key: cord-0954645-9yj7j4ba
authors: Yang, Danzhou
title: G-Quadruplex DNA and RNA
date: 2019-08-23
journal: G-Quadruplex Nucleic Acids
DOI: 10.1007/978-1-4939-9666-7_1
sha: ff1be979fed9e2b6048aed72fe3e5919e0306444
doc_id: 954645
cord_uid: 9yj7j4ba

G-quadruplexes (G4s) have become one of the most exciting nucleic acid secondary structures. A noncanonical, four-stranded structure formed in guanine-rich DNA and RNA sequences, G-quadruplexes can readily form under physiologically relevant conditions and are globularly folded structures. DNA is widely recognized as a double-helical structure essential in genetic information storage. However, only ~3% of the human genome is expressed in protein; RNA and DNA may form noncanonical secondary structures that are functionally important. G-quadruplexes are one such example which have gained considerable attention for their formation and regulatory roles in biologically significant regions, such as human telomeres, oncogene-promoter regions, replication initiation sites, and 5′- and 3′-untranslated region (UTR) of mRNA. They are shown to be a regulatory motif in a number of critical cellular processes including gene transcription, translation, replication, and genomic stability. G-quadruplexes are also found in nonhuman genomes, particularly those of human pathogens. Therefore, G-quadruplexes have emerged as a new class of molecular targets for drug development. In addition, there is considerable interest in the use of G-quadruplexes for biomaterials, biosensors, and biocatalysts. The First International Meeting on Quadruplex DNA was held in 2007, and the G-quadruplex field has been growing dramatically over the last decade. The methods used to study G-quadruplexes have been essential to the rapid progress in our understanding of this exciting nucleic acid secondary structure.

G-quadruplexes (G4s) are noncanonical four-stranded nucleic acid structures formed in guanine-rich DNA and RNA sequences ( Fig. 1) . They have emerged as one of the most exciting nucleic acid secondary structures. DNA is widely recognized as a doublehelical structure essential in genetic information storage. Results from the ENCODE project [1] indicate that only~3% of the human genome is expressed in protein and that RNA and DNA may form noncanonical secondary structures that are functionally important. G-quadruplexes are one such example which have gained considerable attention for their formation and regulatory 

G-quadruplexes have been found to form in specific human guanine-rich sequences with functional significance, such as telomeres, oncogene-promoter regions, and 5 0 -and 3 0 -untranslated region (UTR) of mRNA, as well as in nonhuman genomes.

The first biologically relevant G-quadruplex was observed in telomeric DNA. Telomeres are specific DNA-protein complexes at the ends of linear chromosomes, providing protection against gene erosion from cell divisions, chromosomal nonhomologous end-joinings, and nuclease attacks [19] [20] [21] . Telomeric G-quadruplexes were first reported as novel intramolecular structures containing guanine-guanine base-pairs in single-stranded telomeric sequences of several organisms [22] , and as guaninetetrads between hairpin loops of the Tetrahymena telomeric DNA [23] . The importance of monovalent cations in the stabilization of G-quadruplex structures was revealed by Williamson, Cech in their monovalent cation-induced square-planar G-quartet model using the Oxytricha and Tetrahymena telomeric DNA [14] . Human telomeres consist of tandem repeats of the hexanucleotide d (TTAGGG) n 5-10 kb in length, which terminate in a singlestranded 3 0 -overhang of 35-600 bases [24] . Telomeres of cancer cells do not shorten upon replication, mainly due to the activation of a reverse transcriptase, telomerase, that extends the telomeric sequence at the chromosome ends [25] . Telomerase is activated in 80-85% of human cancer cells to maintain telomere length and malignant phenotype [25] [26] [27] . The G-quadruplex formation can inhibit the activity of telomerase [28] , making it an attractive target for cancer therapeutic intervention. In addition to the formation at the telomere end, which most likely involves intramolecular G-quadruplex structures, intermolecular G-quadruplex formation may also be involved in the T-loop invasion complex [29, 30] . Recently, telomeric repeat-containing RNA (TERRA) G-quadruplex was identified and found to inhibit telomerase [31, 32] .

