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Nucleic Acids Res. 2010 November; 38(20): 7332–7342.
Published online 2010 July 8. doi:  10.1093/nar/gkq600
PMCID: PMC2978371

Double-stranded DNA-templated cleavage of oligonucleotides containing a P3′→N5′ linkage triggered by triplex formation: the effects of chemical modifications and remarkable enhancement in reactivity

Abstract

We recently reported double-stranded DNA-templated cleavage of oligonucleotides as a sequence-specific DNA-detecting method. In this method, triplex-forming oligonucleotides (TFOs) modified with 5′-amino-2′,4′-BNA were used as a DNA-detecting probe. This modification introduced a P3′→N5′ linkage (P–N linkage) in the backbone of the TFO, which was quickly cleaved under acidic conditions when it formed a triplex. The prompt fission of the P–N linkage was assumed to be driven by a conformational strain placed on the linkage upon triplex formation. Therefore, chemical modifications around the P–N linkage should change the reactivity by altering the microenvironment. We synthesized 5′-aminomethyl type nucleic acids, and incorporated them into TFOs instead of 5′-amino-2′,4′-BNA to investigate the effect of 5′-elongation. In addition, 2′,4′-BNA/LNA or 2′,5′-linked DNA were introduced at the 3′- and/or 5′-neighboring residues of 5′-amino-2′,4′-BNA to reveal neighboring residual effects. We evaluated the triplex stability and reaction properties of these TFOs, and found out that chemical modifications around the P–N linkage greatly affected their reaction properties. Notably, 2′,5′-linked DNA at the 3′ position flanking 5′-amino-2′,4′-BNA brought significantly higher reactivity, and we succeeded in indicating that a TFO with this modification is promising as a DNA analysis tool.

INTRODUCTION

DNA-templated reactions have been widely used not only in the area of DNA sensing (1–23) but also for synthesis and selection of small molecules (24–27). The reaction on the template would reflect the microenvironment around the reactive site. In fact, especially in the area of DNA sensing via DNA-templated reactions, probes with delicate modifications, which will change the microenvironment around the reactive site, have exhibited dramatic differences in their reactivity, sequence selectivity, and/or turnover numbers (1–6). These observations suggest that it is important to optimize the reactivity of the probes to make these analytical tools practical.

We recently reported on a double-stranded DNA (dsDNA)-templated cleavage of oligonucleotides as a sequence-specific DNA detecting method (28). In this method, triplex-forming oligonucleotides (TFOs) modified with 5′-amino-2′-O,4′-C-methylene bridged nucleic acid (5′-amino-2′,4′-BNA) were used (28). This modification introduced a P–N linkage in the backbone of the TFO, instead of the P–O linkage generally found in phosphodiester moieties of oligonucleotides. Although it is well known that a P–N linkage is cleavable under mild acidic conditions (29), we found out that the cleaving reaction of the P–N linkage was greatly accelerated when the TFO formed a triplex with its target dsDNA in a sequence-specific manner under mild acidic conditions (Scheme 1A) (28,30). We demonstrated that this dsDNA-templated cleavage combined with fluorescence resonance energy transfer (FRET) technology was useful as a DNA detecting method, distinguishing a single nucleotide mismatch (28).

Scheme 1.
(A) Target dsDNA and acids act as catalysts for the cleavage of the P–N linkage. (B) Strategy to change the microenvironment around the P-N linkage.

Because the rate of the reaction is an important factor for sensitivity and quickness of the analysis, we became interested in enhancing the reactivity of the probe. In a previous report, we proposed that the acid-mediated cleavage of the P–N linkage triggered by triplex formation should be driven by a conformational strain on the P–N linkage (28). This interested us in the effects of modifications in changing the microenvironment around the P–N linkage. In the present study, we investigated the relationship between those chemical modifications and the reactivity of the acid-mediated cleavage of TFOs triggered by triplex formation. At first, we synthesized 5′-aminomethyl-type nucleic acids, and incorporated them into TFOs instead of 5′-amino-2′,4′-BNA to investigate the effect of 5′-elongation (Scheme 1B, left). We also synthesized oligonucleotides containing 2′-O,4′-C-methylene bridged nucleic acid (2′,4′-BNA)/locked nucleic acid (LNA) (31–34) or 2′,5′-linked DNA (35,36) as 5′ and/or 3′ neighboring residues of 5′-amino-2′,4′-BNA in TFO to reveal the neighboring residual effects (Scheme 1B, right). Here we revealed the effects of chemical modifications around the P–N linkage on dsDNA-templated cleavage of TFO, and detailed investigation was performed on one of the eminent TFOs to elucidate its potential as an analytical tool.

