RESUMEN
Riboswitches are segments of noncoding RNA that bind with metabolites, resulting in a change in gene expression. To understand the molecular mechanism of gene regulation in a fluoride riboswitch, a base-pair opening dynamics study was performed with and without ligands using the Bacillus cereus fluoride riboswitch. We demonstrate that the structural stability of the fluoride riboswitch is caused by two steps depending on ligands. Upon binding of a magnesium ion, significant changes in a conformation of the riboswitch occur, resulting in the greatest increase in their stability and changes in dynamics by a fluoride ion. Examining hydrogen exchange dynamics through NMR spectroscopy, we reveal that the stabilization of the U45·A37 base-pair due to the binding of the fluoride ion, by changing the dynamics while maintaining the structure, results in transcription regulation. Our results demonstrate that the opening dynamics and stabilities of a fluoride riboswitch in different ion states are essential for the genetic switching mechanism.
Asunto(s)
Bacillus cereus/genética , Emparejamiento Base , Fluoruros/química , Genes Bacterianos , Riboswitch , Aptámeros de Nucleótidos , Secuencia de Bases , Catálisis , Enlace de Hidrógeno , Espectroscopía de Resonancia Magnética , Modelos Moleculares , Conformación de Ácido Nucleico , Motivos de NucleótidosRESUMEN
Polymerase η (Polη) is one of the Y-family polymerases that is recruited by monoubiquitinated proliferating cell nuclear antigen (Ub-PCNA) to DNA damage sites during translesion synthesis (TLS). This interaction is mediated by an ubiquitin-binding zinc-finger (UBZ) domain and a PCNA-interacting protein (PIP) box in Polη, which binds to ubiquitin and PCNA, respectively. Here, we show that without the UBZ domain, the PIP box of yeast Polη has a novel binding function with ubiquitin. Furthermore, the UBZ domain and the PIP box share the same binding surfaces for ubiquitin. The interaction with ubiquitin via the PIP box stabilizes the Ub-PCNA/Polη complex. Moreover, the PIP residues I624 and L625 contribute to Polη function in TLS in vivo.
Asunto(s)
ADN Polimerasa Dirigida por ADN/química , ADN Polimerasa Dirigida por ADN/metabolismo , Saccharomyces cerevisiae/química , Saccharomyces cerevisiae/metabolismo , Ubiquitina/química , Ubiquitina/metabolismo , Secuencia de Aminoácidos , ADN/biosíntesis , Daño del ADN , Replicación del ADN , Isoleucina/metabolismo , Leucina/metabolismo , Espectroscopía de Resonancia Magnética , Modelos Moleculares , Antígeno Nuclear de Célula en Proliferación/metabolismo , Unión Proteica , Dominios Proteicos , Saccharomyces cerevisiae/enzimología , Saccharomyces cerevisiae/genética , Dedos de ZincRESUMEN
Retinoic acid-inducible gene I (RIG-I) is responsible for innate immunity via the recognition of short double-stranded RNAs in the cytosol. With the clue that G-U wobble base pairs in the influenza A virus's RNA promoter region are responsible for RIG-I activation, we determined the complex structure of RIG-I ΔCARD and a short hairpin RNA with G-U wobble base pairs by X-ray crystallography. Interestingly, the overall helical backbone trace was not affected by the presence of the wobble base pairs; however, the base pair inclination and helical axis angle changed upon RIG-I binding. NMR spectroscopy revealed that RIG-I binding renders the flexible base pair of the influenza A virus's RNA promoter region between the two G-U wobble base pairs even more flexible. Binding to RNA with wobble base pairs resulted in a more flexible RIG-I complex. This flexible complex formation correlates with the entropy-favoured binding of RIG-I and RNA, which results in tighter binding affinity and RIG-I activation. This study suggests that the structure and dynamics of RIG-I are tailored to the binding of specific RNA sequences with different flexibility.
