Human Telomeric G-quadruplex Structures Research Articles

Selective aggregation of natural ligands into efficient AIEgens on a human telomeric duplex-G-quadruplex junction.

DNA structures with the potential to concurrently recruit multiple ligands are promising in pharmaceutical and sensing applications when concentrated in a local environment. Herein, we found that human telomeric G-quadruplex (htG4) structures with a junction can selectively aggregate a natural ligand of tetrahydropalmatine (THP) into AIEgens. The htG4 monomer favors formation of a THP dimer emitting at ∼525 nm. In addition, only a hybrid htG4 folding supports formation of the emissive THP dimer. However, overhanging a duplex beyond the 5' end of the hybrid htG4 structure preferentially forms THP J-aggregates with member molecularity being more than two. It is demonstrated that the junction between the duplex and the hybrid htG4 structure is responsible for formation of the THP J-aggregates, as confirmed by the fact that the pairing state of the junction affects the molecularity of the J-aggregates. Nevertheless, such J-aggregates cannot be grown at the junction of two tandem htG4s. Therefore, G4-initiated ligand aggregation (GILA) for natural compounds provides a new way to design pharmaceuticals and sensors with a high local concentration at the site of interest.

Flanking Effect on the Structure and Stability of Human Telomeric G-Quadruplex in Varying Salt Concentrations.

The stability of the human telomere G-quadruplex (G4) is directly linked to cancer disease. The human telomere is mostly associated with the flanking nucleobases, which can affect the stability of G4. Hence, in this study, the effect of the flanking nucleobases in the context of their chemical nature, number, and position on the structure and stability of G4 has been investigated in varying concentrations of KCl mimicking the normal and cancer KCl microenvironments. The addition of flanking nucleobases does not alter the G4 topology. However, the presence of merely a single flanking nucleobase destabilizes the telomeric G4. This destabilizing effect is more prominent for thymine than adenine flanking nucleobase, probably due to the formation of the intermolecular G4 topology by thymine. Interestingly, the change in the stability of the telomeric G4 in the presence of thymine flanking nucleobase is sensitive to the concentration of KCl relevant to the normal and cancerous microenvironments, in contrast to adenine. Flanking nucleobases have a greater impact at the 5' end compared to the 3' end, particularly noticeable in KCl concentrations resembling the normal microenvironment rather than the cancerous one. These findings indicate that the effect of the flanking nucleobases on telomeric G4 is different in the KCl salt relevant to normal and cancerous microenvironments. This study may be helpful in attaining molecular-level insight into the role of G4 in telomeric length regulation under normal and cancerous KCl salt conditions.

Insights into the free energy landscape and salt-controlled mechanism of the conformational conversions between human telomeric G-quadruplex structures

G-quadruplexes have become attractive drug targets in cancer therapy. However, due to the polymorphism of G-quadruplex structures, it is difficult to experimentally verify the relevant structures of multiple intermediates and transition states in dynamic equilibrium. Hence, understanding the mechanism by which structural conversions of G-quadruplexes occur is still challenging. We conducted targeted molecular dynamics simulation with umbrella sampling to investigate how salt affects the conformational conversion of human telomeric G-quadruplex. Our results explore a unique view into the structures and energy barrier of the intermediates and transition states in the interconversion process. The pathway of G-quadruplex conformational interconversion was mapped out by a free energy landscape, consisting of branched parallel pathways with multiple energy basins. We propose a salt-controlled mechanism that as the salt concentration increases, the conformational conversion mechanism switches from multi-pathway folding to sequential folding pathways. The hybrid-I and hybrid-II structures are intermediates in the basket-propeller transformation. In high-salt solutions, the conformational conversion upon K+ binding is more feasible than upon Na+ binding. The free energy barrier for conformational conversions ranges from 1.6 to 4.6 kcal/mol. Our work will be beneficial in developing anticancer agents.

Spectroscopic and molecular docking studies for the binding and interaction aspects of curcumin-cysteine conjugate and rosmarinic acid with human telomeric G-quadruplex DNA

The binding and interaction aspects of potential anticancer ligands like: curcumin-cysteine (CC) and rosmarinic acid (RA) with human telomeric G-quadruplex DNA, a novel anticancer target, have been probed by spectroscopic and molecular docking approach. The circular dichroism study unravels the conformational switching from mixed hybrid to parallel structure for the short sequence of human telomeric G-quadruplex structure in the presence of both the ligands. Further a good correlation for binding affinity has been established from the emission and absorption binding spectrum analysis. Further our spectroscopic and molecular docking studies have suggested that the CC having better binding capability than RA to human telomeric G-quadruplex. The presence of L-cysteine moiety in CC ligand is responsible factor for its binding via both minor as well as major groove of human telomeric G-quadruplex DNA where-as RA binds only via minor groove of telomeric G-DNA.