MATERIALS AND METHODS

General aspects and instrumentations

Natural oligonucleotides, such as the target dsDNAs 5′-d(GCTAAAAAGAMAGAGAGATCG)-3′, 5′-d(CGATCTCTCTNTCTTTTTAGC)-3′, where M and N were A, C, G or T; and TFO0 5′-d(TTTTTCTTTCTCTCT)-3′, where C represents 2′-deoxy-5-methylcytidine, were purchased from Hokkaido System Science Co., Ltd and Gene Design Inc, respectively. The stoichiometry of oligonucleotides was calculated using the following extinction coefficients (l/mol/cm); A, 15000; G, 12500; C, 7500; T, 8500; 5-MeC, 6000.

Syntheses of TFOs

TFO′ and TFO* were prepared according to previous reports (28,29). Syntheses of TFO1–TFO9 were performed at a 0.2 µmol scale on an automated DNA synthesizer (Applied Biosystems, ExpediteTM 8909) using the standard phosphoramidite protocol on CPG supports except for coupling time of certain couplings (90 s in the standard protocol). The coupling time of amidite 9, 15 and 5′-amino-2′,4′-BNA-T (NMe) amidite was extended to 15, 15 and 10 min, respectively. In addition, the coupling time for P–N bond formation in TFO3, TFO5, TFO6 and TFO8 was extended to 5 min. The phosphoramidite derivatives of 2′,4′-BNA-T (34), which is also commercially available as LNA, and 5′-amino-2′,4′-BNA-T (NMe) (28) were prepared according to previous reports. The phosphoramidite derivative monomer of 2′,5′-linked DNA-T (3′-dT CE phosphoramidite) was purchased from Glen Research. Other reagents for oligonucleotide synthesis were purchased from Proligo. As an activator, 1H-tetrazole was used for every coupling step. Syntheses of TFOs were performed on DMTr-OFF mode. Cleavage from the CPG support was accomplished using 28% aqueous ammonia solution at room temperature for 1.5 h, and the solution containing TFO was kept at 55°C for 20 h. The crude TFOs were purified with a gel filtration column (General Electric Company, NAPTM 10 Column) and RP-HPLC (Waters XterraTM MS C18, 2.5 µm 10 × 50 mm) [buffer A, 0.1 M TEAA (pH 7.0); Buffer B, 0.1 M TEAA (pH 7.0) /MeCN = 1:1; linear gradient, B 12–24%/30 min; flow rate, 3.0 ml/min]. The composition of TFOs was confirmed by MALDI–TOF–MS analysis using 3-hydroxypicolinic acid and diammonium hydrogen citrate as the matrix. The isolated yield and MALDI–TOF–MS data for TFO1–TFO9 were summarized in Supplementary Table S1.

UV melting experiments

UV melting experiments were carried out on SHIMADZU UV-1650PC, and SHIMADZU UV-1650B spectrometers. The UV melting profiles were recorded in a solution whose pH was 6.0 or 4.0. The pH 6.0 solution contained 140 mM KCl, 10 mM MgCl2, 1.0 mM sodium phosphate buffer, 10 mM sodium citrate buffer, and was used for TFO′, TFO* and TFO0–TFO9. The pH 4.0 solution contained 140 mM KCl, 10 mM MgCl2, 1.0 mM sodium phosphate buffer, 10 mM sodium citrate–HCl buffer and was used for TFO0. The final pH was actually measured using Twin pH Meter B-212 (Horiba, Ltd). The scan rate was 0.5°C/min with detection at 260 nm. The final concentration of each oligonucleotide was 1.5 µM, which was calculated from the extinction coefficients. The solution containing oligonucleotides was heated and subsequently cooled to 10°C to generate the triplex. The melting temperatures were obtained as maxima of the first derivative of the melting curve.