Human telomeric DNA is structurally polymorphic and may adopt different intramolecular G-quadruplex conformations, including two equilibrating hybrid-type structures [33-39] and a 2-tetrad structure [40] [41] [42] 

More recently, DNA G-quadruplexes were found to form in the gene promoter regions and function as transcriptional regulators [53, 54] , which has been the most active area for G-quadruplex DNA in the past decade. The first experiments that suggested the existence of unusual forms of DNA associated with runs of guanines in gene promoters were reported in 1982 for the chicken β-globulin gene based upon the nuclease hypersensitivity of promoter elements [55] [56] [57] . Since then, the occurrence of these elements in the human gene promoters has been reported, including in those of insulin . The potential occurrence of DNA G-quadruplexes has been discovered in the promoter regions of human genes involved in growth and proliferation [53, 78, 79] ; these genes all contain G-rich/C-rich tracts in the proximal regions of promoters and are mostly TATAless. In addition, the potential for quadruplex formation is higher within oncogenes as compared to tumor suppressor genes [80] . Computational analyses showed significant enrichment of G-quadruplex-forming sequences in the promoter regions of human genes near transcription start sites (TSS) [81] . The driving force of the formation of promoter G-quadruplexes appears to be the transcription-induced dynamic negative superhelicity [82] [83] [84] [85] . The c-MYC gene promoter is the most extensively studied system for the promoter G-quadruplex [54, 86] . A highly conserved G-rich nuclease hypersensitivity element III 1 in the proximal region of the c-MYC promoter controls 80-90% of the transcriptional activity regardless of whether the P1 or P2 promoter is used [87] [88] [89] [90] . This element in the c-MYC promoter is highly dynamic in its conformation [91] , and can form G-quadruplex structures, which function as a transcriptional silencer [54, 59] .

In contrast to the repeating tandems in the telomeric sequence, the promoter G-quadruplex-forming sequences are each unique in their number and length of G-tracts and intervening bases. The promoter G-rich sequences often contain more than four G-tracts with unequal numbers of guanines and can form multiple G-quadruplexes through utilizing varying combinations of G-tracts or different loop isomers through utilizing varying guanines on one G-tract [18] . Parallel structures are common to the promoter G-quadruplexes, usually with a three-tetrad core. Structural studies showed that each promoter G-quadruplex adopts . A notable feature in the promoter G-quadruplexes is the prevalence of the G 3 NG 3 motif, a robust parallel-stranded structural motif with a 1-nt propeller loop. This motif was first observed in the major G-quadruplex structure formed in the c-MYC promoter, which showed that the 1-nt propeller loop conformation is highly favored [ [109] [110] [111] . The variations in promoter G-quadruplexes give rise to different overall structure properties that could be specifically recognized by proteins or small-molecule ligands for transcriptional regulation. Moreover, inherent polymorphism and equilibrium between different conformations may provide an additional layer of transcriptional modulation.

G-quadruplexes have been found in other regions of the human genome, such as immunoglobulin class switch regions [112] [113] [114] , ribosomal DNA [115] , mitochondrial DNA [116] [117] [118] [119] , replication initiation regions [120] , the LINE-1 retrotransposon [121] [122] [123] , DNA:RNA hybrid-G-quadruplexes in transcription [124] , as well as in the extended repeat sequences in neurodegenerative diseases at both DNA and RNA levels, such as the (CGG) n repeat in the 5 0 -UTR of the FMR1 gene in the Fragile X syndrome (FXS) [125] [126] [127] 

