An increasingly comprehension of the folding intermediate states of DNA G-quadruplexes (G4s) is currently an important scientific challenge, especially for the human telomeric (h-tel) G4s-forming sequences, characterized by a highly polymorphic nature. Despite the G-triplex conformation was proposed as one of the possible folding intermediates for the antiparallel and hybrid h-tel G4s, for the parallel h-tel topology with an all-anti guanine orientation, a vertical strand-slippage involving the G-triplets was proposed in previous works through microseconds-long standard molecular dynamics simulations (MDs). Here, in order to get further insights into the vertical strand-slippage and the folding intermediate states of the parallel h-tel G4s, we have carried out a Well-Tempered Metadynamics simulation (WT-MetaD), which allowed us to retrieve an ensemble of six G4s having two/G-tetrad conformations derived by the G-triplets vertical slippage. The insights highlighted in this work are aimed at rationalizing the mechanistic characterisation of the parallel h-tel G4 folding process.
G-quadruplexes1,2 (G4s) are non canonical DNA structures present at the telomere ends and involved in the genome stability and in the inhibition of the telomerase enzyme, a reverse transcriptase responsible for the cellular immortalization3,4 and up-regulated in ~85% of human tumors3. The evidence that G4s formation at the 3′-end of telomere DNA can effectively hamper telomerase from adding further repeats3 suggests G4s as a promising target for anticancer therapy5,6,7. In order to identify new compounds as potential anticancer drugs, the structure-based drug design targeting G4s could be a crucial step in gaining accurate information about the structural features of G4s8,9,10,11,12,13. Unfortunately, the rational design of novel G4 binders is hampered both by the structural polymorphism of these non-canonical conformations and by the lack of a well-defined ligand binding site. Therefore, enhanced sampling methods, like Metadynamics, have been required in order to deeply define the ligand binding mode14,15. Monomolecular G4s of the human telomeric sequence d[AG3(TTAGGG)3] (h-tel) can adopt different folding topologies according to the relative orientations of the four strands16. In fact, while the arrangement of the h-tel monomolecular G4s has been well characterized by NMR in Na+ to adopt a basket-type conformation with the single strands assuming an antiparallel orientation17, in presence of K+ ions the folding topology of the h-tel monomolecular G4s includes both parallel-stranded and hybrid (mixed parallel/antiparallel) conformations, raising the question of which conformation is biologically more favoured. In 2006, the NMR hybrid syn/anti conformation was proposed as the most favoured one under K+ physiological conditions18, whose folding organization is different from that reported in K+ ions by crystallography consisting, instead, in the parallel-stranded topology with three G-tetrads and three symmetrical external d(TTA) loops in a propeller-like arrangement19, considered not predominant in solution20. Later, in 2007 Xue et al. reported that the same parallel-stranded conformation found by X-ray is adopted also in K+ solution under molecular crowding conditions21. Given the molecular crowding nature of the intracellular environment22, these observations led to the hypothesis that the propeller-type parallel-stranded conformation might be more biologically favoured under such conditions. These evidences were confirmed in 2011 with the first NMR h-tel G4s in K+ containing crowded solutions, partially keeping a structural similarity with the crystallographic conformation23. Computational and experimental studies about the kinetics and folding pathways have suggested the formation of a G-triplex structure with three G-triad planes, as plausible intermediate state in the G4 folding pathway of the antiparallel24,25 and both hybrid-1 and hybrid-2 topologies26,27,28,29. Fewer efforts have been dedicated, instead, to define the intermediate states of the propeller-type parallel topology of the native human telomere sequence for which the G-triplex intermediate has been not experimentally identified yet. The most recent example for the parallel propeller-type folding was probed through microsecond-scale molecular dynamics simulations (MDs) performed on a truncated sequence (d[A(G3T2A)2G3]) of the parallel propeller-like G4. On the basis of such simulation data, it was suggested that G-triplexes with all-anti guanines conformation are quite unstable and therefore unlikely to contribute to the folding of the human telomere G4, but rather to its unfolding. For the all-anti guanine monomolecular (and tetramolecular) G4s (Fig. 1A), the most natural arrangement is the vertical strand-slippage movement involving the G-triplets (Fig. 1B,C), that leads to a reduced number of G-tetrad planes (two G-tetrads and one G-triad), as demonstrated by standard MDs. By contrast, the same arrangement is prevented by the steric conflict between the alternation of syn- and anti- nucleotides in the hybrid and antiparallel topologies30,31.
All the above reported examples suggest the existence of other possible intermediate substrates perhaps with specific cellular functions. However, despite the large amount of all-atom computer simulations performed so far, a detailed atomistic picture of the folding process of the parallel monomolecular G4s is still unclear due to the time scale limitations of unrestrained standard simulations. To this aim, the use of enhanced sampling methods is mandatory.
In the light of the previous findings30,31, we have investigated the folding process of the native 22-nt monomolecular DNA G4 d[AGGG(TTAGGG)3] (PDB ID: 1KF1)19, considered as the most probable at cellular level21,32, through Well-Tempered Metadynamics simulations (WT-MetaD) in explicit solvent and K+ ions. In this way, the time-scale limitation problem is overcome and the so-called “rare events” are accelerated33. The aim of our work was to obtain a clear scenery of the possible vertical slippage combinations and the identification of the most relevant ensemble structures deriving from each arrangement. It is worth to underline that, in K+ solutions, NMR data indicate d[AGGG(TTAGGG)3] sequence as an equilibrium mixture of more than one conformer34, making its experimental determination impossible under usual conditions. Nevertheless, an experimental structure of a G-rich sequence, having one G-triad and two G-tetrad planes and derived by the G-triplet slippage, has been recently retrieved by NMR (PDB ID: 2N60)35. Based on these observations, here we analysed the folding process of the G4 parallel topology, by including further insights of the vertical slippage mechanism and of the formation of all the possible ensemble conformations. The results presented in this work could help to integrate the current knowledge on the G4 folding processes, which are essential to stabilize the nucleic structures and to understand their formation in the genome.