POT1 stability and binding measured by fluorescence thermal shift assays.

The protein POT1 (Protection of Telomeres 1) is an integral part of the shelterin complex that protects the ends of human chromosomes from degradation or end fusions. It is the only component of shelterin that binds single-stranded DNA. We describe here the application of two separate fluorescent thermal shift assays (FTSA) that provide quantitative biophysical characterization of POT1 stability and its interactions. The first assay uses Sypro Orange™ and monitors the thermal stability of POT1 and its binding under a variety of conditions. This assay is useful for the quality control of POT1 preparations, for biophysical characterization of its DNA binding and, potentially, as an efficient screening tool for binding of small molecule drug candidates. The second assay uses a FRET-labeled human telomeric G-quadruplex structure that reveals the effects of POT1 binding on thermal stability from the DNA frame of reference. These complementary assays provide efficient biophysical approaches for the quantitative characterization of multiple aspects of POT1 structure and function. The results from these assays provide thermodynamics details of POT1 folding, the sequence selectivity of its DNA binding and the thermodynamic profile for its binding to its preferred DNA binding sequence. Most significantly, results from these assays elucidate two mechanisms for the inhibition of POT1 -DNA interactions. The first is by competitive inhibition at the POT1 DNA binding site. The second is indirect and is by stabilization of G-quadruplex formation within the normal POT1 single-stranded DNA sequence to prevent POT1 binding.

Human POT1 unfolds G-quadruplexes by conformational selection

The reaction mechanism by which the shelterin protein POT1 (Protection of Telomeres 1) unfolds human telomeric G-quadruplex structures is not fully understood. We report here kinetic, thermodynamic, hydrodynamic and computational studies that show that a conformational selection mechanism, in which POT1 binding is coupled to an obligatory unfolding reaction, is the most plausible mechanism. Stopped-flow kinetic and spectroscopic titration studies, along with isothermal calorimetry, were used to show that binding of the single-strand oligonucleotide d[TTAGGGTTAG] to POT1 is both fast (80 ms) and strong (−10.1 ± 0.3 kcal mol−1). In sharp contrast, kinetic studies showed the binding of POT1 to an initially folded 24 nt G-quadruplex structure is four orders of magnitude slower. Fluorescence, circular dichroism and analytical ultracentrifugation studies showed that POT1 binding is coupled to quadruplex unfolding, with a final complex with a stoichiometry of 2 POT1 per 24 nt DNA. The binding isotherm for the POT1-quadruplex interaction was sigmoidal, indicative of a complex reaction. A conformational selection model that includes equilibrium constants for both G-quadruplex unfolding and POT1 binding to the resultant single-strand provided an excellent quantitative fit to the experimental binding data. POT1 unfolded and bound to any conformational form of human telomeric G-quadruplex (antiparallel, hybrid, parallel monomers or a 48 nt sequence with two contiguous quadruplexes), but did not avidly interact with duplex DNA or with other G-quadruplex structures. Finally, molecular dynamics simulations provided a detailed structural model of a 2:1 POT1:DNA complex that is fully consistent with experimental biophysical results.

Abstract 1856: Targeting human telomeres by binding of epiberberine to telomeric G-quadruplex