G-quadruplexes have been identified in nonhuman genomes. As in the human genome, these G-quadruplexes predominantly occur in regions of regulatory importance. Particularly, G-quadruplexes are found in genomes of human pathogens [144] . Many examples of G-quadruplexes were identified in viruses [145, 146] , including human immunodeficiency virus (HIV) [147] [148] [149] [150] , multiple species of herpes virus [151] [152] [153] [154] [155] , human papillomavirus (HPV) [156] , hepatitis C [157] , Zika [158] , Ebola [159] , and a G-quadruplexbinding protein was found in severe acute respiratory syndrome (SARS) coronavirus [160] . In bacteria, G-quadruplexes are found in Escherichia coli [161] , Neisseria gonorrhoeae [162] , Neisseria meningitidis [163] , Mycobacterium tuberculosis [164] , and Deinococcus radiodurans [165] . G-quadruplexes were also found in ciliates [14], malaria parasites [166, 167] , and yeasts [168, 169] . Notably, helicases that resolve G-quadruplex structures, such as RecQ [170, 171] and Pif1 [142] families, were found in both nonhuman and human systems. Most recently, the presence of G-quadruplexes in plant genomes has also emerged [172] .

There has been significant progress in the detection of G-quadruplexes structures in vivo [173] . The first direct evidence of the in vivo existence of G-quadruplexes was established by using G-quadruplex-specific single chain variable fragment (scFv) of an antibody to detect G-quadruplexes formed at telomeres in macronuclei of the ciliate Stylonychia lemnae, which was shown to be cell cycle-dependent [174] and controlled by telomere end-binding proteins TEBPα and TEBPβ phosphorylation [175] . More recently, using a G-quadruplex-specific antibodies BG4 (scFv) [176] and 1H6 (monoclonal antibody) [177] , G-quadruplex structures were visualized in human cells at both telomeric and non-telomeric sites on chromosomes, and G4-loci number increased after exposure of live cells to G-quadruplex ligands [176] or in the absence of FANCJ, a G-quadruplex DNA-specific helicase [177] . Using BG4 to map endogenous G-quadruplex structures by G4 ChIP-seq in human cells,~10,000 endogenous G-quadruplex structures were detected in immortalized precancerous HaCaT cells, 10 times higher than in normal human NHEK cells [178] . G-quadruplex structures were found to be enriched in nucleosome-depleted regulatory regions including the promoters, such as c-MYC, and 5 0 UTRs, of highly transcribed genes. The detected G-quadruplexes in cells account for less than 1% of the genomic G4-sites identified by G4-seq [179] or predicted by G4 algorithms [81] , suggesting the in vivo formation of G-quadruplex is highly context-dependent. In addition, the endogenous potential G4 sites were detected in live human cells by chemical footprinting combined with high-throughput sequencing and were found to enrich in regions involving chromatin reorganization and gene transcription [180] . G-quadruplex formation in vivo was also detected by small molecules probes, such as the radiolabeled Gquadruplex-ligands 360A [181] , and fluorescent G-quadruplexligands BMVC [182, 183] and DAOTA-M2 [184] .

Recognition of the biological significance of G-quadruplexes has promoted research and development of G-quadruplex-interactive small molecule ligands (G4-ligands). The identification of genomic G-quadruplex structures in regions of functional importance, such as human telomeres and oncogene promoters, has created the opportunity to selectively target these globular DNA structures for cancer-specific drug development [17, [185] [186] [187] [188] [189] [190] . The therapeutic possibilities of targeting telomeric G-quadruplexes to inhibit telomerase were first reported in 1997 [191] and have been actively pursued [185] [186] [187] [188] . G-quadruplex-ligands were also shown to inhibit the alternative lengthening of telomeres (ALT) pathway which maintains telomere stability in a telomerase-independent manner in~15% of cancer cells [192] [193] [194] [195] . The discovery of the perylene derivative PIPER to inhibit helicase Sgs1-mediated G-quadruplex unfolding suggested the existence of a broader mechanism for G-quadruplex-ligands [196] . In 2002, a small molecule that stabilizes the G-quadruplex formed in the c-MYC promoter was shown to inhibit c-MYC expression, suggesting therapeutic opportunity of targeting promoter G-quadruplexes for transcriptional modulation [54, 197] . Different groups of compounds, such as quindolines and ellipticines, were reported to suppress c-MYC transcription by stabilization of the c-MYC promoter G-quadruplex [198] [199] [200] [201] . Subsequently, transcriptional repression of other oncogenes was shown by compounds stabilizing promoter G-quadruplexes, such as c-KIT [202] , BCL-2 [203] , KRAS [204] [205] [206] . More recently, G-quadruplex-stabilizing compounds were shown to cause DNA damage and genomic instability and exhibit synergistic effect with inhibitors or deficiency of DNA-repair mechanisms [207] [208] [209] [210] [211] . Specifically, G-quadruplexstabilizing compounds were shown to induce selective lethality in BRCA-deficient cancers by targeting the inherent DNA doublestrand break (DSB) repair deficiency [212, 213] .