General methods for hydrolysis experiments

An amount of 2.0 µl of 50 mM sodium phosphate buffer (pH 7.0), 10 µl of 100 mM MgCl2, 14 µl of 1.0 M KCl, 13.4 µl of 25 µM TFO with or without 13.4 µl of 25 µM target dsDNA were mixed, and deionized water was added to adjust the volume to 90 µl. This solution was maintained at 40°C, after being heated and subsequently cooled to generate a triplex. Then, 10 µl of 100 mM sodium citrate-based buffer was added for acidification, and the final composition of the solution was 140 mM KCl, 1.0 mM sodium phosphate buffer, 10 mM sodium citrate-based buffer, 10 mM MgCl2 and 3.35 µM each strand. The final pH was actually measured using Twin pH Meter B-212 (Horiba, Ltd). After the incubation for the indicated amount of time at 40°C, 10 µl of the reaction mixture was removed, added to 160 µl of 0.10 M triethylammonium acetate buffer (pH 9.0) to stop the reaction, and analyzed by HPLC system (Shimadzu Prominence) to determine the proportion of intact TFO. Replacement of KCl with NaCl or exclusion of MgCl2 from reaction mixture did not have significant effects on the reactivity (data not shown). The HPLC system used for the analysis of the reaction is described in the Supplementary Data.

Kinetics of acid-mediated cleavage of TFOs triggered by triplex formation

The reaction was performed as is described in the general method for hydrolysis experiments. An amount of 10 µl of 100 mM sodium citrate–HCl buffer (pH 4.0) was used to adjust the pH to 4.0. The reaction mixture was incubated for 0, 5, 10, 20 and 60 min (TFO1–TFO9), or 0, 30, 60, 120 and 240 min (TFO′).

Effects of pH on reactivity

The reaction was performed as described in the general method for hydrolysis experiments. The reactivity at different pH was evaluated for TFO4 and TFO8 with the full match target dsDNA. 10 µl of 100 mM sodium citrate–HCl buffers (pH 4.5 and 5.0) were used to adjust the pH to 4.3 and 4.5, and 10 µl of 100 mM sodium citrate buffer (pH 5.5) was used to adjust the pH to 4.9. The reaction mixture was incubated for 0, 5, 10, 20 and 60 min.

Sequence selectivity

The reaction was performed as described in the general method for hydrolysis experiments. The sequence selectivity of TFO8 was evaluated in the presence of full match, misT, misC and misG target dsDNAs (Figure 1) or in the absence of the target dsDNA, and 10 µl of 100 mM sodium citrate–HCl buffer (pH 3.0) was used to adjust the pH to 3.3. The reaction mixture was incubated for 2 min.

Figure 1.
Sequence of the target dsDNA used in the present study. Bar indicates a site where each TFO could bind. MN: AT (full match), TA (misT), CG (misC), GC (misG).

Molecular modeling

As the initial structure, the triplex containing dsDNA (5′-AAAAAGAAAGAGAGA-3′/3′-TTTTTCTTTCTCTCT-5′) and TFO0 was generated with default parameters of Discovery Studio 2.5TM (Accelrys Software, Inc.). Then, the structure of TFO* was constructed by the replacement of the P–O linkage in the middle of the sequence of TFO0 with the P–N linkage, and insertion of O2′ atom and methylene bridge over O2′ and C4′ atom. The obtained triplex structure was exported to MacroModel 9.1TM (Schrödinger, LLC), and it was modified to each triplex structure (TFO7, TFO8 and TFO9). On each structure (TFO*, TFO7, TFO8 and TFO9) was performed energy minimization using AMBER* as a force field and GB/SA solvation model of water as implemented in MacroModel 9.1TM. The minimization was performed using PRCG method to obtain structures optimized to within a gradient of 0.05 kJ/mol Å.