Asunto(s)
Proteína 58 DEAD Box/química , Proteína 58 DEAD Box/metabolismo , ARN Bicatenario/química , ARN Bicatenario/metabolismo , Receptores Inmunológicos/química , Receptores Inmunológicos/metabolismo , Emparejamiento Base , Cristalografía por Rayos X , Entropía , Células HEK293 , Humanos , Hidrógeno/química , Interferón gamma/metabolismo , Espectroscopía de Resonancia Magnética , Modelos Moleculares , ProtonesRESUMEN
Human RNA editing enzyme ADAR1 deaminates adenosine in pre-mRNA to yield inosine. The Zα domain of human ADAR1 (hZαADAR1) binds specifically to left-handed Z-RNA as well as Z-DNA and stabilizes the Z-conformation. To answer the question of how hZαADAR1 can induce both the B-Z transition of DNA and the A-Z transition of RNA, we investigated the structure and dynamics of hZαADAR1 in complex with 6-base-pair Z-DNA or Z-RNA. We performed chemical shift perturbation and relaxation dispersion experiments on hZαADAR1 upon binding to Z-DNA as well as Z-RNA. Our study demonstrates the unique dynamics of hZαADAR1 during the A-Z transition of RNA, in which the hZαADAR1 protein forms a thermodynamically stable complex with Z-RNA, similar to Z-DNA, but kinetically converts RNA to the Z-form more slowly than DNA. We also discovered some distinct structural features of hZαADAR1 in the Z-RNA binding conformation. Our results suggest that the A-Z transition of RNA facilitated by hZαADAR1 displays unique structural and dynamic features that may be involved in targeting ADAR1 for a role in recognition of RNA substrates.
Asunto(s)
Adenosina Desaminasa/química , ADN de Forma Z/química , Resonancia Magnética Nuclear Biomolecular/métodos , Proteínas de Unión al ARN/química , ARN/genética , HumanosRESUMEN
STING, a central protein in the innate immune response to cytosolic DNA, has emerged as a hot target for the development of vaccine-adjuvants and anticancer drugs. The discovery of potent human-STING (hSTING) agonist is expected to revolutionize the current cancer immunotherapy. Inspired by the X-ray crystal structure of DMXAA (5,6-dimethylxanthenone-4-acetic acid) and hSTINGG230I complex, we designed various DMXAA derivatives that contain a hydrogen bonding donor/acceptor or a halide at the C7 position. While 7-bromo- and 7-hydroxyl-DMXAA showed notable binding to mouse-STING (mSTING), our newly synthesized C7-functionalized DMXAA derivatives did not bind to hSTING. Nevertheless, our newly developed synthetic protocol for the C7-functionalization of DMXAA would be applicable to access other C7-substituted DMXAA analogues as potential hSTING agonists.
Asunto(s)
Diseño de Fármacos , Proteínas de la Membrana/agonistas , Xantonas/farmacología , Humanos , Modelos Moleculares , Estructura Molecular , Relación Estructura-Actividad , Temperatura , Xantonas/síntesis química , Xantonas/químicaRESUMEN
Retinoic acid-inducible gene I (RIG-I) recognizes double-stranded viral RNAs (dsRNAs) containing two or three 5' phosphates. A few reports of 5'-PPP-independent RIG-I agonists have emerged, but little is known about the molecular principles underlying their recognition. We recently found that the bent duplex RNA from the influenza A panhandle promoter activates RIG-I even in the absence of a 5'-triphosphate moiety. Here, we report that non-canonical synthetic RNA oligonucleotides containing G-U wobble base pairs that form a bent helix can exert RIG-I-mediated antiviral and anti-tumor effects in a sequence- and site-dependent manner. We present synthetic RNAs that have been systematically modified to enhance their efficacy and we outline the basic principles for engineering RIG-I agonists applicable to immunotherapy.
RESUMEN
Cyclic GMP-AMP synthase (cGAS) is a DNA-sensing enzyme in the innate immune system. Recent studies using core-cGAS lacking the N terminus investigated the mechanism for binding of double-stranded (ds) DNA and synthesis of 2',3'-cyclic GMP-AMP (cGAMP), a secondary messenger that ultimately induces type I interferons. However, the function of the N terminus of cGAS remains largely unknown. Here, we found that the N terminus enhanced the activity of core-cGAS in vivo. Importantly, the catalytic activity of core-cGAS decreased as the length of double-stranded DNA (dsDNA) increased, but the diminished activity was restored by addition of the N terminus. Furthermore, the N terminus deoligomerized the 2 : 1 complex of corecGAS and dsDNA into a 1 : 1 complex, suggesting that the N terminus enhanced the activity of corecGAS by facilitating formation of a monomeric complex of cGAS and DNA.