A G-quadruplex targeting drug, Quarfloxin (CX-3543) [115] , based on the fluoroquinolone compounds developed by Laurence Hurley [214, 215] showed excellent in vivo activity in various solid tumors and had reached Phase II clinical trials. Its secondgeneration compound, CX-5461, is currently in clinical trials for BRCA1/2 deficient tumors (Canadian trial, NCT02719977) [213] . Diverse families of other small molecule compounds that interact with G-quadruplexes were developed and studied. For example, TMPyP4, a tetra-(N-methyl-4-pyridyl)-porphyrin, is a structure-based designed compound that exhibits significant selectivity for quadruplex DNA over duplex DNA and inhibits telomerase and ALT [216, 217] . Its positional isomer TMPyP2 is a poor G-quadruplex-interactive compound and can be used as a negative control of TMPyP4 [218] . Later studies revealed that TMPyP4 interacts with the c-MYC promoter G-quadruplex and downregulates c-MYC [54, 197] . TMPyP4 and TMPyP2 have been one of the most widely used molecules in G-quadruplex research. Telomestatin is a natural product isolated from Streptomyces anulatus 3533-SV4 to be a highly potent inhibitor of telomerase [219] and active against human cancers by stabilizing telomeric G-quadruplex and inhibit telomere-protein binding [220] [221] [222] [223] . BRACO19 is a rationally designed trisubstituted acridine to directly target telomeric G-quadruplex [224] and was shown to inhibit telomerase and induce telomere uncapping in human cancer cells [195] and have high in vivo activity against different cancer xenograft models [225, 226] . 12459 is a triazine G4-ligand that exhibits anti-telomerase activity but also appears to involve BCL-2 and hTERT splicing [192, 227, 228] . Closely related pyridine dicarboxamide derivatives 360A/307A and bisquinolinium compounds Phen-DC(3)/Phen-DC(6) are highly selective G-quadruplex ligands and were shown to be active against both telomeric and c-MYC G-quadruplex and inhibit c-MYC gene transcription in tumor cells, as well as bind to a G-quadruplex formed in the 5 0 -UTR of TRF2 mRNA to repress translation [133, [229] [230] [231] [232] . Phen-DC was also shown to trigger genetic instability in Saccharomyces cerevisiae [207] . PDS is a pyridostatin compound which shows potent G-quadruplex-stabilization and has been widely used to study G-quadruplex functions and G-quadruplex-induced DNA damage [176, [210] [211] [212] 233] . In addition, G-quadruplex DNA was also shown to be potential cancer therapeutics. AS1411 (Antisoma, London, UK) is an unmodified 26-nt G-quadruplex forming oligonucleotide that has been in Phase II trials for treatment of renal cancer and acute myeloid leukemia [234] .

G-quadruplex-interactive compounds have contributed immensely to understanding G-quadruplex functions and potential as a therapeutic target. Different G-quadruplex-ligands show various levels of selectivity, between G-quadruplex structures over other forms of DNA and between different G-quadruplexes, and this selectivity is likely to be related to their biological activity. Conventional and in silico screening methods as well as structure-based rational drug design were actively pursued in the development of G-quadruplex-targeting small molecules. A common feature among the G-quadruplex-ligands is the presence of a fused ring system that is capable of stacking with the terminal G-tetrads. In addition, a crescent-shaped asymmetric pharmacophore that can recruit a DNA base and cationic side chain substituents that have the propensity to interact with G-quadruplex grooves can give rise to specific interactions (Fig. 1d) [235, 236] . Structural data of G-quadruplex-ligand complexes has been playing an important role in the understanding of small molecule recognition of G-quadruplexes and the design of G-quadruplex-ligands [18, 237] . This includes a handful NMR solution structures of intramolecular G-quadruplex-ligand complexes, including c-MYC G-quadruplex-ligand complexes [235, [238] [239] [240] and telomeric G-quadruplex-ligand complexes [236, [241] [242] [243] , and X-ray crystallographic structures of intramolecular and intermolecular telomeric G-quadruplex-ligand complexes [43, 237, [244] [245] [246] [247] [248] [249] [250] .