RESULTS

Synthesis of 5′-aminomethyl-2′,4′-BNA (NMe)

As shown in Scheme 2, the synthesis of an amidite 9 was performed starting from 1 (37). Utilizing the Dess-Martin reagent, 1 was oxidized to give an aldehyde 2, which was treated with methyltriphenylphosphonium bromide to give a 4′-vinyl nucleoside 3. Hydroboration followed by oxidation gave an 5′-elongated nucleoside 4. After mesylation of the hydroxy group of 4, the 3′-benzyl group was removed by Pd(OH)2-catalized hydrogenolysis to give 6. The mesylate group of 6 was substituted to a methylamino group by treating with methylamine in a sealed tube to give an 5′-aminomethyl nucleoside analogue 7. The 4-methoxytritylation of 7 treated with 4-methoxytrityl chloride (MMTrCl) followed by phosphitylation gave an amidite 9. The procedure for the synthesis is described in the Supplementary Data.

Scheme 2.
Reagents and conditions: (a) Dess-Martin reagent, CH2Cl2, rt, 1 h; (b) Ph3PBrCH3, n-BuLi, THF, rt, 1 h, 57% over two steps; (c) BH3, THF, NaOH, H2O2, rt, 40 min, 50%; (d) MsCl, pyridine, rt, 1 h, 87%; (e) Pd(OH)2-C, cyclohexene, ...

Synthesis of 5′-aminomethyl-DNA (NMe)

The synthesis of an amidite 15 was performed from 10 (38) in a similar manner to that of an amidite 9 as shown in Scheme 3. Mesylation of the hydroxy group of 10 followed by substitution to a methylamino group gave 12. 4-Methoxytritylation, removal of the TBDMS group followed by phosphitylation afforded an amidite 15. The procedure for the synthesis is described in the Supplementary Data.

Scheme 3.
Reagents and conditions: (a) MsCl, pyridine, rt, 1 h, 85%; (b) liquid MeNH2 in a sealed tube, rt, 48 h; (c) MMTrCl, Et3N, pyridine, rt, 2 h, 93% over two steps; (d) TBAF, THF, rt, 1.5 h, 72%; (e) (i-Pr2)N2POCH2CH2CN, diisopropylammonium ...

Syntheses of TFOs

TFO1–TFO9 were synthesized by conventional phosphoramidite chemistry on an automated DNA synthesizer as described in the Materials and methods section. The TFOs were purified by reversed-phase HPLC (RP-HPLC) and characterized by MALDI–TOF–MS. Cleavage of TFO1 took place under measurement of MALDI–TOF–MS, and only fragment signals were observed instead of intact ones. Therefore, the composition of TFO1 was confirmed by its fragments signal. The sequences of each TFO are given in Table 1.

Table 1.
Sequences, Tm values and hydrolysis rate constants of each TFO

Thermal stability of TFOs in triplexes

Initially, we investigated the triplex-forming ability of TFO′, TFO* and TFO0–TFO9 by means of UV melting experiments, and the Tm values of triplexes containing the full match target dsDNA (Figure 1) and each TFO are summarized in Table 1. Although we wished to evaluate the triplex stability of each TFO under the conditions used in the hydrolysis experiments, it was not possible due to the cleavage of the P–N linkage. Therefore, we performed the melting experiments at less acidic pH (pH 6.0). At the same time the Tm value of TFO0, which contains no P–N linkage, was examined under acidic conditions (pH 4.0). Since triplex formation requires the protonation on the cytidines in TFO, the Tm of a triplex is known to increase in proportion to the decrease of pH (39,40). Hence, we supposed that it would be able to estimate the triplex-forming ability of the other TFOs containing the P–N linkage under acidic conditions, comparing the Tm values of TFO0 at pH 4.0 and 6.0. At pH 6.0, triplexes melted directly to single-stranded state, except for TFO2, TFO7, and TFO9 (Supplementary Figure S1). Tm of the target dsDNA was also measured, and found to be 61°C. The Tm values of TFO′, and TFO* were 57 and 61°C while those of TFO1–TFO9 were 61, 52, 65, 63, 75, 66, 53, 61 and 52°C, respectively (Table 1). As is well known (39–41), acidic conditions greatly stabilized triplex containing TFO0 (Tm; 59°C at pH 6.0 to 71°C at pH 4.0). While the thermal stability of the triplex containing TFO1 was as the same with that of TFO*, the removal of the 2′,4′-bridge led to lower triplex stability (TFO2). As previously reported (34), 2′,4′-BNA/LNA modifications (TFO3–TFO6) stabilized the triplex. TFOs modified with 2′,5′-linked DNA exhibited a less or equivalent triplex-forming ability depending on the modification positions (TFO7, TFO8 and TFO9) compared to TFO*. Considering the triplex-forming ability of TFO0 under acidic conditions, we estimated that almost all the fraction of TFO′, TFO* and TFO1–TFO9 formed triplexes at pH 4.0, 40°C.

