Parallel G-quadruplex DNA Research Articles

Interaction of water soluble phthalocyanine compounds with parallel and hybrid G-quadruplex DNA molecules

G-quadruplex DNAs are secondary DNA structures formed in guanine-rich genome sequences, such as telomeres. Due to the increased metabolic activities of cancer cells, the formation probability of G-quadruplex structures increases. Since the formation of G-quadruplex structures and their stabilization with various ligands prevents DNA’s turning into straight strands, which are necessary for some processes such as transcription and translation, it may cause disruptions in cell proliferation. Therefore, these DNA constructs are important for anticancer drug targets. In the present study, the interactions of water-soluble MnPc and ZnPc compounds with G-quadruplex DNAs with parallel and hybrid conformation were investigated. KD constants were calculated with spectroscopic titration data. Stoichiometric ratios of DNA-phthalocyanine interactions were determined by Job’s method and found between 1:1 to 1:2 for MnPc and 1:1 for ZnPc. The effect of phthalocyanine on the G-quadruplex conformation was investigated by circular dichroism (CD) spectroscopy. Capillary gel electrophoresis studies supported the existence of interactions. DNA polymerase stop assay further supported stabilizing AS1411 and Tel21 G-quadruplex structures with Pc compounds. This work is on a molecular level study. The in vitro and in vivo images can be different because MPcs are localized in the cytoplasmic organelles but rare in the nucleus.

Parallel G-Quadruplex DNA Structures from Nuclear and Mitochondrial Genomes Trigger Emission Enhancement in a Nonfluorescent Nano-aggregated Fluorine-Boron-Based Dye.

Molecular self-assembly is a powerful tool for the development of functional nanostructures with adaptive optical properties. However, in aqueous solution, the hydrophobic effects in the monomeric units often afford supramolecular architectures with typical side-by-side π-stacking arrangement with compromised emissive properties. Here, we report on the role of parallel DNA guanine quadruplexes (G4s) as supramolecular disaggregating-capture systems capable of coordinating a zwitterionic fluorine-boron-based dye and promoting activation of its fluorescence signal. The dye's high binding affinity for parallel G4s compared to nonparallel topologies leads to a selective disassembly of the dye's supramolecular state upon contact with parallel G4s. This results in a strong and selective disaggregation-induced emission that signals the presence of parallel G4s observable by the naked eye and inside cells. The molecular recognition strategy reported here will be useful for a multitude of affinity-based applications with potential in sensing and imaging systems.

GW-2974 and SCH-442416 modulators of tyrosine kinase and adenosine receptors can also stabilize human telomeric G-quadruplex DNA.

GW-2974 is a potent tyrosine kinase receptor inhibitor while SCH-442416 is a potent adenosine receptors' antagonist with high selectivity towards human adenosine A2A receptor over other adenosine receptors. The two compounds were reported to possess anti-cancer properties. This study aimed to investigate whether stabilization of human telomeric G-quadruplex DNA by GW-2974- and SCH-442416 is a plausible fundamental mechanism underlying their anti-cancer effects. Human telomeric G-quadruplex DNA with sequence AG3(TTAGGG)3 was used. The study used ultraviolet-visible (UV-Vis), fluorescence, fluorescence quenching, circular dichroism (CD), melting temperatures (Tm) and molecular docking techniques to evaluate interactions. The results showed that GW-2974 and SCH-442416 interacted with G-quadruplex DNA through intercalation binding into two types of dependent binding sites. Binding affinities of 1.3 × 108-1.72 × 106 M-1 and 1.55 × 107-3.74 × 105 M-1 were obtained for GW-2974 and SCH-442416, respectively. An average number of binding sites between 1 and 2 was obtained. Additionally, the melting temperature curves indicated that complexation of both compounds to G-quadruplex DNA provided more stability (ΔTm = 9.9°C and 9.6°C, respectively) compared to non-complexed G-quadruplex DNA. Increasing the molar ratios over 1:1 (drug:G-quadruplex) showed less stabilization effect on DNA. Furthermore, GW-2974 and SCH-442516 have proven ≥ 4.0 folds better selective towards G-quadruplex over double-stranded ct-DNA. In silico molecular docking and dynamics revealed favorable exothermic binding for the two compounds into two sites of parallel and hybrid G-quadruplex DNA structures. The results supported the hypothesis that GW-2974 and SCH-442416 firmly stabilize human telomeric G-quadruplex DNA in additions to modulating tyrosine kinase and adenosine receptors. Consequently, stabilizing G-quadruplex DNA could be a mechanism underlying their anti-cancer activity.

