TABLE 1.
Representative list of rG4 structure-targeting tools with their binding characteristics and biological effects
| Name | Target rG4 | Biophysical approaches | Biological effects | Reference |
|---|---|---|---|---|
| Small molecules | ||||
| TMPyP4 | NRAS rG4, KRAS rG4 | UV-Vis and fluorescence titrations, Job plot (target:ligand = 4:1), fluorescence spectroscopy (Kd = 301 ± 45 nM [NRAS]) | Cell lines used: Panc-1; inhibit KRAS and NRAS expression. | Ferino et al. 2020 |
| TERRA rG4 | UV-Vis absorption spectroscopy (redshift: 20 nm, hypochromicity: 35%), fluorescence spectroscopy (Kd = 1.92 × 106 M−1), induced circular dichroism (ICD), extensive triplet decay kinetics experiments, Job plot (1:1), NMR | NA | Qi et al. 2019 | |
| miRNA-1587 G4 | Circular dichroism (CD) | Cell lines used: HeLa; unwind G4 and enhances miRNA-1587 regulation of the target mRNA. | Li et al. 2019 | |
| Pre-miRNA-149 G4 | CD titrations, UV-Vis absorption spectroscopy (redshift: 20 nm, hypochromicity: 65%, Kd = 240 nM), Isothermal Titration Calorimetry (ITC), NMR | Cell lines used: MCF-7; restore endogenous miRNA-149 expression and inhibit cell proliferation. | Ghosh et al. 2019 | |
| FMR1 r(CGG) n G4 | Native gel electrophoresis | Cell lines used: HEK293; unwind G4 and enhance mRNA expression. | Ofer et al. 2009 | |
| MT3-MMP rG4 | UV-Vis absorption spectroscopy (redshift: 22 nm, hypochromicity: 75%), CD, NMR, native gel electrophoresis | Cell lines used: HeLa; unwind G4 and enhance reporter gene expression. | Morris et al. 2012 | |
| C9orf72 r(GGGGCC)8 repeat G4 | Native gel electrophoresis, visible absorption spectroscopy (redshift: 17 nm, hypochromicity: 64%), CD, UV melting | Unwind G4 and block interaction of RNA-binding proteins. | Zamiri et al. 2014 | |
| SARS-CoV-2 rG4 | CD melting (ΔTm = 23.8°C) | Cell lines used: Vero E6; inhibit SARS-CoV-2 RNA expression, SARS-CoV-2 infection (EC50 = 8.87 μM), and lung inflammation in virus-infected animal models. | Qin et al. 2022 | |
| Zaire ebolavirus L rG4 | CD melting (ΔTm = 11.9°C), competitive fluorescence spectroscopy, native gel electrophoresis | Cell lines used: BSR-T7; inhibit EBOV L-RNA expression. | Wang et al. 2016b | |
| HCV rG4 | CD melting, native gel electrophoresis | Cell lines used: HEK293, Huh-7.5.1; stabilize HCV rG4s and inhibit HCV C gene expression and HCV replication in host cells. | Wang et al. 2016a | |
| rG4 in 3′ UTR of immediate early gene (IE180) of PRV | CD, NMR | Cell lines used: HEK293, PK-15; destabilize IE180 rG4, inhibit IE180 expression and PRV replication. | Zhang et al. 2020b | |
| LANA rG4 of Kaposi's sarcoma-associated herpes virus (KSHV) | NA | Cell lines used: BCBL-1, BJAB-LYFP, B3Z, HEK293; inhibit LANA expression. | Dabral et al. 2020 | |
