The solution structure of d(G(4)T(4)G(3))(2): a bimolecular G-quadruplex with a novel fold

Changes in physicochemical and anticancer properties modulated by chemically modified sugar moieties within sequence-related G-quadruplex structures

We systematically investigated the influence of locked nucleic acid (LNA), unlock nucleic acid (UNA), and 2’-O-methyl-RNA (2’-O-Me-RNA) residues on the thermal stability, structure folding topology, biological activity and enzymatic resistance of three sequence-related DNA G-quadruplexes. In order to better understand the mechanism of action of the studied modifications, a single-position substitution in the loops or G-tetrads was performed and their influence was analyzed for a total of twenty-seven modified G-quadruplex variants. The studies show that the influence of each modification on the physicochemical properties of G-quadruplexes is position-dependent, due to mutual interactions between G-tetrads, loops, and additional guanosine at 5’ or 3’ end. Nevertheless, the anticancer activity of the modified G-quadruplexes is determined by their structure, thus also by the local changes of chemical character of sugar moieties, what might influence the specific interactions with therapeutic targets. In general, UNA modifications are efficient modulators of the G-quadruplex thermodynamic stability, however they are poor tools to improve the anticancer properties. In contrast, LNA and 2’-O-Me-RNA modified G-quadruplexes demonstrated certain antiproliferative potential and might be used as molecular tools for designing novel G-quadruplex-based therapeutics.

G4 Matters-The Influence of G-Quadruplex Structural Elements on the Antiproliferative Properties of G-Rich Oligonucleotides

G-quadruplexes (G4s) are non-canonical structures formed by guanine-rich sequences of DNA or RNA that have attracted increased attention as anticancer agents. This systematic study aimed to investigate the anticancer potential of five G4-forming, sequence-related DNA molecules in terms of their thermodynamic and structural properties, biostability and cellular uptake. The antiproliferative studies revealed that less thermodynamically stable G4s with three G-tetrads in the core and longer loops are more predisposed to effectively inhibit cancer cell growth. By contrast, highly structured G4s with an extended core containing four G-tetrads and longer loops are characterized by more efficient cellular uptake and improved biostability. Various analyses have indicated that the G4 structural elements are intrinsic to the biological activity of these molecules. Importantly, the structural requirements are different for efficient cancer cell line inhibition and favorable G4 cellular uptake. Thus, the ultimate antiproliferative potential of G4s is a net result of the specific balance among the structural features that are favorable for efficient uptake and those that increase the inhibitory activity of the studied molecules. Understanding the G4 structural features and their role in the biological activity of G-rich molecules might facilitate the development of novel, more potent G4-based therapeutics with unprecedented anticancer properties.

Structural basis for stabilization of human telomeric G-quadruplex [d-(TTAGGGT)]4 by anticancer drug epirubicin

Anthracycline anticancer drugs show multiple strategies of action on gene functioning by regulation of telomerase enzyme by apoptotic factors, e.g. ceramide level, p53 activity, bcl-2 protein levels, besides inhibiting DNA/RNA synthesis and topoisomerase-II action. We report binding of epirubicin with G-quadruplex (G4) DNA, [d-(TTAGGGT)]₄, comprising human telomeric DNA sequence TTAGGG, using ¹H and ³¹P NMR spectroscopy. Diffusion ordered spectroscopy, sequence selective changes in chemical shift (~0.33 ppm) and line broadening in DNA signals suggest formation of a well-defined complex. Presence of sequential nuclear Overhauser enhancements at all base quartet steps and absence of large downfield shifts in ³¹P resonances preclude intercalative mode of interaction. Restrained molecular dynamics simulations using AMBER force field incorporating intermolecular drug to DNA interproton distances, involving ring D protons of epirubicin depict external binding close to T1-T2-A3 and G6pT7 sites. Binding induced thermal stabilization of G4 DNA (~36 °C), obtained from imino protons and differential scanning calorimetry, is likely to come in the way of telomerase association with telomeres. The findings pave the way for drug-designing with modifications at ring D and daunosamine sugar.

Structural basis for stabilization of human telomeric G-quadruplex [d-(TTAGGGT)]4 by anticancer drug adriamycin

Besides inhibiting DNA duplication, DNA dependent RNA synthesis and topoisomerase-II enzyme action, anticancer drug adriamycin is found to cause telomere dysfunction and shows multiple strategies of action on gene functioning. We present evidence of binding of adriamycin to parallel stranded intermolecular [d-(TTAGGGT)]₄ G-quadruplex DNA comprising human telomeric DNA by proton and phosphorus-31 nuclear magnetic resonance spectroscopy. Diffusion ordered spectroscopy shows formation of complex between the two molecules. Changes in chemical shift and line broadening of DNA and adriamycin protons suggest participation of specific chemical groups/moieties in interaction. Presence of sequential nuclear Overhauser enhancements at all base quartet steps and absence of large downfield shifts in ³¹P resonances give clear proof of absence of intercalation of adriamycin chromophore between base quartets. Restrained molecular dynamics simulations using observed 15 short intermolecular inter proton distance contacts depict stacking of ring D of adriamycin with terminal G6 quartet by displacing T7 base and external groove binding close to T1-T2-A3 bases. The disappearance of imino protons monitored as a function of temperature and differential scanning calorimetry experiments yield thermal stabilization of 24 °C, which is likely to come in the way of telomerase association with telomeres. The findings pave the way for design of alternate anthracycline based drugs with specific modifications at ring D to enhance induced thermal stabilization and use alternate mechanism of binding to G-quadruplex DNA for interference in functional pathway of telomere maintenance by telomerase enzyme besides their well known action on duplex DNA. Communicated by Ramaswamy H. Sarma.