Evaluation of reactivity of TFOs

To reveal the effects of the chemical modifications on dsDNA-templated cleavage of TFOs, the reactivity of TFO′ and TFO1–TFO9 was investigated at pH 4.0, 40°C. Each TFO was annealed with the target dsDNA to form a triplex, which was followed by acidification to start the reaction, and the remaining amount of intact TFO was analyzed by HPLC (Supplementary Figure S2). A time-course of the cleavage of each TFO is shown in Figure 2 and Supplementary Figure S3, and the pseudo-first order rate constants of the cleaving reaction in the presence (ktriplex) or the absence (kalone) of the target dsDNA are summarized in Table 1.

Figure 2.
Time-course of the cleavage of TFO1, TFO2 and TFO*. TFO1 (filled circles), TFO2 (filled triangles) and TFO* (open squares) with the target dsDNA, respectively, and TFO* (filled squares) without the target dsDNA. Error bars indicate standard deviation ...

As shown in Figure 2 and Table 1, TFO1 exhibited almost the same reactivity with TFO*, and TFO2 exhibited higher reactivity than TFO* in the presence of the target dsDNA. On the other hand, in the absence of the target dsDNA, 5′-aminomethyl-modified TFO1 and TFO2 both exhibited higher reactivity than any other TFOs studied here.

Table 1 shows that the 2′,4′-BNA/LNA modification (Y) at the 5′-neighboring residue of 5′-amino-2′,4′-BNA (X1) (TFO3 and TFO5) significantly reduced the reactivity, while the modification at the 3′ neighboring residue (TFO4) enhanced the reactivity in the presence of the target dsDNA compared to that of TFO*. The TFO containing two 2′,4′-BNA/LNA residues separately (TFO6) showed as high reactivity as TFO4 in the presence of the target dsDNA.

Although the reactivity of the TFOs modified with 2′,4′-BNA/LNA varied by their modification patterns in the presence of the target dsDNA, the reactivity in the single-stranded state was not affected by these modifications.

2′,5′-Linked DNA-modified TFOs showed somewhat similar tendency to 2′,4′-BNA/LNA-modified TFOs (Table 1). In the presence of the target dsDNA, the modification with 2′,5′-linked DNA (L) at the 5′-neighboring residue (TFO7 and TFO9) significantly reduced the reactivity, while the 2′,5′-linked DNA modification at the 3′ neighboring residue of 5′-amino-2′,4′-BNA (TFO8) brought the highest reactivity.

In the absence of the target dsDNA, the reactivity of TFO7 and TFO9 was higher than that of TFO*, and their reaction rates overtook those in the presence of the target dsDNA. On the other hand, the reactivity of TFO8 was quite low in the absence of the target dsDNA.

The relative pseudo-first order rate constants (ktriplex/kalone) could be an important factor of sensitivity. Therefore, the ratios were calculated for each TFO, and these values are given in Table 1. Notably, the ratio of TFO8 was the highest to be 96 ± 9 (that of TFO′ and TFO* was 5.0 ± 1.1 and 29 ± 5, respectively), which indicated that the sensitivity of TFO8 would be ~20 times and three times higher than that of TFO′ and TFO*.