| ZIKV rG4 | ITC | Cell lines used: CCL-81; inhibit ZIKV growth, viral protein synthesis and genome replication in host cells. | Majee et al. 2021 | |
| TMPyP4-C14 | KRAS rG4 | UV-Vis titrations (Kd = 4.7 [±0.6] × 10−7 M [utr1], 3.4 [±0.1] × 10−7 M [utr2]), fluorescence quenching titrations (Kd = 2.8 [±0.5] × 10−7 M [utr2]) | Cell lines used: Panc-1; inhibit endogenous KRAS expression and cell growth. | Faudale et al. 2012 |
| Alkyl cationic porphyrins 2b/2d | KRAS rG4, NRAS rG4 | KRAS rG4: UV-Vis and fluorescence titrations (redshift: 13 nm, hypochromicity: ca. 50% [2b]), Job plot (target:ligand = 6:1 [2b], 9:1 [2d]); NRAS rG4: fluorescence spectroscopy (Kd = 107 ± 11 nM [2b], 32 ± 8 nM [2d]) | Cell lines used: Panc-1; inhibit KRAS and NRAS expression, metabolic activity of pancreatic cancer cells (EC50 (48 h) = 13.7 ± 0.7 nM [2b], 16.4 ± 2.1 nM [2d]), and the growth of a Panc-1 xenograft in SCID mice. | Ferino et al. 2020 |
| PDS | EWSR1 rG4 | Fluorescence titrations (Kd = 4.6 µM) | Cell lines used: TC32, SKNMC, HCT116, PC3, HEK-293T, RD-ES, TC71; block interaction of rG4-binding protein (IC50 = 7.7 μM) and inhibit cell viability (IC50 = 14 μM [TC32], 4.8 μM [SKNMC]). | Neckles et al. 2019 |
| HNF4a rG4 | NA | Inhibit HNF4a expression. | Guo and Lu 2017 | |
| EBNA1 rG4 | FRET melting | Cell lines used: HEK293, B3Z; stabilize EBNA1 rG4 and inhibit EBNA1 expression and antigen presentation. | Murat et al. 2014 | |
| ZIKV rG4 | Surface plasmon resonance (KA = 107–108 M−1), CD melting (ΔTm = 4.6°C–21°C), ITC, immunofluorescence assay (IFA) | Inhibit ZIKV infection (EC50 = 4.2 ± 0.4 μM), genome replication, and protein expression. | Zou et al. 2021 | |
| TMPRSS2 rG4 | FRET melting (ΔTm = 3.48°C), CD melting (ΔTm = 4.00°C), bio-layer interferometry (BLI) assay (Kd = 604.9 ± 2.84 nM), IFA | Cell lines used: H1299, HBE, LLC; inhibit TMPRSS2 expression and SARS-CoV-2 infection in mouse models. | Liu et al. 2022 | |
| cPDS | TERRA rG4 | FRET melting (ΔTm = 20.7 ± 0.1 K) | NA | Di Antonio et al. 2012 |
| PDP | HCV rG4 | FRET kinetic assay, native gel electrophoresis | Cell lines used: HEK-293, Huh-7.5.1; stabilize RNA G4s and inhibit HCV C gene expression and HCV replication in host cells. | Wang et al. 2016a |
| SARS-CoV-2 rG4 | CD melting (ΔTm = 13.9°C), native gel electrophoresis, IFA | Cell lines used: HeLa, HEK293T; inhibit SARS-CoV-2 RNA expression. | Zhao et al. 2021; Qin et al. 2022 | |
| 12459 | hTERT rG4 | Native gel electrophoresis | Alter hTERT alternative RNA splicing. | Gomez et al. 2004 |
| 360A | TRF2 rG4 | Competition FRET | Inhibit the reporter gene expression. | Gomez et al. 2010 |
| Phen-DC3 | TRF2 rG4 | Competition FRET | Inhibit the reporter gene expression. | Gomez et al. 2010 |
| EBNA1 rG4 | Pull-down assay | Cell lines used: H1299, Mutu-1, NPC-6661; block nucleolin–EBNA1 rG4 interaction and promote endogenous EBNA1 expression in EBV-infected cells. | Lista et al. 2017 | |