Dual mode of binding of anti cancer drug epirubicin to G-quadruplex [d-(TTAGGGT)]4 containing human telomeric DNA sequence induces thermal stabilization

Epirubicin exerts its anti cancer action by blocking DNA/RNA synthesis and inhibition of topoisomerase-II enzyme. Recent reports on its influence on telomere maintenance, suggest interaction with G-quadruplex DNA leading to multiple strategies of action. The binding of epirubicin with parallel stranded inter molecular G-quadruplex DNA [d-(TTAGGGT)]₄ comprising human telomeric DNA sequence TTAGGG was investigated by absorption, fluorescence, circular dichroism and nuclear magnetic resonance spectroscopy. The epirubicin binds as monomer to G-quadruplex DNA with affinity, K_b1 = 3.8 × 10⁶ M^-1 and K_b2 = 2.7 × 10⁶ M^-1, at two independent sites externally. The specific interactions induce thermal stabilization of DNA by 13.2-26.3 °C, which is likely to come in the way of telomere association with telomerase enzyme and contribute to epirubicin-induced apoptosis in cancer cell lines. The findings pave the way for drug designing in view of the possibility of altering substituent groups on anthracyclines to enhance efficacy using alternate mechanism of its interaction with G4 DNA, causing interference in telomere maintenance pathway by inducing telomere dysfunction.

Metal Cations in G-Quadruplex Folding and Stability

This review is focused on the structural and physicochemical aspects of metal cation coordination to G-Quadruplexes (GQ) and their effects on GQ stability and conformation. G-quadruplex structures are non-canonical secondary structures formed by both DNA and RNA. G-quadruplexes regulate a wide range of important biochemical processes. Besides the sequence requirements, the coordination of monovalent cations in the GQ is essential for its formation and determines the stability and polymorphism of GQ structures. The nature, location, and dynamics of the cation coordination and their impact on the overall GQ stability are dependent on several factors such as the ionic radii, hydration energy, and the bonding strength to the O6 of guanines. The intracellular monovalent cation concentration and the localized ion concentrations determine the formation of GQs and can potentially dictate their regulatory roles. A wide range of biochemical and biophysical studies on an array of GQ enabling sequences have generated at a minimum the knowledge base that allows us to often predict the stability of GQs in the presence of the physiologically relevant metal ions, however, prediction of conformation of such GQs is still out of the realm.

A Thermodynamic Study of Adenine and Thymine Substitutions in the Loops of the Oligodeoxyribonucleotide HTel

Guanine-rich DNA oligodeoxyribonucleotides (ODN) can form four-stranded structures named quadruplexes (G4s), which are stabilized via the association of four guanine bases. Quadruplexes have a high level of conformational diversity depending on the molecularity, sequence, and the cation conditions of the G4 formation. Monomolecular G4 structures have nonguanine loops that usually consist of between one and four adenine and thymine residues. In the work reported here, we systematically modified the nucleotides in the loops of the 22 nucleotide ODN, HTel, which contains four repeats of the human telomeric sequence, GGGTTA. We studied the effect of different types of bases in the loops on the stability and topology of the G4s formed. We show that lower steric hindrance of pyrimidine residues increases the stability of G4s with a major enthalpic contribution. Stacking of the loop bases onto tetrads could compensate for the loss of rotational freedom. In addition, in the presence of sodium, the stabilities of the G4s are loop dependent. In the presence of potassium, the stability of G4 depend on the sequences of each loop. Lastly, in the presence of potassium ions, the modified HTel ODNs may exist in equilibrium of the two types of the hybrid topology, and these structures are stabilized by the second loop. Modifications of the bases in this loop change the topology and stability of the folded structures.

Correlations between fluorescence emission and base stacks of nucleic acid G-quadruplexes

Correlations between parallel G-quadruplex structures and featured fluorescence emission bands have been built.

Role of Alkali Metal Ions in G-Quadruplex Nucleic Acid Structure and Stability

G-quadruplexes are guanine-rich nucleic acids that fold by forming successive quartets of guanines (the G-tetrads), stabilized by intra-quartet hydrogen bonds, inter-quartet stacking, and cation coordination. This specific although highly polymorphic type of secondary structure deviates significantly from the classical B-DNA duplex. G-quadruplexes are detectable in human cells and are strongly suspected to be involved in a number of biological processes at the DNA and RNA levels. The vast structural polymorphism exhibited by G-quadruplexes, together with their putative biological relevance, makes them attractive therapeutic targets compared to canonical duplex DNA. This chapter focuses on the essential and specific coordination of alkali metal cations by G-quadruplex nucleic acids, and most notably on studies highlighting cation-dependent dissimilarities in their stability, structure, formation, and interconversion. Section 1 surveys G-quadruplex structures and their interactions with alkali metal ions while Section 2 presents analytical methods used to study G-quadruplexes. The influence of alkali cations on the stability, structure, and kinetics of formation of G-quadruplex structures of quadruplexes will be discussed in Sections 3 and 4. Section 5 focuses on the cation-induced interconversion of G-quadruplex structures. In Sections 3 to 5, we will particularly emphasize the comparisons between cations, most often K(+) and Na(+) because of their prevalence in the literature and in cells.

Seven essential questions on G-quadruplexes

The helical duplex architecture of DNA was discovered by Francis Crick and James Watson in 1951 and is well known and understood. However, nucleic acids can also adopt alternative structural conformations that are less familiar, although no less biologically relevant, such as the G-quadruplex. G-quadruplexes continue to be the subject of a rapidly expanding area of research, owing to their significant potential as therapeutic targets and their unique biophysical properties. This review begins by focusing on G-quadruplex structure, elucidating the intermolecular and intramolecular interactions underlying its formation and highlighting several substructural variants. A variety of methods used to characterize these structures are also outlined. The current state of G-quadruplex research is then addressed by proffering seven pertinent questions for discussion. This review concludes with an overview of possible directions for future research trajectories in this exciting and relevant field.