Interaction of 9-Methoxyluminarine with Different G-Quadruplex Topologies: Fluorescence and Circular Dichroism Studies.

The interactions of G–quadruplexes of different topologies with highly fluorescent 9-methoxyluminarine ligand 9-MeLM were investigated by fluorescence and circular dichroism spectroscopy. The results showed that 9-methoxyluminarine was able to interact and did not destabilize any investigated molecular targets. The studied compound was selectively quenched by parallel c-MYC G-quadruplex DNA, whereas hybrid and antiparallel G4 topology caused only a negligible decrease in the fluorescence of the ligand. A high decrease of fluorescence of the ligand after binding with c-MYC G-quadruplex suggests that this molecule can be used as a selective probe for parallel G-quadruplexes.

Spectroscopic and In Silico Studies on the Interaction of Substituted Pyrazolo[1,2-a]benzo[1,2,3,4]tetrazine-3-one Derivatives with c-Myc G4-DNA.

Herein we describe a combined experimental and in silico study of the interaction of a series of pyrazolo[1,2-a]benzo[1,2,3,4]tetrazin-3-one derivatives (PBTs) with parallel G-quadruplex (GQ) DNA aimed at correlating their previously reported anticancer activities and the stabilizing effects observed by us on c-myc oncogene promoter GQ structure. Circular dichroism (CD) melting experiments were performed to characterize the effect of the studied PBTs on the GQ thermal stability. CD measurements indicate that two out of the eight compounds under investigation induced a slight stabilizing effect (2–4 °C) on GQ depending on the nature and position of the substituents. Molecular docking results allowed us to verify the modes of interaction of the ligands with the GQ and estimate the binding affinities. The highest binding affinity was observed for ligands with the experimental melting temperatures (Tms). However, both stabilizing and destabilizing ligands showed similar scores, whilst Molecular Dynamics (MD) simulations, performed across a wide range of temperatures on the GQ in water solution, either unliganded or complexed with two model PBT ligands with the opposite effect on the Tms, consistently confirmed their stabilizing or destabilizing ability ascertained by CD. Clues about a relation between the reported anticancer activity of some PBTs and their ability to stabilize the GQ structure of c-myc emerged from our study. Furthermore, Molecular Dynamics simulations at high temperatures are herein proposed for the first time as a means to verify the stabilizing or destabilizing effect of ligands on the GQ, also disclosing predictive potential in GQ-targeting drug discovery.

Selective alkylation of parallel G-quadruplex structure.

The selective alkylation of nucleic acids is important for a medicinal approach and biological study. We now report a novel selective alkylation of the parallel G-quadruplex structure using the conjugate of the macrocyclic hexaoxazole L2G2-6OTD-1M1PA and vinyl-quinazolinone-S(O)Me (6OTD-VQ-S(O)Me).

Three-Dimensional Structure of RNA Monomeric G-Quadruplex Containing ALS and FTD Related G4C2 Repeat and Its Binding with TMPyP4 Probed by Homology Modeling based on Experimental Constraints and Molecular Dynamics Simulations.

The G-quadruplex-forming hexanucleotide repeat expansion (HRE), d(G4C2)n, within the human C9orf72 gene is the root cause for familial amyotrophic lateral sclerosis-frontotemporal dementia (ALS-FTD). A recent study has shown that TMPyP4 has good potential to work as a RNA G-quadruplex binder in treating ALS and FTD. Although the high-resolution structure of the monomeric DNA antiparallel G-quadruplex form of the monomeric hexanucleotide repeat was recently solved, the RNA parallel G-quadruplex structure and its complex with TMPyP4 are not available yet. In this study, we first constructed the homology model for the parallel monomeric RNA G-quadruplex of r(G4C2)3G4 based on experimental constraints and the parallel monomeric G-quadruplex DNA crystal structure. Although the G-tetra core of the homology model was stable observed in 15 μs molecular dynamics (MD) simulations, we observed that the loops adopt additional conformations besides the initial crystal conformation, where TMPyP4 binding was found to reduce the loop fluctuation of the RNA monomeric G-quadruplex. Next, we probed the elusive binding behavior of TMPyP4 to the RNA monomeric G-quadruplex. Encouragingly, the binding modes observed are similar to the modes observed in two experimental complexes of a parallel DNA G-quadruplex with TMPyP4. We also constructed a Markov state model to provide insights into the binding pathways. Together, the findings from our study may assist future development of G-quadruplex-specific ligands in the treatment of neurodegenerative diseases like ALS and FTD.