| HCV110-131 rG4 | FRET melting (ΔTm = 7.5°C), CD melting | Cell lines used: Huh7; inhibit HCV viral replication. | Jaubert et al. 2018 | |
| Pre-miRNA-149 G4 | Molecular docking simulations | NA | Carvalho et al. 2020 | |
| C8, C8-NH2, phenN2, phen2N4, PDS | Pre-miRNA-149 G4 | Molecular docking simulations | NA | Carvalho et al. 2020 |
| PyDH2 and PhenDH2 series | EBNA1 rG4 | Fluorescence melting, fluorescent indicator displacement (FID) assay (DC50 = 0.26 ± 0.05 μM [PyDH2], 0.30 ± 0.03 μM [PhenDH2]), pull-down assay | Cell lines used: H1299, Mutu-1; block nucleolin–EBNA1 rG4 interaction and enhance antigen presentation. | Reznichenko et al. 2019 |
| RR110 | NRAS rG4 | NMR, agarose gel electrophoresis | Inhibit NRAS expression. | Bugaut et al. 2010 |
| ZnAPC | NRAS rG4 | Visible absorption spectroscopy (Kd = 3.1 ± 0.3 μM), fluorescence spectroscopy, native gel electrophoresis | Cell lines used: MCF-7; photo-cleave NRAS rG4 and inhibit NRAS expression and cell viability. | Kawauchi et al. 2018 |
| Jatrorrhizine derivatives | miRNA-1587 G4 | Electrospray ionization mass spectrometry (ESI-MS) | Induce dimeric miRNA-1587 G4 formation. | Tan et al. 2018 |
| Pseudopalmatine | miRNA-1587 G4 | CD melting (ΔTm = 8°C) | Cell lines used: HeLa; inhibit miRNA-1587 regulation of the target mRNA. | Li et al. 2019 |
| RGB-1 | TERRA rG4 | Size exclusion chromatography (Kd = 5.9 μM, stoichiometry = 1:1.2), CD melting (ΔTm ≥ 5°C) | Cell lines used: HEK293; inhibit TERRA expression. | Katsuda et al. 2016 |
| NRAS rG4 | CD melting | Cell lines used: HEK293; inhibit endogenous NRAS expression. | Katsuda et al. 2016 | |
| PNADOTASQ | TERRA rG4, TRF2 rG4, VEGF rG4 | FRET melting (ΔTm = 21.2°C [TERRA], 10.1°C [TRF2], 12.0°C [VEGF]) | NA | Haudecoeur et al. 2013 |
| Octenidine | NRAS rG4 | FID (DC50 = 1.6 μM), fluorescence quenching (FQ) assay (Kd = 0.49 ± 0.03 μM), CD melting, native gel electrophoresis | Cell lines used: SK-MEL-2; block DHX36/NRAS rG4 interactions (IC50= 2.4 ± 0.4 μM), inhibit NRAS expression and cancer cells viability (IC50 = 2.34 ± 0.09 μM), and suppress tumor growth in mouse models. | Chen et al. 2023 |
| NMM | Influenza A Virus (IAV) rG4 | NMR (stoichiometry = 1:1), native gel electrophoresis | NA | Tomaszewska et al. 2021 |
| BRACO-19 | ZIKV rG4 | Fluorescence spectroscopy (>100-fold), ITC, CD melting (ΔTm = 3.6°C–13.1°C) | Cell lines used: CCL-81; inhibit ZIKV growth, viral protein synthesis, and genome replication in host cells. | Majee et al. 2021 |
| HIV-1 U3 rG4 | CD | Cell lines used: MT-4; inhibit the reverse transcription and block HIV-1 rG4–protein interaction. | Perrone et al. 2014; Butovskaya et al. 2019 | |
| EBNA1 rG4 | Native gel electrophoresis | Cell lines used: Raji, HeLa, BJAB, DG75; inhibit viability of EBV-positive cells and block functions of EBNA1. | Norseen et al. 2009 | |