G-triplex structure and formation propensity

The occurrence of a G-triplex folding intermediate of thrombin binding aptamer (TBA) has been recently predicted by metadynamics calculations, and experimentally supported by Nuclear Magnetic Resonance (NMR), Circular Dichroism (CD) and Differential Scanning Calorimetry (DSC) data collected on a 3' end TBA-truncated 11-mer oligonucleotide (11-mer-3'-t-TBA). Here we present the solution structure of 11-mer-3'-t-TBA in the presence of potassium ions. This structure is the first experimental example of a G-triplex folding, where a network of Hoogsteen-like hydrogen bonds stabilizes six guanines to form two G:G:G triad planes. The G-triplex folding of 11-mer-3'-t-TBA is stabilized by the potassium ion and destabilized by increasing the temperature. The superimposition of the experimental structure with that predicted by metadynamics shows a great similarity, with only significant differences involving two loops. These new structural data show that 11-mer-3'-t-TBA assumes a G-triplex DNA conformation as its stable form, reinforcing the idea that G-triplex folding intermediates may occur in vivo in human guanine-rich sequences. NMR and CD screening of eight different constructs obtained by removing from one to four bases at either the 3' and the 5' ends show that only the 11-mer-3'-t-TBA yields a relatively stable G-triplex.

Structure of the human telomere in Na+ solution: an antiparallel (2+2) G-quadruplex scaffold reveals additional diversity

Single-stranded DNA overhangs at the ends of human telomeric repeats are capable of adopting four-stranded G-quadruplex structures, which could serve as potential anticancer targets. Out of the five reported intramolecular human telomeric G-quadruplex structures, four were formed in the presence of K⁺ ions and only one in the presence of Na⁺ ions, leading often to a perception that this structural polymorphism occurs exclusively in the presence of K⁺ but not Na⁺. Here we present the structure of a new antiparallel (2+2) G-quadruplex formed by a derivative of a 27-nt human telomeric sequence in Na⁺ solution, which comprises a novel core arrangement distinct from the known topologies. This structure complements the previously elucidated basket-type human telomeric G-quadruplex to serve as reference structures in Na⁺-containing environment. These structures, together with the coexistence of other conformations in Na⁺ solution as observed by nuclear magnetic resonance spectroscopy, establish the polymorphic nature of human telomeric repeats beyond the influence of K⁺ ions.

Explaining the varied glycosidic conformational, G-tract length and sequence preferences for anti-parallel G-quadruplexes

Guanine-rich DNA sequences tend to form four-stranded G-quadruplex structures. Characteristic glycosidic conformational patterns along the G-strands, such as the 5'-syn-anti-syn-anti pattern observed with the Oxytricha nova telomeric G-quadruplexes, have been well documented. However, an explanation for these featured glycosidic patterns has not emerged. This work presents MD simulation and free energetic analyses for simplified two-quartet [d(GG)](4) models and suggests that the four base pair step patterns show quite different relative stabilities: syn-anti > anti-anti > anti-syn > syn-syn. This suggests the following rule: when folding, anti-parallel G-quadruplexes tend to maximize the number of syn-anti steps and avoid the unfavorable anti-syn and syn-syn steps. This rule is consistent with most of the anti-parallel G-quadruplex structures in the Protein Databank (PDB). Structural polymorphisms of G-quadruplexes relate to these glycosidic conformational patterns and the lengths of the G-tracts. The folding topologies of G2- and G4-tracts are not very polymorphic because each strand tends to populate the stable syn-anti repeat. G3-tracts, on the other hand, cannot present this repeating pattern on each G-tract. This leads to smaller energy differences between different geometries and helps explain the extreme structural polymorphism of the human telomeric G-quadruplexes.

Influence of backbone on the charge transport properties of G4-DNA molecules: a model-based calculation

We put forward a model Hamiltonian to describe the influence of backbone energetics on charge transport through guanine-quadruplex DNA (G4-DNA) molecules. Our analytical results show that an energy gap can be produced in the energy spectrum of G4-DNA by hybridization effects between the backbone and the base and by on-site energy difference of the backbone from the base. The environmental effects are investigated by introducing different types of disorder into the backbone sites. Our numerical results suggest that the localization length of G4-DNA can be significantly enhanced by increasing the backbone disorder degree when the environment-induced disorder is sufficiently large. There exists a backbone disorder-induced semiconducting-metallic transition in short G4-DNA molecules, where G4-DNA behaves as a semiconductor if the backbone disorder is weak and behaves as a conductor if the backbone disorder degree surpasses a critical value.

Giardia telomeric sequence d(TAGGG)4 forms two intramolecular G-quadruplexes in K+ solution: effect of loop length and sequence on the folding topology

Recently, it has been shown that in K(+) solution the human telomeric sequence d[TAGGG(TTAGGG)(3)] forms a (3 + 1) intramolecular G-quadruplex, while the Bombyx mori telomeric sequence d[TAGG(TTAGG)(3)], which differs from the human counterpart only by one G deletion in each repeat, forms a chair-type intramolecular G-quadruplex, indicating an effect of G-tract length on the folding topology of G-quadruplexes. To explore the effect of loop length and sequence on the folding topology of G-quadruplexes, here we examine the structure of the four-repeat Giardia telomeric sequence d[TAGGG(TAGGG)(3)], which differs from the human counterpart only by one T deletion within the non-G linker in each repeat. We show by NMR that this sequence forms two different intramolecular G-quadruplexes in K(+) solution. The first one is a novel basket-type antiparallel-stranded G-quadruplex containing two G-tetrads, a G x (A-G) triad, and two A x T base pairs; the three loops are consecutively edgewise-diagonal-edgewise. The second one is a propeller-type parallel-stranded G-quadruplex involving three G-tetrads; the three loops are all double-chain-reversal. Recurrence of several structural elements in the observed structures suggests a "cut and paste" principle for the design and prediction of G-quadruplex topologies, for which different elements could be extracted from one G-quadruplex and inserted into another.