The free energy surface (FES) of the parallel DNA G4
The crystal structure of the h-tel (PDB ID: 1KF1)19 was considered for this study. Two different CVs were biased: the first CV (π-πcore), introduced by Giberti et al. to study the nucleation of urea crystals36, here was employed to describe the π-π stacking among the guanine residues of the G-tetrads (for details, see Supplementary Information, including Figure S1); the second was a coordination CV (Hbcore 1KF1), suitable to count the total number of the native Hoogsteen hydrogen-bonds network holding the three G-tetrad planes (for details, see the Supplementary Information, including Tables S1 and S2). The vertical slippage of the G-triplets was observed during 140 ns of WT-MetaD simulation. The recrossing events occurring with the selected biased CVs (Supplementary Information, Figure S2A,B), indicate those CVs as good descriptors of the reaction, since they were able to distinguish the three different energetic states corresponding to the three different minima A, B and C resulting from the Free Energy Surface (FES) (Supplementary Information, Figure S3). Unfortunately, the different conformations found in the two minima B and C were not completely distinguishable in the CVs space, since a partial overlap of the populations was observed as shown in the plots of Figure S3i and Figure S3h, respectively. Since this could lead not only to the lack of the convergence, but also to an inaccuracy in the calculation of the Free Energy value of each slipped structure, we reweighted the FES as function of two unbiased CVs (discussed in the Methods section). This was done by means of the reweighting algorithm that allows calculating the unbiased probabilities from the biased probabilities along the CV and finally reconstructing the FES from the unbiased probabilities37. Looking at the reweighted FES reported in Fig. 2, three main energetic minima were identified. The basin A is the energetically deepest one and it corresponds to parallel G4 motifs with a folding arrangement very similar to that of the 1KF1Cry. The second minimum, basin B, is populated by transition-state structures (TS-structures) with a slightly more unstable barely stacked conformations of G4s characterized by a partial distancing of the guanine residues of the G-tetrad planes. Finally, the most interesting basin C retrieves an ensemble of two G-tetrad planes structures arising from the vertical slippage movement of different G-triplets. Specifically, on the basis of which G-triplet is involved in the vertical slippage and the movement direction, globally six ensembles were identified. A detailed description of basins A and B is addressed in the Supplementary Information (Figures S4–S6 and Table S3), while results retrieved from basin C are reported in the following paragraphs. The convergence of the WT-MetaD simulation is shown in Figure S7 and S8 of the Supplementary Information.
The slipped G4s structures are observed in basin C
At variance with basins A and B, basin C was the energetically highest. It depicted an ensemble of six G4 arrangements with only two G-tetrad planes coming from the vertical slippage movement of different guanine triplets (G-triplets) (Table 1). For clarity reasons, we structurally differentiated each vertical slippage arrangement with an alphanumeric code. Specifically, numbers correspond to the G-triplets involved in the vertical movement, following the 5′-to-3′ direction, while letters explain the direction of the vertical slippage: “u” (up) and “d” (down), when the G-triplet slips towards the 5′-end and the 3′-end positions, respectively (Table 1). Moreover, as reported in Table S2, such structures were also extracted from the basin C through a plumed tool relying on the number of the native Hbcore engaged within the two G-tetrad planes. Their 3D schematic representation is shown in Fig. 2, while their percentage of existence relative to basin C was reported as histograms in the Supplementary Information (Figure S9).
As it can be observed from Fig. 2, most of these structures were characterized by the slippage of a single strand of guanines, in which the G-triplets (in the 2d, 3d and 4d ensembles) moved towards the 3′-end position, thus leading to the disruption of the expected Hoogsteen hydrogen bonds network (Hbcore), as typically found in the G-tetrad of 1KF1cry (Movie S1). This event led to the formation of a G-triad at the 5′-end (Fig. 2a,b,d) with a vacant site of the slipped guanine highly accessible to the water solvent. It is worth to mention that a similar G-triad conformation was previously retrieved with NMR by Heddi and co-workers35. Subsequently, Stefl et al. described the same structure for the tetramolecular d(TGGGGT)4 G4, in which the G-triad arrange in an “open” and “closed” form38. In our study, we also disclosed the formation of both the G-triad forms in the parallel monomolecular h-tel G4 (see Supplementary Information Figure S10A,B). In particular, the “open” G-triad was detected in the 3d, 3u and 4d conformations and it was characterized by the conservation of the Hoogsteen-like hydrogen bond network with a vacant site suitable for small-molecules recognition and a coordinating K+ ion contributing to its stability (for details, see Fig. S10A). Contrarily, the “closed” G-triad occurred only in the 2d structure that was obtained after the transition from 1KF1-like to 2d through the intermediate 24d. It was characterized by a specific rearrangement of the Hoogsteen-like hydrogen bonds without any coordinating K+ ion.
Most of the G-triads observed in our simulation occurred at the 5′-end, while only one G-triad (3u) was observed at the 3′-end (Fig. 2c), with the G-triplet slipping towards the 5′-end direction (up). In addition, only two conformations (24d and 34d) exhibited the simultaneous slippage of two G-triplets leaving just two guanine residues at the 5′-end or the 3′-end (Fig. 2e,f, respectively), thus preventing the G-triad formation.
The free energy associated to the vertical slippage of the G-triplets in basin C was calculated using the reweighting algorithm. In such case, the Hbcore was used as unbiased CV, which is related to the number of their corresponding Hoogsteen hydrogen bonds, such as Hbcore2d, Hbcore3d, Hbcore3u, Hbcore24d and Hbcore34d (for details, see Table S2 and Table 2).