Asunto(s)
ADN/química , Sustancias Macromoleculares/química , Nucleotidiltransferasas/química , Multimerización de Proteína , Animales , Biocatálisis , Calorimetría/métodos , Dicroismo Circular , ADN/genética , ADN/metabolismo , Humanos , Immunoblotting , Cinética , Sustancias Macromoleculares/metabolismo , Espectroscopía de Resonancia Magnética , Ratones , Nucleótidos Cíclicos/biosíntesis , Nucleotidiltransferasas/genética , Nucleotidiltransferasas/metabolismo , Unión ProteicaRESUMEN
Retinoic acid-inducible gene I (RIG-I) recognizes specific molecular patterns of viral RNAs for inducing type I interferon. The C-terminal domain (CTD) of RIG-I binds to double-stranded RNA (dsRNA) with the 5'-triphosphate (5'-PPP), which induces a conformational change in RIG-I to an active form. It has been suggested that RIG-I detects infection of influenza A virus by recognizing the 5'-triphosphorylated panhandle structure of the viral RNA genome. Influenza panhandle RNA has a unique structure with a sharp helical bending. In spite of extensive studies of how viral RNAs activate RIG-I, whether the structural elements of the influenza panhandle RNA confer the ability to activate RIG-I signaling has been poorly explored. Here, we investigated the dynamics of the influenza panhandle RNA in complex with RIG-I CTD using NMR spectroscopy and showed that the bending structure of the panhandle RNA negates the requirement of a 5'-PPP moiety for RIG-I activation.
Asunto(s)
Proteína 58 DEAD Box/metabolismo , Virus de la Influenza A/genética , Conformación de Ácido Nucleico , Polifosfatos/metabolismo , ARN Viral/química , Emparejamiento Base , Calorimetría , Proteína 58 DEAD Box/química , Humanos , Hidrógeno/metabolismo , Interferón beta/metabolismo , Espectroscopía de Resonancia Magnética , Modelos Biológicos , Unión Proteica , Dominios Proteicos , Estabilidad del ARN , ARN Viral/metabolismo , Reacción en Cadena en Tiempo Real de la Polimerasa , Receptores Inmunológicos , TermodinámicaRESUMEN
Z-DNA binding proteins (ZBPs) play important roles in RNA editing, innate immune response and viral infection. Structural and biophysical studies show that ZBPs initially form an intermediate complex with B-DNA for B-Z conversion. However, a comprehensive understanding of the mechanism of Z-DNA binding and B-Z transition is still lacking, due to the absence of structural information on the intermediate complex. Here, we report the solution structure of the Zα domain of the ZBP-containing protein kinase from Carassius auratus(caZαPKZ). We quantitatively determined the binding affinity of caZαPKZ for both B-DNA and Z-DNA and characterized its B-Z transition activity, which is modulated by varying the salt concentration. Our results suggest that the intermediate complex formed by caZαPKZ and B-DNA can be used as molecular ruler, to measure the degree to which DNA transitions to the Z isoform.
Asunto(s)
ADN Forma B/química , ADN de Forma Z/química , Proteínas de Unión al ADN/química , Proteínas de Peces/química , Carpa Dorada/metabolismo , Proteínas Quinasas/química , Secuencia de Aminoácidos , Animales , Sitios de Unión , Clonación Molecular , ADN Forma B/metabolismo , ADN de Forma Z/metabolismo , Proteínas de Unión al ADN/genética , Proteínas de Unión al ADN/metabolismo , Escherichia coli/genética , Escherichia coli/metabolismo , Proteínas de Peces/genética , Proteínas de Peces/metabolismo , Expresión Génica , Cinética , Modelos Moleculares , Datos de Secuencia Molecular , Unión Proteica , Proteínas Quinasas/genética , Proteínas Quinasas/metabolismo , Estructura Secundaria de Proteína , Estructura Terciaria de Proteína , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Alineación de Secuencia , Cloruro de Sodio/química , TermodinámicaRESUMEN
Bacterial small RNAs (sRNAs) are known regulators in many physiological processes. In Escherichia coli, a large number of sRNAs have been predicted, among which only about a hundred are experimentally validated. Despite considerable research, the majority of their functions remain uncovered. Therefore, collective analysis of the roles of sRNAs in specific cellular processes may provide an effective approach to identify their functions. Here, we constructed a collection of plasmids overexpressing 99 individual sRNAs, and analyzed their effects on biofilm formation and related phenotypes. Thirty-three sRNAs significantly affecting these cellular processes were identified. No consistent correlations were observed, except that all five sRNAs suppressing type I fimbriae inhibited biofilm formation. Interestingly, IS118, yet to be characterized, suppressed all the processes. Our data not only reveal potentially critical functions of individual sRNAs in biofilm formation and other phenotypes but also highlight the unexpected complexity of sRNA-mediated metabolic pathways leading to these processes.