Folding topology of a bimolecular DNA quadruplex containing a stable mini-hairpin motif within the diagonal loop

We describe the NMR structural characterisation of a bimolecular anti-parallel DNA quadruplex d(G(3)ACGTAGTG(3))(2) containing an autonomously stable mini-hairpin motif inserted within the diagonal loop. A folding topology is identified that is different from that observed for the analogous d(G(3)T(4)G(3))(2) dimer with the two structures differing in the relative orientation of the diagonal loops. This appears to reflect specific base stacking interactions at the quadruplex-duplex interface that are not present in the structure with the T(4)-loop sequence. A truncated version of the bimolecular quadruplex d(G(2)ACGTAGTG(2))(2), with only two core G-tetrads, is less stable and forms a heterogeneous mixture of three 2-fold symmetric quadruplexes with different loop arrangements. We demonstrate that the nature of the loop sequence, its ability to form autonomously stable structure, the relative stabilities of the hairpin loop and core quadruplex, and the ability to form favourable stacking interactions between these two motifs are important factors in controlling DNA G-quadruplex topology.

Stacking and not solely topology of T3 loops controls rigidity and ammonium ion movement within d(G4T3G4)2 G-quadruplex

A solution state NMR study has shown that d(G4T3G4) in the presence of (15)NH4(+) ions folds into a single bimolecular G-quadruplex structure in which its G-tracts are antiparallel and the two T3 loops span along the edges of the outer G-quartets on the opposite sides of the G-quadruplex core. This head-to-tail topology is in agreement with the topology of the G-quadruplex recently found in the X-ray crystal structure formed by d(G4T3G4) in the presence of K(+) ions [Neidle et al. J. Am. Chem. Soc. 2006, 128, 5480]. In contrast, the presence of K(+) ions in solution resulted in a complex ensemble of G-quadruplex structures. Molecular models based on NMR data demonstrate that thymine loop residues efficiently base-base stack on the outer G-quartets and in this way stabilize a single structure in the presence of (15)NH4(+) ions. The use of heteronuclear NMR enabled us to localize three (15)NH4(+) ion binding sites between pairs of adjacent G-quartets and study the kinetics of their movement. Interestingly, no (15)NH4(+) ion movement within the G-quadruplex was detected at 25 degrees C. At 35 degrees C we were able to observe slow movement of (15)NH4(+) ions from the outer binding sites to bulk solution with the characteristic residence lifetime of 1.2 s. The slow movement of (15)NH4(+) ions from the outer binding sites into bulk solution and the absence of movement from the inner binding site were attributed to steric hindrance imposed by the T3 loops and the rigidity of the G-quadruplex.

G-quadruplex formation by human telomeric repeats-containing RNA in Na+ solution

For a long time, telomeres have been considered to be transcriptionally silent. Very recently, a breaking finding from two groups demonstrated that telomere DNA is transcribed into telomeric repeat-containing RNA in mammalian cells (Azzalin, C. M.; Reichenbach, P.; Khoriauli, L.; Giulotto, E.; Lingner, J. Science 2007, 318, 798-801. Schoefter, S.; Blasco, M. A. Nat. Cell Biol. 2008, 10, 228-236). The telomeric RNA, a newly appeared player in telomere biology, may be a key component of telomere machinery. In the current study, we used a combination of NMR, circular dichroism (CD), matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOFMS), and gel electrophoresis to investigate the structural features of a human telomere RNA sequence. We demonstrated that human telomere RNA can form a parallel G-quadruplex structure in the presence of Na(+). Importantly, we found for the first time that the G-quadruplex forming telomere RNA protects itself from enzymatic digestion. These results provide valuable information to allow understanding of the structure and function of human telomeric RNA.

Direct NMR detection of alkali metal ions bound to G-quadruplex DNA

We describe a general multinuclear (1H, 23Na, 87Rb) NMR approach for direct detection of alkali metal ions bound to G-quadruplex DNA. This study is motivated by our recent discovery that alkali metal ions (Na+, K+, Rb+) tightly bound to G-quadruplex DNA are actually "NMR visible" in solution (Wong, A.; Ida, R.; Wu, G. Biochem. Biophys. Res. Commun. 2005, 337, 363). Here solution and solid-state NMR methods are developed for studying ion binding to the classic G-quadruplex structures formed by three DNA oligomers: d(TG4T), d(G4T3G4), and d(G4T4G4). The present study yields the following major findings. (1) Alkali metal ions tightly bound to G-quadruplex DNA can be directly observed by NMR in solution. (2) Competitive ion binding to the G-quadruplex channel site can be directly monitored by simultaneous NMR detection of the two competing ions. (3) Na+ ions are found to locate in the diagonal T4 loop region of the G-quadruplex formed by two strands of d(G4T4G4). This is the first time that direct NMR evidence has been found for alkali metal ion binding to the diagonal T4 loop in solution. We propose that the loop Na+ ion is located above the terminal G-quartet, coordinating to four guanine O6 atoms from the terminal G-quartet and one O2 atom from a loop thymine base and one water molecule. This Na+ ion coordination is supported by quantum chemical calculations on 23Na chemical shifts. Variable-temperature 23Na NMR results have revealed that the channel and loop Na+ ions in d(G4T4G4) exhibit very different ion mobilities. The loop Na+ ions have a residence lifetime of 220 micros at 15 degrees C, whereas the residence lifetime of Na+ ions residing inside the G-quadruplex channel is 2 orders of magnitude longer. (4) We have found direct 23Na NMR evidence that mixed K+ and Na+ ions occupy the d(G4T4G4) G-quadruplex channel when both Na+ and K+ ions are present in solution. (5) The high spectral resolution observed in this study is unprecedented in solution 23Na NMR studies of biological macromolecules. Our results strongly suggest that multinuclear NMR is a viable technique for studying ion binding to G-quadruplex DNA.

NMR methods for studying quadruplex nucleic acids

Solution NMR spectroscopy has traditionally played a central role in examining quadruplex structure, dynamics, and interactions. Here, an overview is given of the methods currently applied to structural, dynamics, thermodynamics, and kinetics studies of nucleic acid quadruplexes and associated cations.