Effect of pH on the reactivity

The kinetics at different pH was evaluated to elucidate the detail reaction properties of TFO8 (5′-TX1L-3′) in the triplex form. We performed the reaction at pH 4.3, 4.5 and 4.9 in addition to pH 4.0. As a comparison, TFO4 (5′-TX1Y-3′) was also evaluated under the same conditions. This TFO4 was chosen because it was modified as the same way with TFO8 (modified at 3′-neighboring residue of 5′-amino-2′,4′-BNA), and the reaction rates of TFO8 and TFO4 were suitable to be monitored under the same reaction time range. Pseudo-first order rate constants (kobs) obtained from the experiments at different pH were plotted against proton concentration ([H+]) to reveal their mode of the pH dependency (Figure 3). The cleavage of the P–N linkage was slowed down as the [H+] decreased, and the plots of the kobs against [H+] exhibited a good inverse relationship within pH 4.0–4.9 for both TFO8 and TFO4.

Figure 3.
Pseudo-first order rate constants (kobs) of TFO8 (open circles) and TFO4 (open triangles) in the triplex form plotted against proton concentration ([H+]) at 40°C. Error bars indicate standard deviation (n = 3). Conditions: 140 mM ...

Sequence selectivity

As we found out that TFO8 had a great potential as a DNA-detecting probe, its sequence selectivity was evaluated. TFO8 was treated with the full match target dsDNA or target dsDNAs containing different base pairs in the middle of the sequence (misT, misC and misG, Figure 1) at pH 3.3 to compare with TFO*, whose sequence selectivity was evaluated at the previously reported conditions (28). While TFO* exhibited high sequence selectivity after 10 min of incubation under the conditions (28), TFO8 showed even higher contrast within only 2 min (Figure 4). To gather information on the origin of the sequence selectivity, the thermal stability of the mismatch triplexes containing TFO8 was evaluated by means of the UV melting experiments (Supplementary Figure S1E). The triplex stability of the mismatch triplexes was revealed to be quite low compared to that of the full match triplex (Tm: full match, 61°C; misT, 23°C; misC, 35°C; misG, 27°C, Supplementary Figure S1E).

Figure 4.
Percent of intact TFO8 in the presence of the full match or mismatch target dsDNA, misT, misC, and misG, or the absence of the target dsDNA (alone). Error bars indicate standard deviation (n = 3–4). Conditions: 140 mM KCl, ...

DISCUSSION

Effects of 5′-elongation flanking the P–N linkage

In the presence of the target dsDNA, TFO1 containing 5′-aminomethyl-2′,4′-BNA (X2) exhibited comparable reactivity to TFO*, while unbridged TFO2 containing 5′-aminomethyl-DNA (X3) exhibited higher reactivity than TFO*. This relationship was different from the relationship between 5′-amino-2′,4′-BNA (NH)-modified TFO and 5′-amino-DNA (NH)-modified TFO, where 2′,4′-BNA modification brought somewhat higher reactivity (28). We suppose that the combination of restriction of the sugar conformation to the N-type and the insertion of a methylene group was incompatible for the cleaving reaction triggered by triplex formation.

In the absence of the target dsDNA, TFO1 and TFO2 both exhibited higher reactivity than any other TFOs. This result is explainable considering the less steric crowding around their P-N linkages. Thus, the protonation on the phosphoramidate and subsequent nucleophilic attack of water might be easier, leading to higher reactivity in their single-stranded states.

Effects of introduction of 2′,4′-BNA/LNA to neighboring residues

Although the sugar conformation in the third strand of a triplex is still ambiguous, there are reports pointing out that the sugar conformation is altered depending on the positions and/or patterns of 2′,4′-BNA/LNA modifications (42,43). Similarly, 2′,4′-BNA/LNA modifications would affect differently on the strain of the neighboring P-N linkage depending on their modification positions. As a result, the 2′,4′-BNA/LNA (Y) modification at the 3′-neighboring residue of 5′-amino-2′,4′-BNA (X1) (TFO4) is assumed to have increased the strain on the P–N linkage appropriately while the modification at the 5′-neighboring residue (TFO3 and TFO5) almost completely relaxed the strain. As the separation of the 2′,4′-BNA/LNA from the 5′-amino-2′,4′-BNA residue (TFO6) led to high reactivity in the presence of the target dsDNA, the introduction of 2′,4′-BNA/LNA at the 5′-neighbor of the 5′-amino-2′,4′-BNA seems to be critically unfavorable for the cleavage of the P–N linkage.