Asunto(s)
Biopelículas , Escherichia coli/genética , Fimbrias Bacterianas/genética , ARN Bacteriano/metabolismo , Northern Blotting , Escherichia coli/fisiología , Proteínas de Escherichia coli/genética , Proteínas de Escherichia coli/metabolismo , Regulación Bacteriana de la Expresión Génica , Fenotipo , Plásmidos/genética , Plásmidos/metabolismo , ARN Bacteriano/genéticaRESUMEN
FAAP20 (Fanconi anemia-associated protein 20) is a subunit of the Fanconi anemia (FA) core complex that repairs interstrand cross-links. To understand the molecular basis for the FA core complex-mediated recruitment of Rev1 to the DNA lesion, we characterized the interactions among FAAP20-UBZ4, Rev1-BRCT, and ubiquitin using NMR. We found that FAAP20-UBZ4 binds not only ubiquitin but also Rev1-BRCT. Mapping the protein-protein interactions showed that FAAP20-UBZ4 has distinct binding surfaces for ubiquitin and Rev1-BRCT. In addition, the chemical exchange patterns indicated that the interaction between FAAP20-UBZ4 and ubiquitin might enhance the binding affinity between FAAP20-UBZ4 and Rev1-BRCT. These results provide new insight into the Rev1 recognition mechanism by FAAP20.
Asunto(s)
Proteínas del Grupo de Complementación de la Anemia de Fanconi/química , Proteínas Nucleares/química , Nucleotidiltransferasas/química , Estructura Terciaria de Proteína , Secuencia de Aminoácidos , Sitios de Unión/genética , Fenómenos Biofísicos , Proteínas del Grupo de Complementación de la Anemia de Fanconi/genética , Proteínas del Grupo de Complementación de la Anemia de Fanconi/metabolismo , Humanos , Espectroscopía de Resonancia Magnética , Modelos Moleculares , Datos de Secuencia Molecular , Proteínas Nucleares/genética , Proteínas Nucleares/metabolismo , Nucleotidiltransferasas/genética , Nucleotidiltransferasas/metabolismo , Unión Proteica , Mapeo de Interacción de Proteínas , Homología de Secuencia de Aminoácido , Propiedades de Superficie , Ubiquitina/química , Ubiquitina/metabolismoRESUMEN
Although it was only recently identified as a second messenger, c-di-AMP was found to have fundamental importance in numerous bacterial functions such as ion transport. The potassium transporter protein, KtrA, was identified as a c-di-AMP receptor. However, the co-crystallization of c-di-AMP with the protein has not been studied. Here, we determined the crystal structure of the KtrA RCK_C domain in complex with c-di-AMP. The c-di-AMP nucleotide, which adopts a U-shaped conformation, is bound at the dimer interface of RCK_C close to helices α3 and α4. c-di-AMP interacts with KtrA RCK_C mainly by forming hydrogen bonds and hydrophobic interactions. c-di-AMP binding induces the contraction of the dimer, bringing the two monomers of KtrA RCK_C into close proximity. The KtrA RCK_C was able to interact with only c-di-AMP, but not with c-di-GMP, 3',3-cGAMP, ATP, and ADP. The structure of the KtrA RCK_C domain and c-di-AMP complex would expand our understanding about the mechanism of inactivation in Ktr transporters governed by c-di-AMP.