Bimolecular quadruplexes and their transitions to higher-order molecular structures detected by ESI-FTICR-MS

Four individual quadruplexes, which are self-assembled in ammonium acetate solution from telomeric sequences of closely related DNA strands--d(G(4)T(4)G(4)), d(G(3)T(4)G(4)), d(G(3)T(4)G(3)), and d(G(4)T(4)G(3))--have been detected in the gas phase using electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICR-MS). The bimolecular quadruplexes associate with the same number of NH(4)(+) in the gas phase as NMR shows that they do in solution. The quadruplex structures formed in solution are maintained in the gas phase. Furthermore, the mass spectra show that the bimolecular quadruplexes generated by the strands d(G(3)T(4)G(3)) and d(G(4)T(4)G(3)) are unstable, being converted into trimolecular and tetramolecular structures with increasing concentrations of NH(4)(+) in the solution. Circular dichroism (CD) spectra reveal structural changes during the process of strand stoichiometric transitions, in which the relative orientation of strands in the quadruplexes changes from an antiparallel to a parallel arrangement. Such changes were observed for the strand d(G(4)T(4)G(3)), but not for the strand d(G(3)T(4)G(3)). The present work provides a significant insight into the formation of various DNA quadruplexes, especially the higher-order species.

Not All G-Quadruplexes Exhibit Ion-Channel-like Properties: NMR Study of Ammonium Ion (Non)movement within the d(G3T4G4)2 Quadruplex

A solution-state NMR study on 15NH4(+) ion movement within d(G(3)T(4)G(4))(2), a dimeric G-quadruplex consisting of three G-quartets and two T(4) loops, rather unexpectedly demonstrated the absence of 15NH4(+) ion movement between the binding sites U and L along the central axis of the G-quadruplex. Distinct temperature dependences of autocorrelation signals for U and L binding sites have been observed in 15N-1H NzExHSQC spectra which correlate with the local stiffness of the G-quadruplex. The volumes of the cross-peaks, which are the result of 15NH4(+) ion movement, have been interpreted in terms of rate constants, T(1) relaxation, and proton exchange. 15NH4(+) ion movements from the binding sites U and L into the bulk solution are characterized by lifetimes of 139 ms and 1.7 s at 298 K, respectively. The 12 times faster movement from the binding site U demonstrates that 15NH4(+) ion movement is controlled by the structure of T4 loop residues, which through diagonal- vs edge-type orientations impose distinct steric restraints for cations to leave or enter the G-quadruplex. Arrhenius-type analysis has afforded an activation energy of 66 kJ mol(-)1 for the UB process, while it could not be determined for the LB process due to slow rates at temperatures below 298 K. We further the use of the 15NH4(+) ion as an NMR probe to gain insight into the occupancy of binding sites by cations and kinetics of ion movement which are intrinsically correlated with the structural details, dynamic fluctuations, and local flexibility of the DNA structure.

NMR evaluation of ammonium ion movement within a unimolecular G-quadruplex in solution

d[G4(T4G4)3] has been folded into a unimolecular G-quadruplex in the presence of 15NH4+ ions. NMR spectroscopy confirmed that its topology is the same as the solution state structure determined earlier by Wang and Patel (J. Mol. Biol., 1995; 251: 76-94) in the presence of Na+ ions. The d[G4(T4G4)3] G-quadruplex exhibits four G-quartets with three 15NH4+-ion-binding sites (O1, I and O2). Quantitative analysis utilizing 15NH4+ ions as a NMR probe clearly demonstrates that there is no unidirectional 15NH4+ ion movement through the central cavity of the G-quadruplex. 15NH4+ ions move back and forth between the binding sites within the G-quadruplex and exchange with ions in bulk solution. 15NH4+ ion movement is controlled by the thermodynamic preferences of individual binding sites, steric restraints of the G-quartets for 15NH4+ ion passage and diagonal versus edge-type arrangement of the T4 loops. The movement of 15NH4+ ions from the interior of the G-quadruplex to bulk solution is faster than exchange within the G-quadruplex. The structural details of the G-quadruplex define stiffness of individual G-quartets that intimately affects 15NH4+ ion movement. The stiffness of G-quartets and steric hindrance imposed by thymine residues in the loops contribute to the 5-fold difference in the exchange rate constants through the outer G-quartets.

Characterization of structure and stability of long telomeric DNA G-quadruplexes

In the current study, we used a combination of gel electrophoresis, circular dichroism, and UV melting analysis to investigate the structure and stability of G-quadruplexes formed by long telomeric DNAs from Oxytricha and human, where the length of the repeat (n)=4 to 12. We found that the Oxytricha telomeric DNAs, which have the sequence (TTTTGGGG)n, folded into intramolecular and intermolecular G-quadruplexes depending on the ionic conditions, whereas human telomeric DNAs, which have the sequence (TTAGGG)n, formed only intramolecular G-quadruplexes in all the tested conditions. We further estimated the thermodynamic parameters of the intramolecular G-quadruplex. We found that thermodynamic stabilities of G-quadruplex structures of long telomeric DNAs (n=5 to 12) are mostly independent of sequence length, although telomeric DNAs are more stable when n=4 than when n>or=5. Most importantly, when n is a multiple of four, the change in enthalpy and entropy for G-quadruplex formation increased gradually, demonstrating that the individual G-quadruplex units are composed of four repeats and that the individual units do not interact. Therefore, we propose that the G-quadruplexes formed by long telomeric DNAs (n>or=8) are bead-on-a-string structures in which the G-quadruplex units are connected by one TTTT (Oxytricha) or TTA (human) linker. These results should be useful for understanding the structure and function of telomeres and for developing improved therapeutic agents targeting telomeric DNAs.