Effects of introduction of 2′,5′-linked DNA to neighboring residues

Since 2′,5′-linked DNA has a different phosphodiester topology, the introduction of 2′,5′-linked DNA in the neighborhood of the P–N linkage may affect the microenvironment around the linkage. In fact, significantly higher reactivity than TFO* was observed for TFO8 in the presence of the target dsDNA, while the cleavage of the P–N linkage brought by the target dsDNA was completely extinguished in the case of TFO7 and TFO9.

Molecular modeling of the triplex structures containing each TFO (TFO*, TFO7, TFO8 and TFO9) brought us important suggestions to understand the results. First, the phosphorus atom of the P–N linkage in TFO7 and TFO9 was linked to the O2′, drawing the P–N linkage into the inner side of the triplex, and the backside of the P–N linkage was well shielded, which would make it difficult for water molecules to access the phosphorus atom (Figure 5). On the other hand, the P–N linkages of TFO* and TFO8 (Figure 5 and Supplementary Figure S4A) were located outside the triplex, and the access of water molecules seemed easier. Second, the modeling also suggested that the γ dihedral angle (N5′-C5′-C4′-C3′) of the 5′-amino-2′,4′-BNA residue in TFO7, and TFO9 adopted a +ac orientation (Figure 5 and Supplementary Figure S4B), while that for TFO* and TFO8 was estimated to adopt a +sc orientation. According to the report made by Letsinger et al., 1H-NMR study on the solution structure of the single-stranded thymidil 5′-amino-DNA dimer (5′-TX-3′) revealed that the +sc population is low (44). As the single-stranded structure is assumed to reflect the less strained structure, the +sc orientation may be thermodynamically less favorable. Considering the results of the modeling studies that the γ dihedral angle of the highly reactive TFOs was estimated to adopt a +sc orientation in triplex state, the dihedral angle seems to be strongly related to the strain on the P–N linkage by affecting, for example, the π conjugation between the P–N linkage.

Figure 5.
Triplex structure of TFO* (A) and TFO7 (B). The third strands are rendered as stick models colored by elements, and their target dsDNAs are rendered as gray colored CPK model. In TFO*, the γ dihedral angle (N5′-C5′-C4′-C3′) ...

Effect of pH on the reactivity

Hydrolysis experiments were performed at different pH to gather more information on the accelerated cleavage of TFO8. Although linearity might have observed in kobs

equation image
(1)

equation image
(2)

versus [H+] as other group reported on the hydrolysis of N3′→P5′ phosphoramidate dinucleotide (45), inverse relationships were observed when the triplex was formed under our conditions (Figure 3). At pH 4.0–4.9, there is assumed to be the equilibrium between the electrically neutral phosphoramidate (TFOneu) and electrically negative one (TFOani), and the reactant of the P–N cleavage reaction would be only the TFOneu as shown in Scheme 4 (45). Accordingly, the reaction rate (v) would be expressed as Equations 1 and 2, where c, [TFOneu], and k1′ represent the concentration of total TFO, that of TFO with the neutral phosphoramidate (Scheme 4) and first

equation image
(3)

equation image
(4)

equation image
(5)

equation image
(6)

equation image
(7)