Abstract Human telomeres play critical roles in cancer, aging, and genetic stability. Human telomeric DNA consists of tandem repeats of the sequence d(TTAGGG) and can form G-quadruplexes. G-quadruplexes are non-canonical DNA secondary structures formed in G-rich sequences, built upon the H-bonded G-tetrads and stabilized by monovalent cations such as K+ or Na+. Telomerase is a reverse transcriptase activated in 80-85% of human cancers. Small molecules that stabilize the telomeric G-quadruplex have been demonstrated to inhibit telomerase and disrupt telomere capping and maintenance, resulting in cancer cell apoptosis. Thus, the human telomeric G-quadruplex is considered an attractive target for anticancer drug development. G-quadruplexes formed in human telomeres are structurally polymorphic. The hybrid-2 G-quadruplex is the major form in the wild-type human telomeric DNA in the physiologically relevant K+ solution. Protoberberines are medicinal natural products with anticancer and anti-inflammatory activities. We show for the first time that a small molecule (epiberberine) specifically binds and induces the physiologically relevant hybrid-2 human telomeric G-quadruplex and converts other telomeric G-quadruplexes to the hybrid-2 structure, the first such small molecule reported. We determined the molecular structure of the 1:1 complex of epiberberine and hybrid-2 human telomeric G-quadruplex in K+ solution by NMR, which elucidates the molecular basis for this specific recognition. Epiberberine binding induces extensive rearrangement of the previously disordered 5′ flanking and loop segments to form an unprecedented four-layer binding pocket specific to the hybrid-2 human telomeric G-quadruplex. Epiberberine recruits the flanking (-1) adenine to form a “quasi-triad” intercalated between the external G-tetrad and a T:T:A triad, capped by a T:T base-pair. The crucial hydrogen-bonded pair is observed between epiberberine and the flanking (-1) adenine in the human telomeric sequences. This strong recognition determines the epiberberine’s ability to convert other human telomeric G-quadruplex structures to the hybrid-2 structure, regardless of the presence and types of monovalent cation in solution. The deep intercalation of epiberberine in this multi-layer binding pocket explains the significant fluorescence enhancement of epiberberine induced by human telomeric sequences in K+. Our study provides structural insights into rational design of small molecule drugs targeting the hybrid-2 G-quadruplex predominant in the human telomeres in physiologically relevant K+ solution. Furthermore, the human telomeric sequence is polymorphic in nature and various G-quadruplexes can exist in dynamic equilibrium, the discovery of epiberberine provides a potential means to study the specific protein interactions and biological functions of the hybrid-2 telomeric G-quadruplex. Citation Format: Clement Lin, Guanhui Wu, Kaibo Wang, Buket Onel, Saburo Sakai, Danzhou Yang. Targeting human telomeres by binding of epiberberine to telomeric G-quadruplex [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1856.

A propeller-like small molecule as a novel G-quadruplex DNA binder: The study of fluorescent sensing property and preferential interactions with human telo21 structure.

A new propeller-like small molecule was synthesized with three terminal amino side groups. The molecule was found to be a selective nucleic acid binder towards telo21 G-quadruplex DNA compared with other representative nucleic acids including single-stranded DNA (dA21), duplex DNA (ds26) and RNA. The fluorescent signal of the molecule upon interaction with telo21 G-quadruplex structure shows remarkable enhancement (Fmax /F0 =17.9) while interaction with other nucleic acids shows the signal enhancement which is less than 2.1. In addition, a good linear relationship of binding signal correlated with the concentration of telo21 DNA was obtained. Molecular docking study was also performed to acquire the binding behaviour and its interaction modes of the molecule with the structure of human telomeric DNA G-quadruplex. The modelling results show that the three conjugated terminal units (dimethylaminobenzyl groups) associated through the ethylene bridges with the central methylated pyridine ring formed a co-planar conformation upon stacking onto the G-quartets via pi-pi stacking interactions. This could be the key reason that the molecule shows excellent fluorescent signal of binding towards telo21 G-quadruplex DNA rather than other types of nucleic acids.

Binding properties of mono- and dimeric pyridine dicarboxamide ligands to human telomeric higher-order G-quadruplex structures.

Here, we report on the in vitro binding properties of the known pyridine dicarboxamide G-quadruplex ligand 360A and a new dimeric analogue (360A)2A to human telomeric DNA higher-order G-quadruplex (G4) structures. This study points to original binding features never reported for G4 ligands, and reveals a greater efficiency for the dimeric ligand to displace RPA (a ssDNA binding protein involved in telomere replication) from telomeric DNA.

3D QSAR AND DOCKING STUDY OF PERYLENE - DI IMIDES ANALOGUES AS POTENT APOPTOSIS INDUCER AND EFFICACIOUS ANTICANCER AGENT

The human telomeric G-Quadruplex structure is a promising target for the design of cancer drugs. The aim of this study was to investigate the anti-cancer activity of perylene derivatives by using in silico computational approach. The perylene derivatives are designed by QSAR studies using VLife MDS Software and activities for these new compounds are predicted. The best predicted activity compounds are screened by G-Quadruplex Ligand Database. Around 59 compounds are selected for docking study. Molecular docking using G-Quadruplex Ligand Database has been carried out and from the study 9 compounds showed high binding affinities for the targets. Finally, from the QSAR and docking studies, 2 compounds showed good biological activity, possessing a strong correlation coefficient, endorsing the fact that perylene derivatives are having strong affinity with the targets. With these compounds, we also observed best pKi values, which shows that they inhibit the targets and may be effective for anti-cancer therapy.