Asunto(s)
Bacillus subtilis/química , Proteínas Bacterianas/química , Proteínas Bacterianas/metabolismo , Proteínas de Transporte de Catión/química , Proteínas de Transporte de Catión/metabolismo , Fosfatos de Dinucleósidos/metabolismo , Staphylococcus aureus/química , Bacillus subtilis/genética , Bacillus subtilis/metabolismo , Proteínas Bacterianas/genética , Proteínas de Transporte de Catión/genética , Fosfatos de Dinucleósidos/química , Modelos Moleculares , Potasio/metabolismo , Estructura Terciaria de Proteína , Staphylococcus aureus/genética , Staphylococcus aureus/metabolismoRESUMEN
Application of peptide nucleic acid (PNA) in bioanalysis has been limited due to its nonspecific adsorption onto hydrophobic surface in spite of favorable properties such as higher chemical/biological stability, specificity and binding affinity towards target nucleic acids compared to natural nucleic acid probes. Herein, we employed BSA in PNA application to enhance the stability of PNA in hydrophobic containers and improve the sensing performance of the DNA sensor based on graphene oxide (GO) and PNA. Addition of 0.01% BSA in a PNA solution effectively prevented the adsorption of PNA on hydrophobic surface and increased the portion of the effective PNA strands for target binding without interfering duplex formation with a complementary target sequence. In the GO based biosensor using PNA, BSA interrupted the unfavorable adsorption of PNA/DNA duplex on GO surface, while allowing the adsorption of ssPNA, resulting in improvement of the performance of the DNA sensor system by reducing the detection limit by 90-folds.
Asunto(s)
Técnicas Biosensibles/instrumentación , ADN/química , ADN/genética , Hibridación Fluorescente in Situ/instrumentación , Ácidos Nucleicos de Péptidos/química , Albúmina Sérica Bovina/química , Adsorción , ADN/análisis , Diseño de Equipo , Análisis de Falla de Equipo , Grafito/química , Interacciones Hidrofóbicas e Hidrofílicas , Óxidos/química , Reproducibilidad de los Resultados , Sensibilidad y Especificidad , Propiedades de SuperficieRESUMEN
The Zα domains of human ADAR1 (ZαADAR1) bind to Z-DNA via interaction mediated by the α3-core and ß-hairpin. Five residues in the α3 helix and four residues in the ß-hairpin play important roles in Zα function, forming direct or water-mediated hydrogen bonds with DNA backbone phosphates or interacting hydrophobically with DNA bases. To understand the roles of these residues during B-Z transition of duplex DNA, we performed NMR experiments on complexes of various ZαADAR1 mutants with a 6-bp DNA duplex at various protein-to-DNA molar ratios. Our study suggests that single mutations at residues K169, N173, or Y177 cause unusual conformational changes in the hydrophobic faces of helices α1, α2, and α3, which dramatically decrease the Z-DNA binding affinity. 1D imino proton spectra and chemical shift perturbation showed that single mutations at residues K170, R174, T191, P192, P193, or W195 slightly affected the Z-DNA binding affinity. A hydrogen exchange study proved that the K170A- and R174A-ZαADAR1 proteins could efficiently change B-DNA to left-handed Z-DNA via an active B-Z transition pathway, whereas the G2·C5 base pair was significantly destabilized compared to wild-type ZαADAR1.
Asunto(s)
Adenosina Desaminasa/química , Adenosina Desaminasa/metabolismo , ADN Forma B/química , ADN de Forma Z/química , ADN de Forma Z/metabolismo , Mutación , Conformación de Ácido Nucleico , Adenosina Desaminasa/genética , Amidas/química , Secuencia de Aminoácidos , Humanos , Espectroscopía de Resonancia Magnética , Modelos Moleculares , Datos de Secuencia Molecular , Estructura Secundaria de Proteína , Estructura Terciaria de ProteínaRESUMEN
The c-KIT tyrosine kinase has emerged as a potential therapeutic target for an array of diseases. However, there exists a drug resistance that is caused by mutations in c-KIT; therefore, c-KIT remains as a clinical challenge due to limited effective treatment options for therapies. For example, the acquired activating point mutation D816V significantly impairs the efficacy of targeted cancer therapies. Understanding the mechanisms of drug resistance at the molecular level will aid in designing and developing particular inhibitors with the potential to overcome these resistance mutations. We undertake a structure-based de novo design of 7-azaindole as the molecular core using the modified scoring function. This approach led to an identification of new c-KIT inhibitors over 100-fold specific for the D816V mutant relative to the wild-type c-KIT with nanomolar inhibitory activity. More importantly, these compounds potently inhibit clinically relevant D816V mutations of c-KIT in biochemical and cellular studies.