Binding of anticancer drug adriamycin to parallel G-quadruplex DNA [d-(TTAGGGT)]4 comprising human telomeric DNA leads to thermal stabilization: A multiple spectroscopy study.

Adriamycin is known to exert its anti cancer action by inhibiting DNA duplication, RNA transcription and topoisomerase-II enzyme action. Recent findings of its binding to G-quadruplex DNA resulting in telomere dysfunction indicated multiple strategies of its action. The interaction of anticancer drug adriamycin 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 to understand mode of their interaction. The adriamycin binds as monomer to G-quadruplex DNA with affinity (Kb1 = 9.8x105 M-1 and Kb2 = 6.7x105 M-1 ) higher than that reported for daunomycin, at two independent sites, mainly in terminal stacking and groove binding modes. The bound complex formed as a result of specific interactions induces thermal stabilization of DNA by 12.5-28.1°C, which is likely to hinder telomere association with telomerase enzyme and contribute significantly to adriamycin-induced apoptosis in cancer cell lines. The findings have therapeutic potential towards drug designing by way of altering substituent groups on anthracyclines to enhance efficacy using additional mechanism of targeting pathway of telomere maintenance by disrupting telomerase association with telomeres.

Substituent dependent selectivity of fluorescent chemosensors derived from coumarin for biologically relevant DNA structures and anions

In this study, we describe facile synthesis of a series of coumarin appended Schiff base chemosensors for the detection of spesific anions such as F−, CN−, AcO−, and H2PO4−. The sensors have been also employed for signaling singlestranded, doublestranded, as well as parallel, anti-parallel and hybrid G-quadruplex DNA structures and increased specificity was detected towards CN− and parallel G-quadruplex structure. The substituents and their positions (ortho, meta, or para) in relation to the OH impacted significantly on the sensing of the anions as well as the acidity of the OH group, in the recognition of the anions. The deprotonation and addition sensing mechanisms of the probes were investigated through UV–vis, fluorimetric, and NMR titration methods. The two signalling mechanisms also have been confirmed using DFT calculations. The bias studies of all the compounds indicated an immediate visible fluorescence change when CN was added to a partial aqueous mixture of DMSO/tap water (6:4, v/v). Furthermore, the chemosensor were studied in neutral and basic mixtures of DMSO/buffer (6:4, v/v) for absorption and emission spectra in the presence and absence of CN−. In the case of DNA structures, up to 5.5-fold fluorescence enhancement was observed in the presence of parallel G-quadruplex as compared with only 1.3-fold in the presence of duplex DNA. Molecular docking studies revealed that, the selectivity is as a result of increased number of H-bonds between DNA and 2b due to modified substituent. In a nutshell, all the fluorophores can be employed in sensing CN− in partial aqueous solution, while 2a, 2b, 2e and 2f showed strong selectivity towards parallel G-quadruplexes over other DNA topologies. Thermal studies of the compounds have shown that the compounds have enough thermal stability properties for application as optic dye.

Photoinduced binding of malachite green copolymer to parallel G-quadruplex DNA.

Designing ligands that selectively target G-quadruplex DNAs has gained attention due to their possible roles in regulation of gene expression and as anti-cancer agents. In this article, we report irradiation-induced ligand binding to G-quadruplex DNAs which offers a novel approach to targeting specific G-quadruplexes. Photoinduced binding to G-quadruplex DNAs was observed for copolymers of poly(vinyl alcohol) carrying a malachite green moiety (PVAMG). This molecule has an aromatic ring with cationic charge, which after irradiation becomes a binding site for G-quadruplex DNA. PVAMGs acted as neutral polymers with no binding affinity under dark conditions. The photoinduced binding was revealed by fluorescence spectroscopy, NMR spectroscopy, UV melting curve, and DNA polymerase stop assay. PVAMGs showed preference to parallel G-quadruplex structures over mixed parallel/antiparallel structures. PVAMGs were found to be noncytotoxic under both dark and irradiated conditions up to a concentration of 20 μM.