| Topotecan (TPT) and Berbamine (BBM) | rG4s in multiple SARS-CoV-2 host factors, TERRA rG4 | In silico virtual docking (TERRA rG4), microscale thermophoresis (TPT: Kd = 5.20 nM [TERRA], 383.01 nM [Tmprss2], 29.81 nM [Ace2]; BBM: Kd = 11.55 nM [TERRA], 10.78 nM [Tmprss2], 264.76 nM [Ace2]) | Cell lines used: H1299, Vero-E6, hACE2-293T; inhibit the endogenous expression of SARS-CoV-2 host factors and block SARS-CoV-2 pseudovirus entry in cells and in mouse models. | Tong et al. 2023 |
| DANC | TERRA rG4 | CD titrations, fluorescence spectroscopy, FRET, native gel electrophoresis | Unwind rG4 and promote G4 nucleic acid processivity. | Liu et al. 2024 |
| PhpC | NRAS rG4 | Fluorescence quenching assay, competitive FRET melting (ΔΔTm = −0.9°C at 1:1 ratio) | Cell lines used: MCF7; unwind rG4 and enhance gene expression. | Mitteaux et al. 2024 |
| 2′-F C3 | rG4 | FRET, NMR | Cell lines used: HEK293FT; unwind rG4 and enhance gene expression. | Teng et al. 2024 |
| F1 | DHX15 rG4 | SPR (Kd = 12.6 ± 1.0 μM, stoichiometry [target:ligand] = 1:2), FID, CD melting (ΔTm = 3.6°C ± 0.3°C) | Inhibit DHX15 expression (IC50 = 22.9 ± 3.8 μM). | Prestwood et al. 2024 |
| Peptides | ||||
| RHAU | rG4 | Native gel electrophoresis (Kd = 14 nM [tetramolecular rAGA]) | Unwind rG4. | Lattmann et al. 2010; Truong et al. 2020 |
| RGG | sc1 rG4 | NMR (Kd = 3.8 nM) | NA | Phan et al. 2011 |
| TERRA rG4 | Native gel electrophoresis (Kd = 11 ± 1 nM) | NA | Yagi et al. 2018 | |
| Shank1a rG4, postsynaptic density protein 95 (PSD-95) rG4 | Native gel electrophoresis, fluorescence spectroscopy (Kd = 271 ± 21 nM [Shank1a], 92 ± 9 nM [PSD-95]), pull-down assay | NA | Imperatore et al. 2020 | |
| TLSRGG3Y | TERRA rG4 | Native gel electrophoresis, ITC (Kd = 10 ± 1 nM) | NA | Takahama and Oyoshi 2013 |
| MTD3/MTD14-RGG | rG4 | Native gel electrophoresis (Kd = 35 ± 12 nM), CD | Methylate G4-forming RNAs. | Yoshida et al. 2022 |
| TZIP | C2(G4C2)4 of C9orf72 | Native gel electrophoresis (Kd = 77 ± 12 nM), CD | Unwind rG4 and induce formation of high order structure. | Wortman et al. 2020 |
| Pep 11 | hTERC rG4 | MST (Kd = 1.37 ± 0.22 μM [pep11], 449 ± 62 nM [tandem pep11], 377 ± 35 nM [cyclic pep11]), fluorescence spectroscopy, filter binding assay, FRET melting | Cell lines used: HeLa; inhibit reporter gene expression. | Mou and Kwok 2023 |
| Aptamers | ||||
| L-Ap3-7 | rG4 | Native gel electrophoresis (Kd = 99.0 ± 20.3 nM [TERRA rG4]) | Block TERRA rG4–RHAU53 interaction (IC50 = 975.3 ± 1.1 nM). | Chan and Kwok 2020 |
| L-Apt.4-1c | rG4 | Native gel electrophoresis (Kd = 74.9 ± 7.5 nM [hTERC rG4]), MST (Kd = 59.1 ± 11.9 nM [hTERC rG4]) | Inhibit hTERC rG4–nucleolin interaction (IC50 = 1.69 ± 0.1 μM). | Umar and Kwok 2020 |