Asunto(s)
Antineoplásicos/química , Compuestos Aza/química , Indoles/química , Proteínas Proto-Oncogénicas c-kit/antagonistas & inhibidores , Antineoplásicos/síntesis química , Antineoplásicos/farmacología , Apoptosis/efectos de los fármacos , Compuestos Aza/síntesis química , Compuestos Aza/farmacología , Benzamidas/farmacología , Ciclo Celular/efectos de los fármacos , Línea Celular Tumoral , Diseño de Fármacos , Resistencia a Antineoplásicos , Ensayos de Selección de Medicamentos Antitumorales , Humanos , Mesilato de Imatinib , Indoles/síntesis química , Indoles/farmacología , Simulación del Acoplamiento Molecular , Piperazinas/farmacología , Mutación Puntual , Proteínas Proto-Oncogénicas c-kit/genética , Pirimidinas/farmacología , Relación Estructura-ActividadRESUMEN
Influenza RNA polymerase is composed of three subunits, PA, PB1, and PB2, which interact with each other for transcription and replication of the viral RNA genome in the nucleus of infected cells. PB2 RNA-binding 627-domain (residues 535-693), located in the C-terminus, presents a highly basic surface around residue lysine 627 and has been proposed to interact with viral or cellular factors, resulting in host adaptation. However, the function of this domain is not yet characterized in detail. In this study, we identified RNA-binding activity and RNA-binding surfaces in both the N-terminal and basic C-terminal regions of PB2 627-domain using NMR experiments. Through mutagenesis studies, we confirmed which residues directly interact with RNA and mapped their locations on the RNA-binding surface. In addition, by luciferase activity assays, we showed that influenza virus polymerase activity may correlate with the interaction between PB2 and RNA. Representative host adaptive mutations (residues 591 and 627) were found to be located on the RNA-binding surface and were confirmed to directly interact with RNA and to affect polymerase activity. From these results, we suggest that influenza virus polymerase activity may be regulated through the interaction between PB2 627-domain and RNA and that consequently host adaptation of the virus may be influenced.
Asunto(s)
Virus de la Influenza A/genética , Proteínas de Unión al ARN/química , ARN Polimerasa Dependiente del ARN/genética , ARN/química , Proteínas Virales/genética , Secuencia de Aminoácidos/genética , Sustitución de Aminoácidos , Fenómenos Biofísicos , Humanos , Virus de la Influenza A/patogenicidad , Mutagénesis , Mutación , Estructura Terciaria de Proteína/genética , ARN/genética , Proteínas de Unión al ARN/genética , Proteínas de Unión al ARN/metabolismo , ARN Polimerasa Dependiente del ARN/química , ARN Polimerasa Dependiente del ARN/metabolismo , Proteínas Virales/química , Proteínas Virales/metabolismoRESUMEN
RecQ C-terminal (RQC) domain is known as the main DNA binding module of RecQ helicases such as Bloom syndrome protein (BLM) and Werner syndrome protein (WRN) that recognizes various DNA structures. Even though BLM is able to resolve various DNA structures similarly to WRN, BLM has different binding preferences for DNA substrates from WRN. In this study, we determined the solution structure of the RQC domain of human BLM. The structure shares the common winged-helix motif with other RQC domains. However, half of the N-terminal has unstructured regions (α1-α2 loop and α3 region), and the aromatic side chain on the top of the ß-hairpin, which is important for DNA duplex strand separation in other RQC domains, is substituted with a negatively charged residue (D1165) followed by the polar residue (Q1166). The structurally distinctive features of the RQC domain of human BLM suggest that the DNA binding modes of the BLM RQC domain may be different from those of other RQC domains.
Asunto(s)
Resonancia Magnética Nuclear Biomolecular , Dominios y Motivos de Interacción de Proteínas , RecQ Helicasas/química , Secuencia de Aminoácidos , Humanos , Modelos Moleculares , Datos de Secuencia Molecular , Conformación Proteica , Alineación de Secuencia , SolucionesRESUMEN
Through screening by NMR spectroscopy, we discovered a novel scaffold (DPQ: 6,7-dimethoxy-2-(1-piperazinyl)-4-quinazolinamine) that binds specifically to the influenza A virus RNA promoter. The solution structure of the RNA-DPQ complex reported here demonstrates that the internal loop is the binding site of DPQ. The scaffold exhibits antiviral activity against influenza viruses.