A wide variety of experimental tools and methods have been utilized or developed for studying G-quadruplex DNA and RNA. These methods play a pivotal role in enabling researchers to gain an understanding of G-quadruplex structures, properties, and functions. The methods commonly used for studying G-quadruplexes include biophysical, biochemical, molecular biology, and cellular methods, as described in this book.

Biophysical methods are widely used to study physical properties of G-quadruplex such as structures, stability, and binding interactions with ligands and proteins. Circular dichroism (CD) is widely used to study G-quadruplex conformations and stability. Isothermal titration calorimetry (ITC) can directly measure binding enthalpies and provide thermodynamic characterization of G-quadruplex-ligand interactions. Biosensor-surface plasmon resonance (SPR) is a quantitative approach for the study of small molecule and protein ligand-quadruplex nucleic acid interactions in real time. Analytical ultracentrifugation (AUC) method can be used to characterize G-quadruplex formation and to monitor ligand binding. Mass spectroscopy can also be used to characterize G-quadruplex structures and ligand binding. Differential scanning calorimetry (DSC) can be used to obtain thermodynamic and sometimes kinetic parameters of G-quadruplexes. X-ray crystallography and solution NMR spectroscopy provide structural information of G-quadruplexes and ligand complexes, while molecular dynamics simulation can also be used to study G-quadruplex structures and small molecule binding.

Biochemical and molecular biology methods are used to study G-quadruplex formation, functions, and protein interactions. Electrophoretic mobility shift assay (EMSA), dimethyl sulfate (DMS) footprinting, and DNA polymerase stop (Pol-stop) assay are widely used to study G-quadruplex formation, protein complexes, and ligand interactions. Chromatin immunoprecipitation (ChIP) assays are used to probe protein interactions with G-quadruplex-forming DNA sequences. A combination of biochemical and biophysical methods can be used to monitor co-transcriptional formation of G-quadruplexes (transcription assay) and to quantitatively analyze the effects of G-quadruplex formation on DNA replication (replication assay). Single-molecule methods such as optical and magnetic tweezers, atomic-force microscopy (AFM), and singlemolecule fluorescence resonance energy transfer (FRET) microscopy can be used to investigate G-quadruplex conformations, ligand interactions, and protein interactions. In addition, methods are used to discover and develop G-quadruplex-targeting molecules, such as FRET-based high-throughput screening of small molecule ligands, and peptide nucleic acid (PNA) oligomers that are designed to bind to G-quadruplexes. G-quadruplexes are also used in nanoparticle-based assays, and as biocatalysts such as G-quadruplex DNAzymes.

More recent and exciting developments include in-cell methods to study the G-quadruplex formation in vivo, such as in vivo chemical footprinting, G-quadruplex detection and visualization, and in-cell NMR. Chemical probing for G-quadruplex formation inside living cells combined with high-throughput sequencing can provide a snapshot of the DNA conformation over the whole genome in vivo. G4-specific antibodies and fluorescence probes are used to detect and visualize G-quadruplexes in cells. NMR spectroscopy is used to study G-quadruplex structures inside living Xenopus laevis oocytes, while 19 F NMR can be used to study G-quadruplex conformation in vitro and in living cells.

In conclusion, it is our hope that the protocols described herein will be found both informative and useful. 