The reweighted algorithm led us to better characterize each conformation on the basis of their different free energy value. Specifically, structures 2d, 3d, 4d and 34d showed the better free energy profile (Table 2), while, among the conformations with one single G-triplet slippage, 3u, the only characterized by the slippage movement towards the 5′-end direction, owns the highest energetic value and results as the less probable structure. This behaviour could be probably due to the steric hindrance between A1 and G14 residues (Supplementary Information, Figure S15).
In order to verify their geometrical stability, each slipped conformation was submitted to MDs. Interestingly, looking at the progression of the Root Mean Square deviation (RMSd) (Supplementary Information, Figure S11A–F) after 200 ns of MDs, different dynamic behaviours were observed, with only 3d and 4d being the most geometrically stable (all details of 24d, 3d, 3u, 2d and 34d MDs are described in the Supplementary Information Figure S12–S19). This finding is in agreement with the free energy calculation (Table 2), which retrieved 3d and 4d as the most energetically favoured. Given the lowest free energy value of 4d, we investigated more in details its dynamic behaviour by extending its MDs to 1 µs.
4d as the most probable two G-tetrads structure with a well-defined G-triad
1 µs long MDs of 4d globally revealed a good geometrical stability of its G-tetrads (Supplementary Information, Figure S20A). An increase of the RMSd trend, calculated on all the DNA nucleobases, was observed only in the first 200 ns and was caused by the fluctuations of the first and the third loops, as shown in the Root Mean Square Fluctuation (RMSF) plot (Supplementary Information, Figure S20B). Interestingly, the highest fluctuation was observed for the first adenine nucleobase (A1) at 5′, which changed its orientation from anti to syn (for details, see Supplementary Information Movie SM2). This conformational change allowed the stacking of A1 over G20, thus hampering the rearrangement to the native crystallographic structure and stabilizing the two G-tetrad planes. Furthermore, the positioning of A1 on the same plane of the G-triad, together with the water-bridge network among the atoms N7 and H1 of A1 and G14 residues (Fig. 3A, upper panel), concurred to a further stabilization of the G-tetrad. An additional contribution to the stability of the 4d G-triad is due to the bypiramidal coordination of the K+ ion with the O6 atoms of the G-triad and the lower G-tetrad (Fig. 3B, lower plot). Similarly, two water molecules engaged hydrogen bonds with G2:G14 residues, thus miming the slipped G20 residue (Fig. 3A) and favouring a further stability of the G-triad, as clearly emerges after 600 ns of MDs (Fig. 3B, upper plot).
A movie showing the vertical slippage mechanism leading to 4d conformation can be found in the Supplementary Information Movie SM1.
Most of the predicted folding intermediates of the parallel telomeric G4 found in the basin C contain one G-triad and two G-tetrad planes. These structures represent transient metastable states, and it is very difficult to demonstrate experimentally their existence. However, to have some experimental information about the possible existence of such a structure in solution, we investigated the construct obtained by removing the last guanine base from the d[TAG3(TTAGGG)3] sequence (h-tel23), i.e. the 22-nt sequence d[TAG3(TTAGGG)2TTAGG] (hereafter named h-tel22tr). The G4-forming sequence h-tel23 adopts, in a 40% PEG200 containing K+-solution, the same parallel-stranded conformation with three G-tetrad planes found for h-tel by X-ray23. The removal of a single guanine at the 3′ end of the sequence rules out the possibility of forming a monomolecular G4 structure with three G-tetrads. In order to assess the molecularity of h-tel22tr in 40% PEG200 containing K+-solution, non-denaturing gel electrophoresis analysis was performed by using as reference the h-tel23 G4 in the same buffer conditions. As shown in Fig. 4A (see also Supplementary Information, Figure S21), h-tel22tr moves essentially as a single band in the gel, exhibiting a mobility close to h-tel23. This clearly indicates the absence of multimolecular DNA complexes and suggests that h-tel22tr adopts a structure (or structures) comparable to that of h-tel23 under such experimental conditions. Then, a spectroscopic investigation of the species formed upon folding of h-tel22tr sequence was performed in comparison with h-tel23 by circular dichroism (CD). Previous studies have demonstrated that the parallel conformation is not the only populated conformation for the telomeric G4 under the PEG-induced crowding conditions, but a non-negligible amount of hybrid conformation coexists with the parallel one39. Fig. 4B,C show the CD spectra of h-tel23 and h-tel22tr in the PEG-containing buffer, recorded in the range 10–100 °C with temperature increase of 5 °C. In general, the CD bands of DNA molecules are generated when the bases are chirally oriented with respect to each other, i.e. when the DNA is structured. Owing to the heterotypic nature of the two faces of guanines, each G can stack onto the adjacent one through the same or the opposite face, leading to a homopolar or heteropolar stacking, respectively40. The former happens when two contiguous Gs have opposite glycosidic bond angle conformation (e.g. anti-syn), whereas the latter happens when the two Gs have the same glycosidic bond angle (e.g. anti-anti). The CD spectrum of a G-rich oligonucleotide characterized by a positive band at 265 nm and a negative one at 243 nm is typical of parallel G4 structures having heteropolar stacks. On the other hand, a positive band at 295 nm is characteristic of the homopolar stacks of hybrid/antiparallel G4 conformations. In agreement with the presence of the parallel-stranded G4 topology, h-tel23 displayed a positive band at 265 nm and a negative one at 243 nm in the spectra (Fig. 4B). However, at low temperatures (up to about 45 °C), the spectra clearly show a shoulder at around 295 nm. This is in agreement with the presence of a certain amount of hybrid/antiparallel conformation(s). In addition, plotting melting curves from the CD data at two wavelengths, i.e. 265 and 295 nm (Fig. 4D), gave two different T1/2 values (95 ± 2 and 50 ± 1 °C, respectively), thus suggesting the presence of two different species. CD spectra of h-tel22tr as a function of temperature show that the shoulder at around 295 nm is much more pronounced in this case, thus indicating that probably the equilibrium between parallel and hybrid/antiparallel species is more shifted toward the latter than in the case of h-tel23. Plotting melting curves from the h-tel22tr CD data at 265 and 295 nm (Fig. 4E) gave T1/2 values of 63 ± 1 and 45 ± 1 °C, respectively, also suggesting the existence of different species in solution.