Pif1 helicase unfolding of G-quadruplex DNA is highly dependent on sequence and reaction conditions

In addition to unwinding double-stranded nucleic acids, helicase activity can also unfold noncanonical structures such as G-quadruplexes. We previously characterized Pif1 helicase catalyzed unfolding of parallel G-quadruplex DNA. Here we characterized unfolding of the telomeric G-quadruplex, which can fold into antiparallel and mixed hybrid structures and found significant differences. Telomeric DNA sequences are unfolded more readily than the parallel quadruplex formed by the c-MYC promoter in K+ Furthermore, we found that under conditions in which the telomeric quadruplex is less stable, such as in Na+, Pif1 traps thermally melted quadruplexes in the absence of ATP, leading to the appearance of increased product formation under conditions in which the enzyme is preincubated with the substrate. Stable telomeric G-quadruplex structures were unfolded in a stepwise manner at a rate slower than that of duplex DNA unwinding; however, the slower dissociation from G-quadruplexes compared with duplexes allowed the helicase to traverse more nucleotides than on duplexes. Consistent with this, the rate of ATP hydrolysis on the telomeric quadruplex DNA was reduced relative to that on single-stranded DNA (ssDNA), but less quadruplex DNA was needed to saturate ATPase activity. Under single-cycle conditions, telomeric quadruplex was unfolded by Pif1, but for the c-MYC quadruplex, unfolding required multiple helicase molecules loaded onto the adjacent ssDNA. Our findings illustrate that Pif1-catalyzed unfolding of G-quadruplex DNA is highly dependent on the specific sequence and the conditions of the reaction, including both the monovalent cation and the order of addition.

Binding of anticancer drug daunomycin to parallel G-quadruplex DNA [d-(TTGGGGT)]4 leads to thermal stabilization: A multispectroscopic investigation

Guanine rich DNA sequences form four stranded G-quadruplex structures found in telomeric DNA and oncogene promoters. Small molecules binding and stabilizing the G-quadruplex disrupt telomere maintenance and gene regulation, thereby limiting the proliferation of cancer cells. The anti-cancer drug daunomycin binds to both G-quadruplex DNA and duplex DNA. We have undertaken a study of interaction of daunomycin to [d-(TTGGGGT)]4 comprising telomeric DNA sequence from Tetrahymena thermophilia to understand the mechanisms of its action. Absorbance, fluorescence and circular dicroism spectra show significant change on interaction with no change in wavelength maxima. The daunomycin dimers present in free state in solution are disrupted on binding. Presence of all sequential short inter proton distance contacts in nuclear magnetic resonance spectra confirm external binding. The observed inter molecular nuclear Overhauser enhancements, changes in chemical shift and molecular docking studies establish well defined binding of daunomycin at two different sites of G-quadruplex DNA. Thermal stabilization of [d-(TTGGGGT)]4 by 10–15 °C upon daunomycin binding is expected to reduce access of telomerase to its functional site at telomeres. The present studies on mode of action pave the way for alternate derivatives/analogues by chemical modification of anthracyclines to arrive at a more potent telomerase inhibitor.

Thiazole Orange-Modified Carbon Dots for Ratiometric Fluorescence Detection of G-Quadruplex and Double-Stranded DNA.

A new carbon dot (CD)-based nanoprobe for the ratiometric fluorescence detection of DNA was constructed in this work. Thiazole orange (TO), a specific organic small molecular probe toward DNA, is covalently linked to the surface of CDs, acting as the recognition element and the fluorescence response unit. In the absence of DNA, the nanoprobe only emitted the blue fluorescence of CDs, whereas TO was almost nonfluorescent. Upon addition of DNA, a turn-on emission at 530 nm appeared and gradually enhanced along with the increasing of the target DNA, whereas the fluorescence of CDs was unchanged, which realized the ratiometric detection of the target DNA. The CD-TO nanoprobe showed good selectivity to parallel G-quadruplex (G4) and double-stranded (ds) DNA over antiparallel G4 and single-stranded DNA. Moreover, the ratiometric fluorescence nanoprobe exhibited high sensitivity for ssab (a dsDNA) and c-myc (a parallel G4) with a low detection limit of 0.90 and 3.31 nM, respectively. Additionally, the G4/hemin peroxidase activity inhibition experiment demonstrated that CD-TO bound to the G4s through the end-stacking mode.