order rate constant in triplex form at 40°C, respectively. From the Tm analysis, the total concentration of TFO8 and TFO4 was assumed to be approximately equal to the concentration of each TFO in triplex form at pH 4.0–4.9. When Ka is defined as the acid dissociation constant of the corresponding TFOneu in triplex form at 40°C (Scheme 4), the inverse proportion of kobs to [H+] led to an estimation of the pKa, which were calculated from the curve fitting [Figure 3 and Equations 3–5]. The obtained equations containing the parameters for TFO8 and TFO4 are provided in Equations 6 and 7, respectively. The estimated pKas were 4.4 (for TFO8) and 3.8 (for TFO4), and these values were significantly higher than those of simple phosphoramidate N,O-diesters (pKa [congruent with] 2–3) (45–47). The accelerated hydrolysis may be explained by the higher estimated pKa, which increases the proportion of TFOneu to TFOani. The phosphorus atom and nitrogen atom in the P–N linkage are able to form an additional π bond (46), and the highly reactive TFOs would have a strained P–N linkage whose conjugation is restricted, resulting in higher basicity of the phosphoramidate. The consideration made by the modeling studies, which indicated the importance of the γ dihedral angle on the reactivity, seems to be reasonable because the dihedral angle would have a significant impact on the P–N conjugation.

Scheme 4.
Equilibrium of phosphoramidates related to the cleavage of the P–N linkage under mild acidic conditions.

Potential of TFO8 as analytical tool

To elucidate the detail properties of TFO8 as an analytical tool, its sequence selectivity was evaluated. Comparison with a previous report (28) obviously declared that TFO8 had much higher potential as an analytical tool because TFO8 was cleaved to the same level with TFO* within 5 times shorter reaction time, even with lower background noise (in the presence of the mismatch target or the absence of the target dsDNA, Figure 4). The UV melting experiments supported the results of the hydrolysis experiments by indicating that the mismatch triplexes were significantly unstable (Supplementary Figure S1E). Although the kinetic study was not performed at pH 3.3 conditions, the half-life of TFO8 in the presence of the full match target dsDNA could be estimated from Figure 4. As the intact TFO8 was ~20% after 2 min of incubation, the half-life was estimated to be <1 min. The estimated half-life was obviously shorter than that expected from Equation 6 (~4 min). This result may be explained by the emerging of the cationic phosphoramidate as a rather reactive substrate than the neutral phosphoramidate under the conditions (Scheme 5). This form of phosphoramidate was not included in the prerequisite of the Equation 6, and this may be the reason why the reactivity at pH 3.3 was assumed to be much higher than expected.

Scheme 5.
Equilibrium between the neutral form and the cationic form of phosphoramidates.

General overview

We successfully demonstrated that the acid-mediated cleavage of the P–N linkage triggered by triplex formation reflects the microenvironment around the P–N linkage. From the present study, we found that the introduction of 2′,5′-linked DNA to the 3′-neighboring residue of 5′-amino-2′,4′-BNA gave the highest reactivity with high sequence selectivity, and we can conclude that a probe with the modification is promising as a dsDNA-detecting tool.

Through this investigation, we succeeded in supporting our concept on the hydrolysis acceleration triggered by triplex formation. The pKa of phosphoramidates seemed to have a positive correlation with the cleavage rate, which would be reflecting the change in the microenvironment around the P–N linkage. This observation indicates the direction of rational design of further chemical modifications bringing higher reactivity with lower background noise.

We and other groups have made efforts to expand the target sequences in triplex-based technologies through the designs and syntheses of TFOs containing unnatural nucleobases that recognize pyrimidine interruption in a homopurine strand (48–54). Therefore, this triplex-based DNA analysis tool would also be applicable to the analysis of pyrimidine-containing strand in near future. We are now optimizing this analytical tool for key biomedical applications, such as detecting single nucleotide polymorphisms.

SUPPLEMENTARY DATA

Supplementary Data are available at NAR Online.

FUNDING

Precursory Research for Embryonic Science and Technology (PRESTO to S.O.); Japan Science and Technology Agency, Creation and Support Program for Start-ups from Universities (to T.I. and S.O.); Japan Society for the Promotion of Science, KAKENHI; Ministry of Education, Culture Sports, Science and Technology, Japan. Funding for open access charge: Japan Society of Promotion of Science.

Conflict of interest statement. None declared.

Supplementary Material

Supplementary Data:

REFERENCES

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