The parallel topology of the human telomeric sequence d[AG3(TTAGGG)3] can be considered the G4 conformation with the most probable biological role among all G4 structures21,32. Moye et al. demonstrated that the telomerase recognizes and binds different parallel G4s with high affinity, whereas the antiparallel conformations are not good substrates, despite their much higher stability32. Also HMGB1, an ubiquitous non-histone protein engaged in many DNA events, such as DNA repair, transcription and telomere maintenance, has a preference for the unimolecular parallel TelG441. Currently, although it has been found that the stabilization of G4 structure can affect the telomerase enzyme activity with a resultant antineoplastic effect, the characterization of its folding intermediate structures formed in solution are still elusive at atomistic level34. In fact, for the propeller-type conformation, the G-triplex formation was considered as the less probable intermediate state42, while the most natural arrangement for such kind of topology is the vertical strand-slippage movement of the G-triplets that leads to two G-tetrad planes and one G-triad, as demonstrated by standard MDs30.
In several instances, Metadynamics-based approaches allowed a detailed atomistic description of meaningful metastable folded states43,44,45,46,47, supporting, in some cases, even their characterization by means of experimental techniques48,49. In this work, using WT-MetaD simulations, we have provided a comprehensive picture of all the possible ensemble conformations emerging during the folding process of the 22-nt parallel topology G4 in solution, which have never been detected yet, at the best of our knowledge. In addition, we also have employed an innovative CV (π-πcore) to investigate the π-π stacking behavior among all anti-guanines of the G-tetrads, besides the Hoogsteen hydrogen bonds network of the G-tetrads CVs. By reweighting the WT-MetaD37 sampling, we were able to retrieve an ensemble of structures (basin C) having two G-tetrad planes in equilibrium with each other. Thus, our studies enforce the hypothesis that late/early stages of parallel stem formation/disruption may involve cation-stabilized four-stranded intermediates with various degrees of strand slippage and incomplete numbers of tetrads30. These results also support the formation mechanism suggested by Stefl et al. in 200338, according to which the parallel G4 has clear strand slippage capabilities. In agreement with the models reported in the previous literature, the formation of G-triplex intermediates28,30 wasn’t directly detected, while a slowly rearrangement of the slipped strands into the native four-tetrad stem, also consistent with experimental data21, was clearly observed and described in this work. This mechanism leads to the formation of a G-triad plane, which can arrange in an “open” and “closed” form based on the G-triplet involved in the vertical slippage38. The “closed” G-triad, which exhibited a good geometrical stability, was found only in 2d conformation and it is reasonably due to the absence of the coordinating K+ ion within the G-triad. On the other hand, the “open” conformation of the G-triad was stabilized by a water molecules network established in the vacant site of the slipped guanine, similarly to the NMR structure described by Heddi and co-workers, suitable as possible ligand binding site35. However, in the basin C, G4 conformations without a G-triad were also collected and they derived from the simultaneous vertical slippage of two G-triplets. In particular, our WT-MetaD run highlighted that the vertical slippage of two adjacent G-triplets are more probable than the simultaneous movement of two opposed G-triplets. Indeed, the better geometrical stability and probability of existence of 34d is mainly due to the presence of two Hoogsteen pairs of guanines, able to coordinate K+ ions with their O6 oxygens.
Focusing on the directionality of the vertical slippage mechanism, the movement towards the 3′-end position has been found out in almost all the structures collected in the basin C, leading to the observation that the presence of residue A1 at the 5′-end involves a steric hindrance such as to hinder the G-triplets movement in this direction. Therefore, only one structure having 5′-end slippage was found in the basin C, showing also a reduced probability of existence. Its dynamic behavior points out the highest stability of its “open” G-triad coupled to wide fluctuations of the third loop and consequently of the 3′-end position, resulting in agreement with the WT-MetaD as the portion with the most favorable capability for the vertical slippage movement. Going along with these findings, 34d and 4d, the two most probable structures found in basin C, showed the vertical slippage of the G-triplets in the 3′-end portion and can be hypothesized as the two most important cation-stabilized four-stranded intermediates occurring during the late/early stages of parallel stem formation/disruption. In particular, 4d structure is characterized by an “open” G-triad with the best geometrical stability between those found at the 5′-end position.
The whole set of experimental data suggests that the construct obtained by removing the last G from the d[TAG3(TTAGGG)3] sequence forms monomolecular G4-like structures under molecular crowding conditions. Since the removal of the last guanine of the sequence ruled out the possibility of forming G4 structures with three G-tetrads, these structures are supposed to be stabilized by no more than two G-tetrads. Indeed, as expected, they result to be thermally less stable than h-tel23 structures. However, as for h-tel22tr parallel structure, we observed a T1/2 value of 63 °C, which, compared with that of a two-tetrads-G4 under the same experimental conditions (T1/2 = 58.7 °C)47, suggests the presence of additional intramolecular interactions that may arise from an additional G-triad. These results are consistent with the hypothesis that G4s containing two G-tetrads and one G-triad may actually be intermediate in the folding of the parallel telomeric G4.