Structural and biophysical insight into dual site binding of the protoberberine alkaloid palmatine to parallel G-quadruplex DNA using NMR, fluorescence and Circular Dichroism spectroscopy

Plant derived small molecules, which interact with and stabilize G-quadruplex DNA, act as inhibitors of telomere elongation and oncogene expression in humans. The inhibition of telomerase enzyme has immense potential since it is over expressed in most cancer cells. Interaction of palmatine, an antitumor alkaloid, to parallel G-quadruplex DNA, [d(TTGGGGT)]4 and [d(TTAGGGT)]4, has been investigated using Nuclear Magnetic Resonance (NMR), fluorescence and Circular Dichroism (CD) spectroscopy. Titrations were monitored by 1H and 31P NMR spectra and solution structure of palmatine-[d(TTGGGGT)]4 complex was obtained by restrained Molecular Dynamics (rMD) simulations using distance restraints from 2D NOESY spectra. Thermal stabilization of DNA was determined by CD, 1H NMR and Differential Scanning Calorimetry (DSC). Binding of palmatine induces 98% enhancement of fluorescence accompanied by blue shift ∼8 nm. CD spectral bands of DNA show minor changes. Diffusion NMR studies confirm formation of a stable complex. Proton NMR signals of palmatine shift upfield upon binding and NOE cross peaks of H10, H3, H28, 5OCH3 protons with T2, A3/G3, G6 and T7 residues reveal dual recognition sites in both G-quadruplex DNA sequences, resulting in thermal stabilization of G-quadruplex by ∼13–17 °C. Restrained molecular dynamics simulations using NOE distance restraints for 2:1 palmatine-[d(TTGGGGT)]4 complex reveal end-stacking of palmatine at G6pT7 step and groove binding along T2pG3 step. Binding to [d(TTAGGGT)]4 takes place at T2pA3pG4 and G6pT7 steps. Structural features of molecular recognition of two different G-quadruplex DNA sequences by palmatine have relevance in rational drug development for anti-cancer therapy.

WITHDRAWN: Structural and biophysical insight into dual site binding of the protoberberine alkaloid palmatine to parallel G-quadruplex DNA using NMR, fluorescence and circular dichroism spectroscopy

The Publisher regrets that this article is an accidental duplication of an article that has already been published, http://dx.doi.org/10.1016/j.biochi.2018.02.002. The duplicate article has therefore been withdrawn. The full Elsevier Policy on Article Withdrawal can be found at https://www.elsevier.com/about/our-business/policies/article-withdrawal.

Naturally occurring quaternary benzo[c]phenanthridine alkaloids selectively stabilize G-quadruplexes.

In this work, the interaction of six natural benzo[c]phenanthridine alkaloids (macarpine, sanguilutine, sanguirubine, chelerythrine, sanguinarine and chelirubine) with parallel and antiparallel G-quadruplex DNA structures was studied. HT22 corresponding to the end of human telomeres and the modified promoter oncogene c-kit21 and Pu22 sequences have been used. Spectroscopically-monitored melting experiments and fluorescence titrations, competitive dialysis and nuclear magnetic resonance spectroscopy were used for this purpose. The results showed that these alkaloids stabilized G-quadruplex structures in terms of increments of Tm values (from 15 to 25 °C) with high selectivity over duplexes and unfolded DNA. The mode of binding was mainly by stacking on the terminal G-tetrads with stoichiometries of 1 : 2 (DNA : ligand). The presence of non-specific electrostatic interactions was also observed. Overall, the results pointed to a strong stabilization of G-quadruplex structures by these alkaloids.

NMR based structural studies decipher stacking of the alkaloid coralyne to terminal guanines at two different sites in parallel G-quadruplex DNA, [d(TTGGGGT)]4 and [d(TTAGGGT)