An integrated encyclopedia of DNA elements in the human genome

An improved model for the hTERT promoter quadruplex

A pharmacological chaperone molecule induces cancer cell death by restoring tertiary DNA structures in mutant hTERT promoters

Formation of parallel four-stranded complexes by guanine-rich motifs in DNA and its implications for meiosis

Intracellular transcription of G-rich DNAs induces formation of G-loops, novel structures containing G4 DNA

MutS[alpha] binds to and promotes synapsis of transcriptionally activated immunoglobulin switch regions

Anticancer activity of CX-3543: a direct inhibitor of rRNA biogenesis

G-quadruplex structures in RNA stimulate mitochondrial transcription termination and primer formation

A hybrid G-quadruplex structure formed between RNA and DNA explains the extraordinary stability of the mitochondrial R-loop

DNA sequences proximal to human mitochondrial DNA deletion breakpoints prevalent in human disease form G-quadruplexes, a class of DNA structures inefficiently unwound by the mitochondrial replicative twinkle helicase

Direct evidence of mitochondrial G-quadruplex DNA by using fluorescent anti-cancer agents

Unraveling cell type-specific and reprogrammable human replication origin signatures associated with G-quadruplex consensus motifs

The ability to form intrastrand tetraplexes is an evolutionarily conserved feature of the 3 0 end of L1 retrotransposons

G-quadruplex structures within the 3 0 UTR of LINE-1 elements stimulate retrotransposition

Mechanism and manipulation of DNA:RNA hybrid G-quadruplex formation in transcription of G-rich DNA

The fragile-X syndrome D(Cgg)(N) nucleotide repeats form a stable tetrahelical structure

Cgg repeats associated with DNA instability and chromosome fragility form structures that block DNA-synthesis in-vitro

Microarray identification of FMRP-associated brain mRNAs and virus 1 genomic RNA

A dynamic G-quadruplex region regulates the HIV-1 long terminal repeat promoter

Formation of a unique cluster of G-quadruplex structures in the HIV-1 Nef coding region: implications for antiviral activity

U3 region in the HIV-1 genome adopts a G-quadruplex structure in its RNA and DNA sequence

Role for G-quadruplex RNA binding by Epstein-Barr virus nuclear antigen 1 in DNA replication and metaphase chromosome attachment

The herpes simplex virus-1 genome contains multiple clusters of repeated G-quadruplex: implications for the antiviral activity of a G-quadruplex ligand

Genome-wide analysis of G-quadruplexes in herpesvirus genomes

G-quadruplex-interacting compounds alter latent DNA replication and episomal persistence of KSHV

Stabilization of telomere G-quadruplexes interferes with human herpesvirus 6A chromosomal integration

Human papillomavirus G-quadruplexes

A highly conserved G-rich consensus sequence in hepatitis C virus core gene represents a new anti-hepatitis C target

Zika virus genomic RNA possesses conserved G-quadruplexes characteristic of the flaviviridae family

Ebola virus derived G-quadruplexes: thiazole orange interaction

A G-quadruplex-binding macrodomain within the "SARS-unique domain" is essential for the activity of the SARS-coronavirus replication-transcription complex

Genome-wide prediction of G4 DNA as regulatory motifs: role in Escherichia coli global regulation

An alternative DNA structure is necessary for pilin antigenic variation in neisseria gonorrhoeae

Sequence, distribution and chromosomal context of class I and class II pilin genes of Neisseria meningitidis identified in whole genome sequences

Mycobacterium tuberculosis DinG is a structure-specific helicase that unwinds G4 DNA implications for targeting g4 dna as a novel therapeutic approach

Genome-wide study predicts promoter-G4 DNA motifs regulate selective functions in bacteria: radioresistance of D. radiodurans involves G4 DNA-mediated regulation

Putative DNA G-quadruplex formation within the promoters of Plasmodium falciparum var genes

Recombination events among virulence genes in malaria parasites are associated with G-quadruplex-forming DNA motifs

Genomic distribution and functional analyses of potential G-quadruplex-forming sequences in Saccharomyces cerevisiae

Rudimentary G-quadruplex-based telomere capping in Saccharomyces cerevisiae

RecQ helicases: caretakers of the genome

Evidence that a RecQ helicase slows senescence by resolving recombining telomeres