Since a stable G4 structure of a synthetic sequence containing two G-tetrads and one G-triad has already been determined by means of NMR technique30, we can enforce the hypothesis on the existence of the ensemble of conformations found in the basin C, which in any case results very difficult to experimentally demonstrate for their structural heterogeneity. Indeed, in literature it is widely reported the difficulty to obtain the parallel propeller-type G4 structure in diluted solution by means of the NMR technique18. The concept of forming G4s with missing guanines in the G-tetrads as result of the vertical G-triplets slippage movement enriches and extends the current knowledge of the G4 structures. The vacant site in the “open” G-triads can provide a potential binding site for small-molecule and metabolites recognition50, playing a regulatory role in the telomeres elongation and/or in the gene expression and assuming a behavior similar to RNA riboswitches. In fact, several RNA riboswitches are able to bind metabolites, as guanine and guanine derivatives, with associated regulator effect on gene expression51,52,53.
This study aims also to present an alternative computational protocol able to investigate the phase space of other parallel G4 structures, such as the oncogene promoter ones, in order to describe the late/early stages of parallel stem formation/disruption. The discovery of possible four-stranded intermediates with various degrees of strand slippage and incomplete numbers of tetrads for the oncogene promoter G4s would open new scenarios in understanding the process behind the regulation of gene expression.
System setup and MDs
The crystal structure of the parallel stranded G4 with the 22-nt human telomeric sequence d[AG3(T2AG3)3] and a resolution of 2.1 Å (PDB ID: 1KF1), was used as starting conformation for the computational simulations17. K+ ions coordinating the G-tetrad O6 atoms were retained, while all the crystallized water molecules were removed.
The G4 nucleic acid was treated using the standard parm99 Amber force field modified with the recently developed parmbsc056,57, in combination with the recently-developed corrections ε/ζOL1 and χOL4 to improve the description respectively of the ε/ζ and χ G-quadruplex torsions58,59,60,61,62,63.
G4 nucleic acid was solvated in a truncated dodecahedron box with TIP3P66 water solvent model using periodic boundary conditions and it was neutralized by adding 19 K+ ions. Long-range electrostatic interactions were treated using Particle-Mesh Ewald (PME)67,68 with a cut-off of 1.0 nm. Van der Waals (VdW) interactions were calculated using also a cut-off of 1.0 nm. All bonds were dealt with the LINCS algorithm69.
Firstly, the whole system was subjected to a minimization phase using 5000 steps with the steepest descent algorithm to resolve bad steric contacts and then equilibrated under constant pressure and temperature at 1 atm and 300 K for 4 ns using a time step of 2 fs. For the temperature control the V-rescale algorithm has been used70, while the Parrinello-Rahman71 barostat to monitor the pressure. In order to verify the stability of the system, 200-ns-long MDs at room temperature were performed in the NVT ensemble.
Well-tempered metadynamics simulation (WT-MetaD)
To obtain an exhaustively local conformational exploration of the parallel G4, we applied the Well-Tempered variant of Metadynamics (WT-MetaD)33. Initial Gaussians height (W) was set at 2.48 kJ/mol with a deposition rate equal to 1 ps. The bias factor was fixed to 20. Two collective variables (CVs) were used to sample local conformational space of the parallel G4: the Coordination CV to describe the native Hoogsteen hydrogen bonds (Hbcore 1KF1) and the number of stacking interactions among the guanines of each G-triplet (π-πcore) (for more details see Hoogsteen Hydrogen bonds (Hbcore) and π-πcore CV paragraphs in the Supplementary Information, including Figure S1). The first CV was evaluated considering the total number of contacts between the acceptor atoms of the G-tetrad, listed in group G1, and the donor ones, put in group G2 (see Table S1 in Supplementary Information), using a Gaussian width of 0.2. For the second CV, since the lack of a proper CV able to describe such π-π interactions, we have referred to the aromatic packing density which characterizes the environment of a typical G-core likewise has been already addressed by Giberti F. et al.36 for the nucleation of urea crystals. For a better clarity, the function of π-πcore is summarized in the Supplementary Information. A Gaussian width of 0.5 was used for this CV. It is worth to underline that, in order to verify the slippage mechanism involving only the G-tetrads, during the WT-MetaD, a complete unfolding of G4 DNA was prevented by using a potential restraint able to focus the conformational sampling only on those structure having more than five Hbcore 1KF1 and eight π-πcore CVs (for more details see Potential Restraint paragraph in the Supplementary Information).
The reweighted FES
Once the free energy of the WT-MetaD simulation is converged, the FES was reconstructed using the reweighting algorithm37 (Fig. 2) as function of two unbiased CVs: the first CV (named as “RMSd(G-core) vs 1KF1Cry”) corresponds to the RMSd of the G-tetrads superimposed to those of the 1KF1 crystallographic model (the latter hereafter named as 1KF1Cry); as second CV we used a Coordination to describe the number of Hoogsteen hydrogen bonds (Hbcore) formed in the G-tetrads. In particular, as concern the second CV, we defined exactly the number of Hoogsteen hydrogen bonds for each structure having two G-tetrad planes as Hbcore2d, Hbcore3d, Hbcore3u, Hbcore24d and Hbcore34d (see Table S2 in Supplementary Information) with respect to 1KF1Cry (see Table S1 in Supplementary Information). The proper Hbcore value of each structure was assigned following the flow diagram reported in Figure S22.
MDs on G4 conformations representing the basin C
The stability of the slipped G4 conformations found in basin C was assessed calculating the RMSd during 200 ns long MDs, by applying the same protocol previously described for the starting 1KF1Cry. Finally, MDs of 4d structure was extended to 1 µs MDs, in order to better analyze the most stable slipped structure found in basin C.
DNA sample preparation
The d[TAG3(TTAGGG)3] (h-tel23) and d[TAG3(TTAGGG)2TTAGG] (h-tel22tr) sequences were synthesized and purified as already described72. The oligonucleotides were dissolved in 20 mM potassium phosphate buffer (pH 7.0) containing 70 mM KCl, 0.2 mM EDTA, and 40% PEG200. The concentration of oligonucleotides was determined by UV adsorption measurements at 95 °C using appropriate molar extinction coefficient values ε (λ = 260 nm) calculated by the nearest-neighbor model73. Each sample was heated to 95 °C for 5 min, gradually cooled to room temperature overnight, and then incubated for at least 24 h at 4 °C before data acquisition.
