to separation of the folding events (Table S1). In all cases the first transition, corresponding to the triplex, has an overall repulsion of counterions; i.e. as the duplex folds into a triplex, counterions are expelled from the structure. This may be explained by the increase in protonation caused by methylation, as a decreased counterion uptake would be caused by repulsion of the positive counterions by the positive charge of the cytosines. The second transition, corresponding to the duplex, has an overall uptake of counterions as expected, although the values are small compared to typical double stranded DNA. This may be due to the relatively close or simultaneous folding of the triplex soon after the duplex at pH 5.2 for all oligonucleotides. Another possibility is that, as mentioned above, methylation shifts the pK_a of both the Hoogsteen cytosines as well as those in the Crick strand and loop regions to a more physiological pH, leading to the greater protonation observed and which would cause greater counterion exclusion. Taken together, at low pH with full triplex formation, methylated triplexes repel, rather than uptake, counterions.

Figure 5.

Uptake of ions for all triplexes in 10 mM sodium cacolydate at pH 5.2.

3.7 Methylation does not affect immobilization of water molecules

The differential binding of water was calculated using Equation 3. The dependence of T_M on pH was determined from UV melting curves and are shown in Figure S7 for the duplexes and in Figure S8 for the triplexes. The ΔH_cal/RT_M² term was determined from DSC experiments at pH 5.2 and the tabulated values are in Table 4 and displayed in Figure 6. The folding of all triplexes is accompanied by an immobilization of water molecules. The grey bars in Figure 6 represent total water immobilization; Control Tri, 2MeH and 2MeC have identical total water immobilization, in contrast to the results from proton and counterion uptake. It can be seen from the Δn_W values of Control Dup and 2MeC-Dup that methylation does increase the amount of water immobilized. However, the values for the control duplexes are much smaller than Control Tri, indicating that DNA triplexes have a much higher amount of water immobilization than DNA duplexes, in contrast to what was observed for counterion uptake. Surprisingly, despite the results for the other methylated triplexes, 4MeHC has increased water immobilization. It can be seen in Figure 6 that the second transition (black bars) of 4MeHC has increased water immobilization compared to the second transition of 2MeC; this transition corresponds to the duplex and thus if methylation of the Crick strand, which is the methylated strand of the duplex, was responsible for the increased water uptake then 2MeC should also have a higher Δn_W value. Since 4MeHC is the only triplex with increased water immobilization, it can be inferred that methylation of both the Crick and Hoogsteen strand act in conjunction to increase the amount of water immobilized. This may be due to a double chain of methyl groups from the cytosines and thymines in the major groove from both the Crick and Hoogsteen strands which increases the amount of hydration around the triplex. Previous research suggested that the increased hydration from this chain can be disrupted by a single base substitution, and so it can only be seen in 4MeHC.[100]

Figure 6.

Uptake of water for all triplexes in 10 mM sodium cacolydate at pH 5.2.

4. Conclusions

We report here a complete thermodynamic description of the unfolding of an intramolecular triplex containing mixed TAT/C⁺GC base-triplets and the differential binding of protons, counterions and water. Substitution of the cytosines on the Hoogsteen strand with methylated cytosines (2MeH) increased the thermal stability of both the triplex and duplex domain. Methylation of the cytosines on the Crick strand (2MeC) and on both the Hoogsteen and Crick strands (4MeHC) increase the stability of the duplex only. Thus, methylation of the cytosines only on the Hoogsteen strand would lead to stabilization of the triple, but methylation on any other strand or a combination of strands leads to stabilization of the duplex only. This indicates that methylation must be precise in order to prevent genetic mutation caused by strand slippage due to instability of triplexes and their repeat sequences. This is in contrast with previous reports of intermolecular triplexes, where methylation of the Hoogsteen strand caused an increase in stability of triplex formation but did not affect duplex formation.[93–95] The stabilization of the duplex by methylation of cytosines may be a feature specific to intramolecular pyrimidine triplexes.

This study also investigates the binding of protons, counterions and water; DNA is highly hydrated, and binding of counterions is necessary to counteract the negative phosphate backbone, which allows folding of DNA into various secondary and tertiary structures. In addition, pyrimidine triplexes require protonation of the cytosines in order to stabilize the triplex structure. Our studies show that methylation increases the uptake of protons, regardless of methylation position. However, this uptake is dependent solely on the presence of methylation, and not on the position or cumulative amount, i.e. the uptake of protons is same regardless of whether the Hoogsteen, Crick, or both strands are methylated. In essence, methylation increases the apparent pK_a of cytosine to a more physiological pH, leading to higher protonation amounts and may be partially responsible for the increased stability of the duplexes, although it is not solely responsible since 4MeHC is the most stable but does not have significantly higher proton uptake. The increased stability is likely attributed to the hydrophobic effect of the methyl groups that was seen in studies of other methylated triplexes.[92, 94, 95] In conjunction with a higher amount of protonation, methylated triplexes release counterions when folding, a result which is in opposition to duplex DNA which uptakes counterions due to the higher charge density. Although triplexes typically have a much lower uptake of counterions than duplex DNA, release of counterions was only seen for triplexes of mixed bases caused by counterion exclusion from the backbone due to protonation, a feature which is enhanced when the cytosines are methylated. Thus, methylation increases the pK_a of cytosines, increasing the protonation of the cytosines in the third strand at low pH which leads to increased repulsion of the counterions. Interestingly, counterions typically stabilize DNA; in the case of methylated triplexes, the release of counterions should destabilize the triplex but this is counteracted by the increased stability caused by protonation and methylation. Finally, methylation does increase water uptake, but only when there the cytosines on both the Hoogsteen and Crick strands are methylated. The reason for this is unclear, but may possibly due to the increase in structural water that forms when there is a continuous line of methyl groups within the major groove formed by the thymines and methylated cytosines.

Highlights.

• Cytosine methylation on the Hoogsteen strand increases the thermodynamic stability of the triplex.

• Methylation on the Crick or both strands increase the thermodynamic stability of the duplex.

• Methylation increases the amount of protonation that occurs upon triplex formation.

• Cytosine methylation causes a release of sodium ions upon folding of the triplex.

• Immobilization of water is not increased upon methylation until a certain threshold is reached.