G quadruplex in plants: a ubiquitous regulatory element and its biological relevance

DNA G-quadruplexes in the human genome: detection, functions and therapeutic potential

In vitro generated antibodies specific for telomeric guanine-quadruplex DNA react with Stylonychia lemnae macronuclei

Telomere end-binding proteins control the formation of G-quadruplex DNA structures in vivo

Quantitative visualization of DNA G-quadruplex structures in human cells

Detection of G-quadruplex DNA in mammalian cells

G-quadruplex structures mark human regulatory chromatin

High-throughput sequencing of DNA G-quadruplex structures in the human genome

Permanganate/S1 nuclease footprinting reveals non-B DNA structures with regulatory potential across a mammalian genome

Preferential binding of a G-quadruplex ligand to human chromosome ends

BMVC: a potential antitumor agent and fluorescence marker of cancer cells

A handheld device for potential point-of-care screening of cancer

The interactions between a small molecule and G-quadruplexes are visualized by fluorescence lifetime imaging microscopy

G-quadruplexes as targets for drug design

DNA and its associated processes as targets for cancer therapy

G-quadruplex DNA: a target for drug design

Telomere maintenance as a target for anticancer drug discovery

Targeting G-quadruplexes in gene promoters: a novel anticancer strategy?

Quadruplex nucleic acids as targets for anticancer therapeutics

Inhibition of human telomerase by a G-quadruplex-interactive compound

Cell senescence and telomere shortening induced by a new series of specific G-quadruplex DNA ligands

Potent inhibition of telomerase by small-molecule pentacyclic acridines capable of interacting with G-quadruplexes

Evaluation of by disubstituted acridone derivatives as telomerase inhibitors: the importance of G-quadruplex binding

A G-quadruplex telomere targeting agent produces p16-associated senescence and chromosomal fusions in human prostate cancer cells

10-perylenetetracarboxylic diimide, a Gquadruplex-interactive ligand

The cationic porphyrin TMPyP4 downregulates c-MYC and human telomerase reverse transcriptase expression and inhibits tumor growth in vivo

Stabilization of G-quadruplex DNA and downregulation of oncogene c-myc by quindoline derivatives

Inhibition of myc promoter and telomerase activity and induction of delayed apoptosis by SYUIQ-5, a novel G-quadruplex interactive agent in leukemia cells

Novel molecular mechanism for actinomycin D activity as an oncogenic promoter G-quadruplex binder

Demonstration that drug-targeted downregulation of MYC in non-hodgkins lymphoma is directly mediated through the promoter G-quadruplex

G-quadruplex-binding benzo[a]phenoxazines down-regulate c-KIT expression in human gastric carcinoma cells

Turning off transcription of the bcl-2 gene by stabilizing the bcl-2 promoter quadruplex with quindoline derivatives

Synthesis, G-quadruplex stabilisation, docking studies, and effect on cancer cells of indolo[3,2-b] quinolines with one, two, or three basic side chains

KRAS oncogene repression in colon cancer cell lines by G-quadruplex binding indolo

A G-quadruplex-binding compound showing anti-tumour activity in an in vivo model for pancreatic cancer

Genetic instability triggered by G-quadruplex interacting Phen-DC compounds in Saccharomyces cerevisiae

is activated at telomeres upon G4 stabilization: possible target for telomere-based therapy

Inhibition of helicase activity by a small molecule impairs Werner syndrome helicase (WRN) function in the cellular response to DNA damage or replication stress

Small-molecule-induced DNA damage identifies alternative DNA structures in human genes

G-quadruplex DNA as a molecular target for induced synthetic lethality in cancer cells

Tarsounas M (2016) Targeting BRCA1 and BRCA2 deficiencies with G-quadruplex-interacting compounds

CX-5461 is a DNA G-quadruplex stabilizer with selective lethality in BRCA1/2 deficient tumours

Design and synthesis of fluoroquinophenoxazines that interact with human telomeric G-quadruplexes and their biological effects