Native gel electrophoresis analysis was carried out on 15% polyacrylamide gel at 25 °C, which was run at 80 V for 4 h in 1 × TB buffer (pH 7.5) supplemented with 10 mM KCl. A concentration of 50 μM was used for the oligonucleotides, which were prepared in a 40% PEG200 containing K+-buffer. Prior to loading the mixture onto the gel, 1 μL of glycerol solution (60% v/v) was added. The total volume loaded in each well was 10 μL. Gel was imaged by UV-shadowing, using the exposure wavelength of 254 nm for nucleobase detection.
Circular dichroism spectroscopy
CD experiments were recorded on a Jasco J-815 spectropolarimeter equipped with a PTC-423S temperature controller. Spectra were recorded in a quartz cuvette with 1 mm path length in the 220–360 nm wavelength range and averaged over three scans. The scan rate was set to 100 nm/min, with a 1 s response time and 1 nm bandwidth. Buffer baseline was subtracted from each spectrum. Experiments were performed using 10 μM oligonucleotide concentration. CD melting experiments were carried out by collecting data in the range 10–100 °C using a temperature step of 5 °C. The samples were incubated at each temperature for a suitable time to achieve the equilibrium. Reaching equilibrium at each temperature was guaranteed by the achievement of superimposable CD spectra on changing time. The CD melting curves were obtained by following changes of CD signal at 265 and 295 nm. Apparent melting temperatures (T1/2) were determined from curve fit using Origin 7.0 software74.
Parrotta, L. et al. Targeting unimolecular G-quadruplex nucleic acids: a new paradigm for the drug discovery? Expert. Opin. drug. discovery 9, 1167–1187 (2014).
Watson, J. D. & Crick, F. H. Genetical implications of the structure of deoxyribonucleic acid. JAMA 269, 1967–1969 (1993).
Zahler, A. M., Williamson, J. R., Cech, T. R. & Prescott, D. M. Inhibition of telomerase by G-quartet DNA structures. Nature 350, 718–720 (1991).
Counter, C. M. et al. Telomere shortening associated with chromosome instability is arrested in immortal cells which express telomerase activity. Embo J. 11, 1921–1929 (1992).
Ilyinsky, N. S. et al. G-quadruplex ligands: Mechanisms of anticancer action and target binding. Mol. Biol. 48, 778–794 (2014).
Di Leva, F. S. et al. Exploring the chemical space of G-quadruplex binders: discovery of a novel chemotype targeting the human telomeric sequence. J. medicinal Chem. 56, 9646–9654 (2013).
Pagano, B. et al. Looking for efficient G‐quadruplex ligands: evidence for selective stabilizing properties and telomere damage by drug‐like molecules. ChemMedChem 10, 640–649 (2015).
Artese, A. et al. Toward the design of new DNA G-quadruplex ligands through rational analysis of polymorphism and binding data. Eur. J. medicinal Chem. 68, 139–149 (2013).
Alcaro, S. et al. Identification and characterization of new DNA G-quadruplex binders selected by a combination of ligand and structure-based virtual screening approaches. J. medicinal Chem. 56, 843–855 (2013).
Rocca, R. et al. Hit Identification of a Novel Dual Binder for h-telo/c-myc G-Quadruplex by a Combination of Pharmacophore Structure-Based Virtual Screening and Docking Refinement. ChemMedChem 11, 1721–1733 (2016).
Rocca, R. et al. Structure-based virtual screening of novel natural alkaloid derivatives as potential binders of h-telo and c-myc DNA G-quadruplex conformations. Molecules 20, 206–223 (2015).
Rocca, R. et al. Identification of G-quadruplex DNA/RNA binders: structure-based virtual screening and biophysical characterization. Biochimica et. Biophysica Acta -General Subj. 1861, 1329–1340 (2017).
Rocca, R. et al. In silico identification of piperidinyl-amine derivatives as novel dual binders of oncogene c-myc/c-Kit G-quadruplexes. ACS medicinal Chem. Lett. 9, 848–853 (2018).
Moraca, F. et al. Ligand binding to telomeric G-quadruplex DNA investigated by funnel-metadynamics simulations. Proc. Natl. Acad. Sci. USA 114, E2136–E2145 (2017).
Di Leva, F. S. et al. Mechanistic insight into ligand binding to G-quadruplex DNA. Nucleic Acids Res. 42, 5447–5455 (2014).
Burge, S., Parkinson, G. N., Hazel, P., Todd, A. K. & Neidle, S. Quadruplex DNA: sequence, topology and structure. Nucleic Acids Res. 34, 5402–5415 (2006).
Wang, Y. & Patel, D. J. Solution structure of the human telomeric repeat d [AG3(T2AG3)3] G-tetraplex. Structure 1, 263–282 (1993).
Ambrus, A. et al. Human telomeric sequence forms a hybrid-type intramolecular G-quadruplex structure with mixed parallel/antiparallel strands in potassium solution. Nucleic acids Res. 34, 2723–2735 (2006).
Parkinson, G. N., Lee, M. P. H. & Neidle, S. Crystal structure of parallel quadruplexes from human telomeric DNA. Nature 417, 876–880 (2002).
Li, J., Correia, J. J., Wang, L., Trent, J. O. & Chaires, J. B. Not so crystal clear: the structure of the human telomere G-quadruplex in solution differs from that present in a crystal. Nucleic acids Res. 33, 4649–4659 (2005).
Xue, Y. et al. Human telomeric DNA forms parallel-stranded intramolecular G-quadruplex in K+ solution under molecular crowding condition. J. Am. Chem. Soc. 129, 11185–11191 (2007).