Quadruplex DNA: sequence, topology and structure

G-quadruplexes are higher-order DNA and RNA structures formed from G-rich sequences that are built around tetrads of hydrogen-bonded guanine bases. Potential quadruplex sequences have been identified in G-rich eukaryotic telomeres, and more recently in non-telomeric genomic DNA, e.g. in nuclease-hypersensitive promoter regions. The natural role and biological validation of these structures is starting to be explored, and there is particular interest in them as targets for therapeutic intervention. This survey focuses on the folding and structural features on quadruplexes formed from telomeric and non-telomeric DNA sequences, and examines fundamental aspects of topology and the emerging relationships with sequence. Emphasis is placed on information from the high-resolution methods of X-ray crystallography and NMR, and their scope and current limitations are discussed. Such information, together with biological insights, will be important for the discovery of drugs targeting quadruplexes from particular genes.

Predictive modelling of topology and loop variations in dimeric DNA quadruplex structures

We have used a combination of simulated annealing (SA), molecular dynamics (MD) and locally enhanced sampling (LES) methods in order to predict the favourable topologies and loop conformations of dimeric DNA quadruplexes with T2 or T3 loops. This follows on from our previous MD simulation studies on the influence of loop lengths on the topology of intramolecular quadruplex structures [P. Hazel et al. (2004) J. Am. Chem. Soc., 126, 16 405–16 415], which provided results consistent with biophysical data. The recent crystal structures of d(G4T3G4)2 and d(G4BrUT2G4) (P. Hazel et al. (2006) J. Am. Chem. Soc., in press) and the NMR-determined topology of d(TG4T2G4T)2 [A.T. Phan et al. (2004) J. Mol. Biol., 338, 93–102] have been used in the present study for comparison with simulation results. These together with MM-PBSA free-energy calculations indicate that lateral T3 loops are favoured over diagonal loops, in accordance with the experimental structures; however, distinct loop conformations have been predicted to be favoured compared to those found experimentally. Several lateral and diagonal loop conformations have been found to be similar in energy. The simulations suggest an explanation for the distinct patterns of observed dimer topology for sequences with T3 and T2 loops, which depend on the loop lengths, rather than only on G-quartet stability.

Interaction of G-rich GT oligonucleotides with nuclear-associated eEF1A is correlated with their antiproliferative effect in haematopoietic human cancer cell lines

G-rich GT oligonucleotides with a different content of G clusters have been evaluated for their ability to exert cytotoxicity and to bind to nuclear-associated proteins in T-lymphoblast CCRF-CEM cells. Only the oligomers that did not form G-based structures or had a poor structure, under physiological conditions, were able to exert significant cellular growth inhibition effect. The cytotoxicity of these oligomers was related to their binding to the nuclear-associated eEF1A protein, but not to the recognition of nucleolin or other proteins. In particular, GT oligomers adopting a conformation compatible with G-quadruplex, did not exert cytotoxicity and did not bind to eEF1A. The overall results suggest that the ability of oligomers to adopt a G-quadruplex-type secondary structure in a physiological buffer containing 150 mM NaCl is not a prerequisite for antiproliferative effect in haematopoietic cancer cells. The cytotoxicity of G-rich GT oligomers was shown to be tightly related to their binding affinity for eEF1A protein.

Role of loop residues and cations on the formation and stability of dimeric DNA G-quadruplexes

Formation of guanine-quadruplexes by four DNA oligonucleotides with common sequence dG4-loop-dG4 has been studied by a combination of NMR and UV spectroscopy. The loops consisted of 1',2'-dideoxyribose, propanediol, hexaethylene glycol, and thymine residues. The comparison of data on modified and parent oligonucleotides gave insight into the role of loop residues on formation and stability of dimeric G-quadruplexes. All modified oligonucleotides fold into dimeric fold-back G-quadruplexes in the presence of sodium ions. Multiple structures form in the presence of potassium and ammonium ions, which is in contrast to the parent oligonucleotide with dT4 loop. 15N-filtered 1H NMR spectra demonstrate that all studied G-quadruplexes exhibit three 15NH4(+) ion binding sites. Topology of intermolecular G-quadruplexes was evaluated by NMR measurements and diffusion experiments. The spherical, prolate-ellipsoid and symmetric cylinder models were used to interpret experimental translational diffusion constants in terms of diameters and lengths of unfolded oligonucleotides and their respective G-quadruplexes. UV melting and annealing curves show that oligonucleotides with non-nucleosidic loop residues fold faster, exhibit no hysteresis, and are less stable than dimeric d(G4T4G4)2 which can be attributed to the absence of H-bonds, stacking between loop residues and the outer G-quartets as well as cation-pi interactions. Oligonucleotide consisting of hexaethylene glycol linkage with only two phosphate groups in the loop exhibits higher melting temperature and more negative deltaH(o) and deltaG(o) values than oligonucleotides with four 1',2'-dideoxyribose or propanediol residues.

Identification of mixed di-cation forms of G-quadruplex in solution

Multinuclear NMR study has demonstrated that G-quadruplex adopted by d(G₃T₄G₄) exhibits two cation binding sites between three of its G-quartets. Titration of tighter binding K⁺ ions into the solution of d(G₃T₄G₄)₂ folded in the presence of NH4+15 ions uncovered a mixed mono-K⁺-mono-NH4+15 form that represents intermediate in the conversion of di-NH4+15 into di-K⁺ form. Analogously, NH4+15 ions were found to replace Na⁺ ions inside d(G₃T₄G₄)₂ quadruplex. The preference of NH4+15 over Na⁺ ions for the two binding sites is considerably smaller than the preference of K⁺ over NH4+15 ions. The two cation binding sites within the G-quadruplex core differ to such a degree that NH4+15 ions bound to the site, which is closer to the edge-type loop, are always replaced first during titration by K⁺ ions. The second binding site is not taken up by K⁺ ion until K⁺ ion already resides at the first binding site. Quantitative analysis of concentrations of the three di-cation forms, which are in slow exchange on the NMR time scale, at 12 K⁺ ion concentrations afforded equilibrium binding constants. K⁺ ion binding to sites U and L within d(G₃T₄G₄)₂ is more favorable with respect to NH4+15 ions by Gibbs free energies of approximately −24 and −18 kJ mol⁻¹ which includes differences in cation dehydration energies, respectively.