| L-Apt.8f | APP rG4 | Native gel electrophoresis (Kd = 24.06 ± 2.90 nM), MST (Kd = 12.76 ± 2.76 nM in 1 mM MgCl2) | Cell lines used: HeLa; inhibit APP expression. | Zhao et al. 2022 |
| L-Apt12-6 | parallel dG4 and rG4 | Native gel electrophoresis | NA | Ji et al. 2023 |
| L-Apt.1-1 | APP rG4 | Native gel electrophoresis (Kd = 12.48 ± 2.82 nM in 1 mM MgCl2) | Cell lines used: HeLa; inhibit endogenous APP expression. | Lau et al. 2024 |
| L-Apt.T8, L-Apt.T8-10D | HIV-1 U3-III rG4 | Native gel electrophoresis (Kd = 58.1 ± 4.9 nM [L-Apt.T8], 12.5 ± 5.17 nM [L-Apt.T8-10D]), MST (Kd = 54.0 ± 15.6 nM [L-Apt.T8], 8.5 ± 1.50 nM [L-Apt.T8-10D]) | Inhibit U3-III-tRNA3Lys segment interaction (IC50 = 87.9 ± 13.1 nM), U3-III–nucleocapsid interaction (IC50 = 124 ± 17.3 nM), and in vitro HIV-1 minus strand transfer (IC50 = 2.06 ± 0.50 μM). | Feng and Kwok 2024 |
| L-Apt1-12 | EBNA 1 rG4 | Native gel electrophoresis (Kd = 107.4 ± 10.4 nM), MST (Kd = 105.6 ± 30.6 nM) | Cell lines used: HEK293T, C666-1, NPC43, SNU719; inhibit endogenous EBNA1 expression and growth of EBV-positive cancer cells. | Ji et al. 2024 |
| L-apt3.1 | pUG fold | Native gel electrophoresis (Kd = 13.5 ± 2.8 nM) | Inhibit gene silencing in Caenorhabditis elegans. | Liew et al. 2025 |
| Antibody | ||||
| BG4 | TERRA rG4, NRAS rG4, BCL2 rG4 | Native gel electrophoresis (Kd = 18.0 ± 2.1 nM [TERRA], 5.5 ± 0.6 nM [NRAS], 6.5 ± 0.9 nM [BCL2]) | Cell lines used: HUVEC, MRC5, GM847, U2OS, HeLa; visualization of rG4. | Biffi et al. 2014 |
| Other tools | ||||
| dAS2 | EBNA 1 rG4 | Fluorescent trap assays, NMR, native gel electrophoresis, CD titrations | Cell lines used: HEK293E, HEK293KbC2, B3Z; unwind rG4 and enhance endogenous EBNA 1 expression and antigen presentation. | Murat et al. 2014 |
| Anti-H2G4 ASO | H2AFY rG4 | Native gel electrophoresis | Cell lines used: HEK293, Caco-2; unwind rG4 and enhance H2AFY expression. | Rouleau et al. 2015 |
| P7C and P7H | rG4 in aptamer RDQ | UV melting (ΔTm = ∼30°C [P7H]), CD, fluorescence spectroscopy (Kd = 8.1 × 108 M−1 [P7C]), Job plot (target:ligand = 1:1 [P7C], 1:2 [P7H]) | Affect G4 folding. | Marin and Armitage 2005 |
| γPNA | rG4 | SPR (Kd = 4.2 nM [γ5′], 1.9 nM [γ3′], 2.8 nM [γCen′]) | Inhibit reporter gene expression (IC50 [37°C)] = 15 nM [γ5′], 75 nM [γ3′], 90 nM [γCen′]). | Oyaghire et al. 2016 |
| WNV NS5B rG4 | CD, thermal difference spectroscopy (TDS), UV melting (ΔTm ≥ 37°C), fluorescence spectroscopy (Kd [37°C] = [2.1 ± 0.3] × 10−16 M) | Unwind rG4 | Sarkar and Armitage 2021 | |
| GRPC | G-vacancy-bearing rG4: MYOG-3332, MYOG-3333, ABTB2-3233 | CD, photo-cross-linking, FRET melting (ΔTm =41.2°C [MYOG-3332], 26°C [ABTB2-3233]), native gel electrophoresis (Kd = 40.6 ± 13.2 nM [MYOG-3333]) | Stabilize rG4 and inhibit in vitro RNA reverse transcription (IC50 = 0.14 μM [MYOG-3332], 0.065 μM [ABTB2-3233]) and RNA translation. | He et al. 2020 |