Zimmerman, S. B. & Trach, S. O. Estimation of macromolecule concentrations and excluded volume effects for the cytoplasm of Escherichia coli. J. Mol. Biol. 222, 599–620 (1991).
Heddi, B. & Phan, A. T. Structure of human telomeric DNA in crowded solution. J. Am. Chem. Soc. 133, 9824–9833 (2011).
Mashimo, T., Yagi, H., Sannohe, Y., Rajendran, A. & Sugiyama, H. Folding pathways of human telomeric type-1 and type-2 G-quadruplex structures. J. Am. Chem. Soc. 132, 14910–14918 (2010).
Koirala, D. et al. Intramolecular folding in three tandem guanine repeats of human telomeric DNA. Chem. Commun. 48, 2006–2008 (2012).
Gray, R. D., Trent, J. O. & Chaires, J. B. Folding and unfolding pathways of the human telomeric G-quadruplex. J. Mol. Biol. 426, 1629–1650 (2014).
Jiang, H. X. et al. Divalent cations and molecular crowding buffers stabilize G-triplex at physiologically relevant temperatures. Sci. Rep. 5, 9255 (2015).
Bian, Y. et al. Atomistic picture for the folding pathway of a hybrid-1 type human telomeric DNA G-quadruplex. PLoS Comput. Biol. 10, e1003562 (2014).
Luo, D. & Mu, Y. Computational Insights into the Stability and Folding Pathways of Human Telomeric DNA G-Quadruplexes. J. Phys. Chem. B. 120, 4912–4926 (2016).
Stadlbauer, P., Krepl, M., Cheatham, T. E., Koča, J. & Šponer, J. Structural dynamics of possible late-stage intermediates in folding of quadruplex DNA studied by molecular simulations. Nucleic Acids Res. 41, 7128–7143 (2013).
Stadlbauer, P. et al. Hairpins participating in folding of human telomeric sequence quadruplexes studied by standard and T-REMD simulations. Nucleic acids Res. 43, 9626–9644 (2015).
Moye, A. L. et al. Telomeric G-quadruplexes are a substrate and site of localization for human telomerase. Nature communications 6 (2015).
Barducci, A., Bussi, G. & Parrinello, M. Well-tempered metadynamics: a smoothly converging and tunable free-energy method. Phys. Rev. Lett. 100, 020603 (2008).
Mergny, J. L., Phan, A. T. & Lacroix, L. Following G-quartet formation by UV-spectroscopy. FEBS Lett. 435, 74–78 (1998).
Heddi, B. et al. G-quadruplexes with (4n-1) guanines in the G-tetrad core: formation of a G-triad· water complex and implication for small-molecule binding. Nucleic acids Res. 44, 910–916 (2015).
Giberti, F., Salvalaglio, M., Mazzotti, M. & Parrinell, M. Insight into the nucleation of urea crystals from the melt. Chem. Eng. Sci. 121, 51–59 (2015).
Bonomi, M., Barducci, A. & Parrinello, M. Reconstructing the equilibrium Boltzmann distribution from well-tempered metadynamics. J. Comput. Chem. 30, 1615–1621 (2009).
Stefl, R. et al. Formation pathways of a guanine quadruplex DNA revealed by molecular dynamics and thermodynamic analysis of the substrates. Biophys. J. 85, 1787–1804 (2003).
Petraccone, L., Malafronte, A., Amato, J. & Giancola, C. G-quadruplexes from human telomeric DNA: how many conformations in PEG containing solutions? J. Phys. Chem. B. 116, 2294–305 (2012).
Randazzo, A., Spada, G. P. & Webba da Silva, M. Circular dichroism of quadruplex structures. Top. Curr. Chem. 330, 67–86 (2013).
Naganathan, A. N., Doshi, U., Fung, A., Sadqi, M. & Munoz, V. Dynamics, energetics, and structure in protein folding. Biochem. 45, 8466–8475 (2006).
Amato, J. et al. Insights into telomeric G-quadruplex DNA recognition by HMGB1 protein. Nucleic acids Res. 47, 9950–9966 (2019).
Stadlbauer, P., Trantírek, L., Cheatham, T. E., Koča, J. & Šponer, J. Triplex intermediates in folding of human telomeric quadruplexes probed by microsecond-scale molecular dynamics simulations. Biochim. 105, 22–35 (2014).
Branduardi, D., Gervasio, F. L. & Parrinello, M. From A to B in free energy space. J. Chem. Phys. 126, 054103 (2007).
Bonomi, M., Branduardi, D., Gervasio, F. L. & Parrinello, M. The unfolded ensemble and folding mechanism of the C-terminal GB1 betahairpin. J. Am. Chem. Soc. 130, 13938–13944 (2008).
Pietrucci, F. & Laio, A. A collective variable for the efficient exploration of protein beta-sheet structures: application to SH3 and GB1. J. Chem. Theory Comput. 5, 2197–2201 (2009).
Todorova, N., Marinelli, F., Piana, S. & Yarovsky, I. Exploring the folding free energy landscape of insulin using bias exchange metadynamics. J. Phys. Chem. B 113, 3556–3564 (2009).
Miyoshi, D., Karimata, H. & Sugimoto, N. Hydration regulates thermodynamics of G-quadruplex formation under molecular crowding conditions. J. Am. Chem. Soc. 128, 7957–7963 (2006).
Limongelli, V. et al. The G-triplex DNA. Angew. Chem. Int. Ed. Engl. 52, 2269–73 (2013).
Cerofolini, L. et al. G-triplex structure and formation propensity. Nucleic acids Res. 42, 13393–13404 (2014).
Pang, S. M., Heddi, B., Martin-pintado, N., Serimbetov, Z. & Phan, A.T. Interaction between guanosine and a G-quadruplex with a vacant site [Abstract No Wed-P30] 5th International Meeting on Quadruplex Nucleic Acids: G4thering in Bordeaux, Bordeaux, France (May 26–28 2015).