BackgroundTelomere elongation by telomerase gets inhibited by G-quadruplex DNA found in its guanine rich region. Stabilization of G-quadruplex DNA upon ligand binding has evolved as a promising strategy to target cancer cells in which telomerase is over expressed. MethodsInteraction of anti-leukemic alkaloid, coralyne, to tetrameric parallel [d(TTGGGGT)]4 (Ttel7), [d(TTAGGGT)]4 (Htel7) and monomeric anti-parallel [dGGGG(TTGGGG)3] (Ttel22) G-quadruplex DNA has been studied using Circular Dichroism (CD) spectroscopy. Titrations of coralyne with Ttel7 and Htel7 were monitored by 1H and 31P NMR spectroscopy. Solution structure of coralyne-Ttel7 complex was obtained by restrained Molecular Dynamics (rMD) simulations using distance restraints from 2D NOESY spectra. Thermal stabilization of DNA was determined by absorption, CD and 1H NMR. Results and conclusionsBinding of coralyne to Ttel7/Htel7 induces negative CD band at 315/300nm. A significant upfield shift in all GNH, downfield shift in T2/T7 base protons and upfield shift (1.8ppm) in coralyne protons indicates stacking interactions. 31P chemical shifts and NOE contacts of G3, G6, T2, T7 protons with methoxy protons reveal proximity of coralyne to T2pG3 and G6pT7 sites. Solution structure reveals stacking of coralyne at G6pT7 and T2pG3 steps with two methoxy groups of coralyne located in the grooves along with formation of a hydrogen bond. Binding stabilizes Ttel7/Htel7 by ~25–35°C in 2:1 coralyne-Ttel7/Htel7 complex. General significanceThe present study is the first report on solution structure of coralyne-Ttel7 complex showing stacking of coralyne with terminal guanine tetrads leading to significant thermal stabilization, which may be responsible for telomerase inhibition.

Characterization of the interaction between heme and a parallel G-quadruplex DNA formed from d(TTGAGG)

Structure-function relationships of complexes between heme and G-quadruplex DNAs have attracted interest from researchers in related fields. A carbon monoxide adduct of a complex between heme and a parallel G-quadruplex DNA formed from hexanucleotide d(TTGAGG) (heme-[d(TTGAGG)]4 complex) has been characterized using 1H NMR spectroscopy, and the obtained results were compared with those for the heme-[d(TTAGGG)]4 complex previously studied in order to elucidate the effect of the incorporation of an A-quartet into stacked G-quartets in the 3′-terminal region of the DNA on the structure of the heme-DNA complex. We found that a π-π stacking interaction between the porphyrin moiety of the heme and the 3′-terminal G-quartet of the DNA is affected by the nature of the stacked G-quartets. This finding provides novel insights as to the design of the molecular architecture of a heme-DNA complex.This article is part of a Special Issue entitled "G-quadruplex" Guest Editor: Dr. Concetta Giancola and Dr. Daniela Montesarchio.

Binding of the alkaloid coralyne to parallel G-quadruplex DNA [d(TTGGGGT)]4 studied by multi-spectroscopic techniques

Binding of coralyne to tetra-molecular parallel G-quadruplex DNA [d(TTGGGGT)]4 was evaluated for the first time using biophysical techniques. Absorbance titrations show hypo/hyper-chromism accompanied by 12nm red shift with binding constant Kb=0.2–4.0×106M−1. Binding induces a negative circular dichroism band of coralyne at 315nm. Quenching of fluorescence (~64%) along with 10nm blue shift in emission maxima indicates proximity of coralyne to guanine bases. Job plot indicates existence of multiple complexes. The observed two fluorescence life times, 6 and 12ns, with relative abundance 33% and 63%, respectively suggest two binding sites/conformations in complex. 1D 1H NMR spectra reveal significant broadening and upfield shift of G3NH, G6NH and G3H8 proton signals upon binding. The NOESY spectra reveal sequence specific non-intercalative interaction of coralyne in monomeric form at two sites close to A3/G3 and G6 bases of [d(TTGGGGT)]4 and [d(TTAGGGT)]4, which has implications in anti-cancer drug action.

Nuclear magnetic resonance studies reveal stabilization of parallel G-quadruplex DNA [d(T2G4T)]4 upon binding to protoberberine alkaloid coralyne

Stabilization of G-quadruplex DNA structures in human telomeric and proto-oncogenic promoter regions upon ligand binding has evolved as a viable anti-cancer strategy. We have studied interaction of coralyne, a human telomerase inhibiting protoberberine alkaloid, with parallel stranded tetrameric G-quadruplex DNA [d(T2G4T)]4 using Circular Dichroism (CD) and nuclear magnetic resonance (NMR) spectroscopy. Appearance of induced CD band and the Diffusion Ordered NMR Spectroscopy (DOSY) experiments confirm the formation of well defined coralyne–DNA complex. 1H and 31P NMR studies reveal that coralyne specifically recognizes T2pG3 and G6pT7 steps in DNA. Guanine imino protons indicate that coralyne binding induces thermal stabilization of the G-quadruplex DNA by >20°C. The observed specific changes and thermal stabilization of DNA upon binding may be attributed to inhibition of telomerase by coralyne.