Selectivity of major isoquinoline alkaloids from Chelidonium majus towards telomeric G-quadruplex: A study using a transition-FRET (t-FRET) assay

BackgroundNatural bioproducts are invaluable resources in drug discovery. Isoquinoline alkaloids of Chelidonium majus constitute a structurally diverse family of natural products that are of great interest, one of them being their selectivity for human telomeric G-quadruplex structure and telomerase inhibition. MethodsThe study focuses on the mechanism of telomerase inhibition by stabilization of telomeric G-quadruplex structures by berberine, chelerythrine, chelidonine, sanguinarine and papaverine. Telomerase activity and mRNA levels of hTERT were estimated using quantitative telomere repeat amplification protocol (q-TRAP) and qPCR, in MCF-7 cells treated with different groups of alkaloids. The selectivity of the main isoquinoline alkaloids of Chelidonium majus towards telomeric G-quadruplex forming sequences were explored using a sensitive modified thermal FRET-melting measurement in the presence of the complementary oligonucleotide CT22. We assessed and monitored G-quadruplex topologies using circular dichroism (CD) methods, and compared spectra to previously well-characterized motifs, either alone or in the presence of the alkaloids. Molecular modeling was performed to rationalize ligand binding to the G-quadruplex structure. ResultsThe results highlight strong inhibitory effects of chelerythrine, sanguinarine and berberine on telomerase activity, most likely through substrate sequestration. These isoquinoline alkaloids interacted strongly with telomeric sequence G-quadruplex. In comparison, chelidonine and papaverine had no significant interaction with the telomeric quadruplex, while they strongly inhibited telomerase at transcription level of hTERT. Altogether, all of the studied alkaloids showed various levels and mechanisms of telomerase inhibition. ConclusionsWe report on a comparative study of anti-telomerase activity of the isoquinoline alkaloids of Chelidonium majus. Chelerythrine was most effective in inhibiting telomerase activity by substrate sequesteration through G-quadruplex stabilization. General significanceUnderstanding structural and molecular mechanisms of anti-cancer agents can help in developing new and more potent drugs with fewer side effects. Isoquinolines are the most biologically active agents from Chelidonium majus, which have shown to be telomeric G-quadruplex stabilizers and potent telomerase inhibitors.

Assessment of human telomeric G-quadruplex structures using surface-enhanced Raman spectroscopy.

G-Quadruplex (G4) structures of a human telomeric 24-mer (5'-TTAGGGTTAGGGTTAGGGTTAGGG-3') sequence (Tel24) stabilized by sodium and potassium ions have been assessed using surface-enhanced Raman scattering (SERS) spectroscopy. The distinctive SERS spectra of Tel24 in the presence of 100mM Na+ and 100mM K+ were obtained and the SERS bands characteristic of the antiparallel basket-type and the mixed hybrid (3+1) structures, respectively, were identified and assigned. The influence of the SERS - active substrate on the scattering enhancement was studied using citrate- and chloride-covered silver nanoparticles, in the absence and presence of the aggregating agent (0.1M Na2SO4 and 0.1M K2SO4). The highly reproducible SERS spectra of Tel24 obtained in various SERS active media indicated the same adsorption mechanism of the cation - stabilized G-quadruplexes onto the metal surface, regardless of the silver colloid. The remarkable resemblance between the circular dichroism (CD) spectra of the Tel24 structures with and without the colloid confirmed that interaction with the enhancing silver surface did not affectthe stability of the formed G4 structures. The presented study pointed to a great potential of the SERS spectroscopy for the sensitive structural analysis of various G4 topologies. Graphical Abstract SERS spectroscopy allowed identification of Na+ stabilized antiparallel basket-type and K+ stabilized hybrid (3+1) structures of the same 24-mer human telomeric sequence.