Nudler, E. & Mironov, A. S. The riboswitch control of bacterial metabolism. Trends biochemical Sci. 29.1, 11–17 (2004).
Serganov, A. et al. Structural basis for discriminative regulation of gene expression by adenine-and guanine-sensing mRNAs. Chem. Biol. 11.12, 1729–1741 (2004).
Serganov, A. & Patel, D. J. Molecular recognition and function of riboswitches. Curr. Opin. Struct. Biol. 22, 279–286 (2012).
Hess, B., Kutzner, C., van der Spoel, D. & Lindahl, E. GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. J. Chem. Theory Comput. 4, 435–447 (2008).
Bonomi, M. et al. PLUMED: A portable plugin for free energy calculations with molecular dynamics. Comput. Phys. Comm. 180, 1961–1972 (2009).
Case, D. A. et al. AMBER 14, University of California, San Francisco (2014).
Guy, A. T., Piggot, T. J. & Khalid, S. Single-stranded DNA within nanopores: Conformational dynamics and implications for sequencing; a molecular dynamics simulation study. Biophys. J. 103, 1028–1036 (2012).
Cornell, W. D. et al. A new force field for molecular mechanical simulation of nucleic acids and proteins. J. Am. Chem. Soc. 117, 5179–5197 (1995).
Cheatham, T. E. III, Cieplak, P. & Kollman, P. A. A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat. J. Biomol. Struct. Dyn. 16, 845–862 (1999).
Pérez, A. et al. Refinement of the AMBER force field for nucleic acids: improving the description of α/γ conformers. Biophys. J. 92, 3817–3829 (2007).
Zgarbová, M. et al. Toward improved description of dna backbone: Revisiting epsilon and zeta torsion force field parameters. J. Chem. Theory Comput. 9, 2339–2354 (2013).
Krepl, M. Reference simulations of noncanonical nucleic acids with different chi variants of the AMBER force field: Quadruplex DNA, quadruplex RNA, and Z-DNA. J. Chem. Theory Comp. 8, 2506–2520 (2012).
Li, M. H., Luo, Q., Xue, X. G. & Li, Z. S. Toward a full structural characterization of G-quadruplex DNA in aqueous solution: Molecular dynamics simulations of four G-quadruplex molecules. J. Mol. Structure: THEOCHEM 952, 96–102 (2010).
Case, D. et al. AMBER 12. University of California, San Francisco, 2012.
Sousa da Silva, A. W. & Vranken, W. F. ACPYPE - AnteChamber PYthon Parser interfacE. BMC Res. Notes 5.1, 367 (2012).
Jorgensen, W. L. & Madura, J. D. Quantum and statistical mechanical studies of liquids. 25. Solvation and conformation of methanol in water. J. Am. Chem. Soc. 105, 1407–1413 (1983).
Darden, T., York, D. & Pedersen, L. Particle mesh Ewald: An N·log(N) method for Ewald sums in large systems. J. Chem. Phys. 98, 10089–10092 (1993).
Essmann, U. et al. A smooth particle mesh ewald potential. J. Chem. Phys. 103, 8577–8592 (1995).
Hess, B., Bekker, H., Berendsen, H. J. & Fraaije, J. G. LINCS: a linear constraint solver for molecular simulations. J. Comput. Chem. 18, 1463–1472 (1997).
Bussi, G., Donadio, D. & Parrinello, M. Canonical sampling through velocity-rescaling. J. Chem. Phys. 126, 014101–014108 (2007).
Parrinello, M. & Rahman, A. Polymorphic transitions in single crystals: A new molecular dynamics method. J. Appl. Phys. 52, 7182–7190 (1981).
Amato, J. et al. Toward the Development of Specific G-Quadruplex Binders: Synthesis, Biophysical, and Biological Studies of New Hydrazone Derivatives. J. Med. Chem. 59, 5706–5720 (2016).
Cantor, C. R., Warshaw, M. M. & Shapiro, H. Oligonucleotide interactions. 3. Circular dichroism studies of the conformation of deoxyoligonucleotides. Biopolym. 9, 1059–1070 (1970).
R.R. and F.P. acknowledge the Swiss Center for Scientific Computing (CSCS) [project ID s370] and the Brutus HPC cluster at ETH Zürich for providing the computational resources. The authors thank Matteo Salvalaglio and Federico Giberti for helping with the application of the proper collective variables to describe the guanines stacking interactions. The authors are grateful also to prof. Vittorio Limongelli for critically reading the manuscript and to prof. Michele Parrinello for having assisted the research with his expertise. This work was supported by: the Italian Ministry of Education ‘Funding for Investments of Base Research’ (FIRB) [code FIRB-IDEAS RBID082ATK]; R.R. was supported by the ‘Programma Operativo Regionale’ (POR) Calabria ‘Fondo Sociale Europeo’ (FSE) 2007–2013 “HEMMAS” Fellowship; G.C. was supported by the University “Magna Græcia” (UMG) grant dedicated to the memory of Anna and Ninì Barbieri. S.A. and G.C. acknowledge the PRIN 2017 research project “Novel anticancer agents endowed with multitargeting mechanism of action” (201744BN5T). F.M was supported by the grant from Regione Campania-POR Campania FESR 2014/2020 [Project n. B61C17000070007 (SATIN)]. J.A., B.P. and A.R. acknowledge Regione Campania-POR Campania FESR 2014/2020 [B61G18000470007].
The authors declare no competing interests.
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Rocca, R., Palazzesi, F., Amato, J. et al. Folding intermediate states of the parallel human telomeric G-quadruplex DNA explored using Well-Tempered Metadynamics. Sci Rep 10, 3176 (2020). https://doi.org/10.1038/s41598-020-59774-x
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