d(G3T4G4) forms unusual dimeric G-quadruplex structure with the same general fold in the presence of K+, Na+ or NH4+ ions

We have recently communicated that DNA oligonucleotide d(G(3)T(4)G(4)) forms a dimeric G-quadruplex in the presence of K(+) ions [J. Am. Chem. Soc.2003, 125, 7866-7871]. The high-resolution NMR structure of d(G(3)T(4)G(4))(2) G-quadruplex exhibits G-quadruplex core consisting of three stacked G-quartets. The two overhanging G3 and G11 residues are located at the opposite sides of the end G-quartets and are not involved in G-quartet formation. d(G(3)T(4)G(4))(2) G-quadruplex represents the first bimolecular G-quadruplex where end G-quartets are spanned by diagonal (T4-T7) as well as edge-type loops (T15-T18). Three of the G-rich strands are parallel while one is anti-parallel. The G12-G22 strand demonstrates a sharp reversal in strand direction between residues G19 and G20 that is accommodated with the leap over the middle G-quartet. The reversal in strand direction is achieved without any extra intervening residues. Here we furthermore examined the influence of different monovalent cations on the folding of d(G(3)T(4)G(4)). The resolved imino and aromatic proton resonances as well as (sequential) NOE connectivity patterns showed only minor differences in key intra- and interquartet NOE intensities in the presence of K(+), Na(+) and NH(4)(+) ions, which were consistent with subtle structural differences while retaining the same folding topology of d(G(3)T(4)G(4))(2) G-quadruplex.

Molecular dynamics simulations of Guanine quadruplex loops: advances and force field limitations

A computational analysis of d(GGGGTTTTGGGG)(2) guanine quadruplexes containing either lateral or diagonal four-thymidine loops was carried out using molecular dynamics (MD) simulations in explicit solvent, locally enhanced sampling (LES) simulations, systematic conformational search, and free energy molecular-mechanics, Poisson Boltzmann, surface area (MM-PBSA) calculations with explicit inclusion of structural monovalent cations. The study provides, within the approximations of the applied all-atom additive force field, a qualitatively complete analysis of the available loop conformational space. The results are independent of the starting structures. Major conformational transitions not seen in conventional MD simulations are observed when LES is applied. The favored LES structures consistently provide lower free energies (as estimated by molecular-mechanics, Poisson Boltzmann, surface area) than other structures. Unfortunately, the predicted optimal structure for the diagonal loop arrangement differs substantially from the atomic resolution experiments. This result is attributed to force field deficiencies, such as the potential misbalance between solute-cation and solvent-cation terms. The MD simulations are unable to maintain the stable coordination of the monovalent cations inside the diagonal loops as reported in a recent x-ray study. The optimal diagonal and lateral loop arrangements appear to be close in energy although a proper inclusion of the loop monovalent cations could stabilize the diagonal architecture.

Kinetics of tetramolecular quadruplexes

The melting of tetramolecular DNA or RNA quadruplexes is kinetically irreversible. However, rather than being a hindrance, this kinetic inertia allows us to study association and dissociation processes independently. From a kinetic point of view, the association reaction is fourth order in monomer and the dissociation first order in quadruplex. The association rate constant k (on), expressed in M(-3) x s(-1) decreases with increasing temperature, reflecting a negative activation energy (E (on)) for the sequences presented here. Association is favored by an increase in monocation concentration. The first-order dissociation process is temperature dependent, with a very positive activation energy E (off), but nearly ionic strength independent. General rules may be drawn up for various DNA and RNA sequence motifs, involving 3-6 consecutive guanines and 0-5 protruding bases. RNA quadruplexes are more stable than their DNA counterparts as a result of both faster association and slower dissociation. In most cases, no dissociation is found for G-tracts of 5 guanines or more in sodium, 4 guanines or more in potassium. The data collected here allow us to predict the amount of time required for 50% (or 90%) quadruplex formation as a function of strand sequence and concentration, temperature and ionic strength.

Propeller-type parallel-stranded G-quadruplexes in the human c-myc promoter

The nuclease-hypersensitivity element III1 in the c-myc promoter is a good anticancer target since it largely controls transcriptional activation of the important c-myc oncogene. Recently, the guanine-rich strand of this element has been shown to form an equilibrium between G-quadruplex structures built from two different sets of G-stretches; two models of intramolecular fold-back antiparallel-stranded G-quadruplexes, called "basket" and "chair" forms, were proposed. Here, we show by NMR that two sequences containing these two sets of G-stretches form intramolecular propeller-type parallel-stranded G-quadruplexes in K(+)-containing solution. The two structures involve a core of three stacked G-tetrads formed by four parallel G-stretches with all anti guanines and three double-chain-reversal loops bridging three G-tetrad layers. The central loop contains two or six residues, while the two other loops contain only one residue.

15NH4+ ion movement inside d(G4T4G4)2 G-quadruplex is accelerated in the presence of smaller Na+ ions

2D NMR studies demonstrate that the residence lifetime of 15NH4+ ions within the bimolecular G-quadruplex adopted by d(G4T4G4) is reduced from 270 ms in the presence of ammonium ions alone to 36 ms in the presence of Na+ ions.

Selective interactions of ethidiums with G-quadruplex DNA revealed by surface-enhanced Raman scattering

Complexes formed between G-quadruplex (G4)-conformed oligonucleotides and four ethidium derivatives were studied by surface-enhanced Raman spectroscopy (SERS) to detail the topology of complexes that support a G4 stabilization. Ethidium bromide (EB), which presents a weak ability to stabilize oligonucleotides in G4 conformation, displayed no SERS intensity modification when bound to G4, as compared with the free EB. Three ethidium derivatives have been selected due to their higher ability to stabilize G4 than EB. Bound with G4-conformed oligonucleotides, SERS intensity of these three ethidiums decreased by factors of about 6, 3.5, and 15. The high SERS quenching was interpreted as a loss of accessibility of silver colloids for G4-bound ethidiums. This could represent a new selective parameter useful to identify G4-stabilizing molecules. To apraise the role of the oligonucleotide sequence on the interaction mode, complexes were formed with eight G4-conformed oligonucleotides in which the three loops were either 5'-TTA-3' or 5'-AAA-3'. Spectra of ethidiums were sensitive to both lateral loops, opposite to the 3' and 5' G4 ends. The sequence of these loops are believed to be selective in the interaction mode of ethidiums for G4.