Probing the Folding Dynamics of Human Telomeric G-Quadruplex with Single-Molecule FRET

Guanine-rich sequences consisting of several tandem repeats of TTAGGG are abundant in human telomeric DNA. They have been shown to fold into unique secondary structures under physiological conditions. One of these is the G-quadruplex structure that can undergo complex folding pathways [1-3]. Single-molecule fluorescence microscopy combined with Forster resonance energy transfer (FRET) allows for probing the conformation and dynamics of individual G-quadruplex molecules without time and population averaging and thus resolving their structural heterogeneity that is otherwise hidden in ensemble experiments [4,5].Here we utilize single-molecule FRET microscopy to probe the K+-induced folding dynamics of human telomeric G-quadruplex DNA. Our single-molecule experiments identify several distinct FRET states populated along the folding of G-quadruplexes. We find that initial dynamic interconversion occurs between three states - the unfolded state and two transient folded states, followed by transition into a dominant long-lived folded G-quadruplex conformation. Additional single-molecule FRET measurements, employing specific chemically modified G-quadruplex sequences, and advanced molecular modeling enabled linking the experimentally observed FRET states to particular G-quadruplex conformations. Our results thus allow uncovering a possible folding pathway of the human telomeric G-quadruplex structures.(1) Bochman, M. L.; Paeschke, K.; Zakian, V. A. Nature Reviews Genetics 2012, 13, 770.(2) Biffi, G.; Tannahill, D.; McCafferty, J.; Balasubramanian, S. Nature Chemistry 2013, 5, 182.(3) Gray, R. D.; Trent, J. O.; Chaires, J. B. J. Mol. Biol. 2014, 426, 1629.(4) Single-Molecule Techniques - A Laboratory Manual; Selvin, P. R.; Ha, T., Eds.; Cold Spring Harbor, NY, 2008.(5) Lee, J. Y.; Okumus, B.; Kim, D. S.; Ha, T. J. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 18938.

Myricetin arrests human telomeric G-quadruplex structure: a new mechanistic approach as an anticancer agent.

The use of small molecules to arrest G-quadruplex structure has become a potential strategy for the development and design of a new class of anticancer therapeutics. We have studied the interaction of myricetin, a plant flavonoid and a putative anticancer agent, with human telomeric G-quadruplex TTAGGG(TTAGGG)3 DNA. Reverse transcription PCR data revealed significant repression in hTERT expression in MCF-7 breast cancer cells upon increasing the concentration of myricetin. Further, we conducted a telomeric repeat amplification protocol assay to confirm the inhibition of telomerase by myricetin. Optical spectroscopic techniques like circular dichroism, UV spectroscopy and fluorescence spectroscopy revealed the formation of a stable myricetin-G-quadruplex complex. The thermodynamic parameters of myricetin-G-quadruplex complex formation, presented through isothermal titration calorimetry studies, indicate the binding process to be thermodynamically favorable. In addition, high resolution NMR spectroscopy in conjunction with molecular dynamics simulation is employed to provide detailed mechanistic insights into the binding in the myricetin-G-quadruplex complex at the atomic level. Our results thus propose a new mode of action of myricetin as an anticancer agent via arresting telomeric G-quadruplex structure.

Folding dynamics and conformational heterogeneity of human telomeric G-quadruplex structures in Na+ solutions by single molecule FRET microscopy.

G-quadruplex structures can occur throughout the genome, including at telomeres. They are involved in cellular regulation and are potential drug targets. Human telomeric G-quadruplex structures can fold into a number of different conformations and show large conformational diversity. To elucidate the different G-quadruplex conformations and their dynamics, we investigated telomeric G-quadruplex folding using single molecule FRET microscopy in conditions where it was previously believed to yield low structural heterogeneity. We observed four FRET states in Na+ buffers: an unfolded state and three G-quadruplex related states that can interconvert between each other. Several of these states were almost equally populated at low to medium salt concentrations. These observations appear surprising as previous studies reported primarily one G-quadruplex conformation in Na+ buffers. Our results permit, through the analysis of the dynamics of the different observed states, the identification of a more stable G-quadruplex conformation and two transient G-quadruplex states. Importantly these results offer a unique view into G-quadruplex topological heterogeneity and conformational dynamics.