Design, synthesis, and biological evaluation of a series of fluoroquinoanthroxazines with contrasting dual mechanisms of action against topoisomerase II and G-Quadruplexes

Cationic porphyrins as telomerase inhibitors: the interaction of tetra-(N-methyl-4-pyridyl)porphine with quadruplex DNA

The different biological effects of telomestatin and TMPyP4 can be attributed to their selectivity for interaction with intramolecular or intermolecular G-quadruplex structures

Interactions of TMPyP4 and TMPyP2 with quadruplex DNA. Structural basis for the differential effects on telomerase inhibition

Telomestatin, a novel telomerase inhibitor from Streptomyces anulatus

Telomestatin, a potent telomerase inhibitor that interacts quite specifically with the human telomeric intramolecular G-quadruplex

Telomerase inhibition with a novel Gquadruplex-interactive agent, telomestatin: in vitro and in vivo studies in acute leukemia

The G-quadruplex ligand telomestatin inhibits POT1 binding to telomeric sequences in vitro and induces GFP-POT1 dissociation from telomeres in human cells

G-Quadruplex stabilization by telomestatin induces TRF2 protein dissociation from telomeres and anaphase bridge formation accompanied by loss of the 3 0 telomeric overhang in cancer cells

Structure-based design of selective and potent G-quadruplexmediated telomerase inhibitors

Overcoming the immortality of tumour cells by telomere and telomerase based cancer therapeutics -current status and future prospects

The G-quadruplex-interactive molecule BRACO-19 inhibits tumor growth, consistent with telomere targeting and interference with telomerase function

Overexpression of Bcl-2 is associated with apoptotic resistance to the G-quadruplex ligand 12459 but is not sufficient to confer resistance to long-term senescence

Telomerase downregulation induced by the G-quadruplex ligand 12459 in A549 cells is mediated by hTERT RNA alternative splicing

Stabilization of the c-myc gene promoter quadruplex by specific ligands' inhibitors of telomerase

Apoptosis related to telomere instability and cell cycle alterations in human glioma cells treated by new highly selective G-quadruplex ligands

Quadruplex ligands may act as molecular chaperones for tetramolecular quadruplex formation

Highly efficient G-quadruplex recognition by bisquinolinium compounds

BRCT domains: phosphopeptide binding and signaling modules

Discovery and development of the G-rich oligonucleotide AS1411 AS a novel treatment for cancer

Solution structure of a 2:1 quindoline-c-MYC G-quadruplex: insights into G-quadruplexinteractive small molecule drug design

Molecular recognition of the hybrid-2 human telomeric G-quadruplex by epiberberine: insights into conversion of telomeric g-quadruplex structures

The structures of quadruplex nucleic acids and their drug complexes

Small-molecule interaction with a five-guanine-tract G-quadruplex structure from the human MYC promoter

Solution structure of a G-quadruplex bound to the bisquinolinium compound Phen-DC(3)

NMR structure of a triangulenium-based long-lived fluorescence probe bound to a G-quadruplex

Solution structure of an intramolecular (3 + 1) human telomeric G-quadruplex bound to a telomestatin derivative

Solution NMR structure of a ligand/hybrid-2-Gquadruplex complex reveals rearrangements that affect ligand binding

Solution structures of multiple G-quadruplex complexes induced by a platinum (II)-based tripod reveal dynamic binding

Structure of the first parallel DNA quadruplex-drug complex

Structure of a G-quadruplex-ligand complex

Structural basis for binding of porphyrin to human telomeres

Topology conservation and loop flexibility in quadruplex-drug recognition: crystal structures of inter-and intramolecular telomeric DNA quadruplex-drug complexes

Structural basis of DNA quadruplex recognition by an acridine drug

Structural basis for telomeric G-quadruplex targeting by naphthalene diimide ligands

The crystal structure of human telomeric DNA complexed with berberine: an interesting case of stacked ligand to G-tetrad ratio higher than 1:1

This research was supported by the National Institutes of Health, R01CA122952, 1R01 GM083117, R01CA177585, and P30CA023168 (Purdue Center for Cancer Research).