Two-repeat Tetrahymena telomeric d(TGGGGTTGGGGT) Sequence interconverts between asymmetric dimeric G-quadruplexes in solution

Recently, the two-repeat human telomeric d(TAGGGTTAGGGT) sequence has been shown to form interconverting parallel and antiparallel G-quadruplex structures in solution. Here, we examine the structures formed by the two-repeat Tetrahymena telomeric d(TGGGGTTGGGGT) sequence, which differs from the human sequence only by one G-for-A replacement in each repeat. We show by NMR that this sequence forms two novel G-quadruplex structures in Na+-containing solution. Both structures are asymmetric, dimeric G-quadruplexes involving a core of four stacked G-tetrads and two edgewise loops. The adjacent strands of the G-tetrad core are alternately parallel and antiparallel. All G-tetrads adopt syn.syn.anti.anti alignments, which occur with 5'-syn-anti-syn-anti-3' alternations along G-tracks. In the first structure (head-to-head), two loops are at one end of the G-tetrad core; in the second structure (head-to-tail), two loops are located on opposite ends of the G-tetrad core. In contrast to the human telomere counterpart, the proportions of the two forms here are similar for a wide range of temperatures; their unfolding rates are also similar, with an activation enthalpy of 153 kJ/mol.

Association of DNA quadruplexes through G:C:G:C tetrads. Solution structure of d(GCGGTGGAT)

The structure formed by the DNA sequence d(GCGGTGGAT) in a 100 mM Na(+) solution has been determined using molecular dynamics calculations constrained by distance and dihedral restraints derived from NMR experiments performed at isotopic natural abundance. The sequence folds into a dimer of dimers. Each symmetry-related half contains two parallel stranded G:G:G:G tetrads flanked by an A:A mismatch and by four-stranded G:C:G:C tetrads. Each of the two juxtaposed G:C:G:C tetrads is composed of alternating antiparallel strands from the two halves of the dimer. For each single strand, a thymine intersperses a double chain reversal connecting the juxtaposed G:G:G:G tetrads. This architecture has potential implications in genetic recombination. It suggests a pathway for oligomerization involving association of quadruplex entities through GpC steps.

A thymine tetrad in d(TGGGGT) quadruplexes stabilized with Tl+/Na+ ions

We report two new structures of the quadruplex d(TGGGGT)4 obtained by single crystal X-ray diffraction. In one of them a thymine tetrad is found. Thus the yeast telomere sequences d(TG1-3) might be able to form continuous quadruplex structures, involving both guanine and thymine tetrads. Our study also shows substantial differences in the arrangement of thymines when compared with previous studies. We find five different types of organization: (i) groove binding with hydrogen bonds to guanines from a neighbour quadruplex; (ii) partially ordered groove binding, without any hydrogen bond; (iii) stacked thymine triads, formed at the 3'ends of the quadruplexes; (iv) a thymine tetrad between two guanine tetrads. Thymines are stabilized in pairs by single hydrogen bonds. A central sodium ion interacts with two thymines and contributes to the tetrad structure. (v) Completely disordered thymines which do not show any clear location in the crystal. The tetrads are stabilized by either Na+ or Tl+ ions. We show that by using MAD methods, Tl+ can be unambiguously located and distinguished from Na+. We can thus determine the preference for either ion in each ionic site of the structure under the conditions used by us.

Small change in a G-rich sequence, a dramatic change in topology: new dimeric G-quadruplex folding motif with unique loop orientations

NMR study has shown that DNA oligonucleotide d(G(3)T(4)G(4)) adopts an asymmetric bimolecular G-quadruplex structure in solution. The structure of d(G(3)T(4)G(4))(2) is composed of three G-quartets, overhanging G11 residue and G3, which is part of the loop. Unique structural feature of d(G(3)T(4)G(4))(2) fold is the orientation of the two loops. Thymidine residues T4-T7 form a diagonal loop, whereas T15-T18 form an edge type loop. The G-quadruplex core of d(G(3)T(4)G(4))(2) consists of two stacked G-quartets with syn-anti-anti-anti alternation of dG residues and one G-quartet with syn-syn-anti-anti alternation. Another unusual structural feature of d(G(3)T(4)G(4))(2) is a leap between G19 and G20 over the middle G-quartet and chain reversal between G19 and G20 residues. The presence of one antiparallel and three parallel strands reveals the hitherto unknown G-quadruplex folding motif consisting of antiparallel/parallel strands and diagonal as well as edge type loops. Further examination of the influence of different monovalent cations on the folding of d(G(3)T(4)G(4)) showed that it forms a bimolecular G-quadruplex in the presence of K+, Na+, and NH4+ ions with the same general fold.

The structure of telomeric DNA

The telomere is a nucleoprotein complex located at the ends of eukaryotic chromosomes. It is essential for maintaining the integrity of the genome. It is not a linear structure and, for much of the cell cycle, telomeric DNA is maintained in a loop structure, which serves to protect the vulnerable ends of chromosomes. Many of the key proteins in the telomere have been identified, although their interplay is still imperfectly understood and structural data are only available on a few. Telomeric DNA itself comprises simple guanine-rich repeats for most of its length, culminating in a short overhang of single-stranded sequence at the extreme 3' ends. This can, at least in vitro, fold into a wide variety of four-stranded quadruplex structures, many of whose arrangements are being revealed by crystallographic and NMR studies.