Pyridostatins selectively recognize two different forms of the human telomeric G-quadruplex structures and their anti-tumor activities in vitro

G-quadruplex as a therapeutic target to develop novel anti-cancer agents has attracted a growing interest. Among all the ligands of G-quadruplexes, pyridostatin derivatives play a very important role. Here, we first reported the recognition of the fundamental skeleton pyridostatin I, which was simply synthesized. Compared to pyridostatin II comprising terminal amino groups, pyridostatin I selectively stabilized intramolecular anti-parallel telomeric G-quadruplex by raising the melting temperature about 20 °C at 295 nm of H22, while pyridostatin II preferred to stabilize intermolecular parallel telomeric G-quadruplex by raising the melting temperature about 25 °C at 265 nm of H7, maybe due to the suited size measurements between G-quadruplex hosts and pyridostatin guests. MTT assays indicated that pyridostatin II had better cytotoxic effects against HCT-8 and A549 cell lines obviously, indicating positively charged side chains may be required for improving the water solubility and cellular uptake of the apolar central skeleton.

Molecular dynamics and principal components of potassium binding with human telomeric intra-molecular G-quadruplex.

Telomere assumes intra-molecular G-quadruplex that is a significant drug target for inhibiting telomerase maintenance of telomeres in cancer. Metal cations have been recognized as playing important roles in stabilizing G-quadruplex, but their binding processes to human telomeric G-quadruplex remain uncharacterized. To investigate the detailed binding procedures, molecular dynamics simulations were conducted on the hybrid [3 + 1] form-one human telomeric intra-molecular G-quadruplex. We show here that the binding of a potassium ion to a G-tetrad core is mediated by two alternative pathways. Principal component analysis illustrated the dominant concerted motions of G-quadruplex occurred at the loop domains. MM-PBSA calculations revealed that binding was energetically favorable and driven by the electrostatic interactions. The lower binding site was found more constructive favorable for binding. Our data provide useful information on a potassium-mediated stable structure of human telomeric intra-molecular G-quadruplex, implicating in ion disorder associated conformational changes and targeted drug design.Electronic supplementary materialThe online version of this article (doi:10.1007/s13238-015-0155-3) contains supplementary material, which is available to authorized users.

Positional impact of fluorescently modified G-tetrads within polymorphic human telomeric G-quadruplex structures.

Emissive C8-aryl-2'-deoxyguanosines placed within G-tetrads of G-quadruplex structures are useful probes for distinguishing G-quadruplexes from duplex structures using fluorescence spectroscopy. Here, we report the positional impact of C8-furyl-dG ((Fur)dG) on G-quadruplex folding in the human telomere 22-mer oligonucleotide (HTelo22, (d[AG3(T2AG3)3])). The (Fur)dG probe was inserted into four different positions within the three unique G-tetrads of HTelo22, and G-quadruplex folding was monitored by UV-vis thermal denaturation, circular dichroism, and fluorescence spectroscopy. Our studies demonstrate the impacts of C8-aryl-dG adduct formation on G-quadruplex polymorphism in K(+) solution and in the presence of the additives and cosolutes, CH3CN, polyethylene glycol (PEG-600), and N-methyl mesoporphyrin IX (NMM). Our experiments predict that C8-aryl-dG derivatives can serve as useful tools for various in vitro studies aimed at understanding both the implications of DNA adduct formation within G-quadruplex structures and the unique implications imposed by various folding topologies on biological function/recognition.

Molecular crowding effects on conformation and stability of G-quadruplex DNA structure: Insights from molecular dynamics simulation

Intracellular space is highly crowded with different biomolecules such as proteins, nucleic acids and ions. Therefore molecular crowding is a crucial factor in determining the structure, stability and function of G-quadruplexs. The effect of crowding on the DNA G-quadruplexes structure and stability has been studied by experimental methods, but it hasn’t been known how crowding agents stabilize the G-quadruplex structure in molecular level yet. Here, we present a molecular dynamics investigation over the effect of molecular crowding, imitated here by ethanol, on the stability of G-quadruplex structure both in presence and absence of stabilizing K+ cations. It was demonstrated that G-quadruplex structure in the water collapses in the absence of this cation, while ethanol stabilizes the structure of G-quadruplex by the excluded volume and decreases the water activity. The presence of ethanol can increase the stability of the Hoogsteen hydrogen bonds within the G-quartet. To understand the importance of cations, simulation has been performed on the cation containing G-quadruplex in the presence of ethanol with different concentrations. Molecular dynamics simulations of the structure and stability of human telomeric G-quadruplex in ethanol containing solution has enhanced our understanding on how the parallel-stranded G-quadruplex is affected in a condition where the water content is reduced.

Correction: Structure and Stability of Human Telomeric G-Quadruplex with Preclinical 9-Amino Acridines

This article was republished on December 3rd, 2013 because of incorrect figure order. Please download this article again to view the figures.