RNA Aptamer In Complex Research Articles

The complex formed between a synthetic RNA aptamer and the transcription repressor TetR is a structural and functional twin of the operator DNA-TetR regulator complex.

RNAs play major roles in the regulation of gene expression. Hence, designer RNA molecules are increasingly explored as regulatory switches in synthetic biology. Among these, the TetR-binding RNA aptamer was selected by its ability to compete with operator DNA for binding to the bacterial repressor TetR. A fortuitous finding was that induction of TetR by tetracycline abolishes both RNA aptamer and operator DNA binding in TetR. This enabled numerous applications exploiting both the specificity of the RNA aptamer and the efficient gene repressor properties of TetR. Here, we present the crystal structure of the TetR-RNA aptamer complex at 2.7 Å resolution together with a comprehensive characterization of the TetR–RNA aptamer versus TetR–operator DNA interaction using site-directed mutagenesis, size exclusion chromatography, electrophoretic mobility shift assays and isothermal titration calorimetry. The fold of the RNA aptamer bears no resemblance to regular B-DNA, and neither does the thermodynamic characterization of the complex formation reaction. Nevertheless, the functional aptamer-binding epitope of TetR is fully contained within its DNA-binding epitope. In the RNA aptamer complex, TetR adopts the well-characterized DNA-binding-competent conformation of TetR, thus revealing how the synthetic TetR-binding aptamer strikes the chords of the bimodal allosteric behaviour of TetR to function as a synthetic regulator.

Structure of an RNA aptamer in complex with the fluorophore tetramethylrhodamine.

RNA aptamers—artificially created RNAs with high affinity and selectivity for their target ligand generated from random sequence pools—are versatile tools in the fields of biotechnology and medicine. On a more fundamental level, they also further our general understanding of RNA-ligand interactions e. g. in regard to the relationship between structural complexity and ligand affinity and specificity, RNA structure and RNA folding. Detailed structural knowledge on a wide range of aptamer–ligand complexes is required to further our understanding of RNA–ligand interactions. Here, we present the atomic resolution structure of an RNA–aptamer binding to the fluorescent xanthene dye tetramethylrhodamine. The high resolution structure, solved by NMR-spectroscopy in solution, reveals binding features both common and different from the binding mode of other aptamers with affinity for ligands carrying planar aromatic ring systems such as the malachite green aptamer which binds to the tetramethylrhodamine related dye malachite green or the flavin mononucleotide aptamer.

Using Pyridinium Styryl Dyes as the Standards of Time-Resolved Instrument Response.

In this paper, two pyridinium styryl dyes, [2-(4-dimethylamino-phenyl)-vinyl]-1-methylpyridinium iodide (DASPMI), were synthesized and characterized by steady state fluorescence spectroscopy as well as picosecond and femtosecond time-resolved fluorescence spectroscopies. Both dyes exhibit large Stokes shifts and fluorescence decays equivalent to the instrument response function (IRF) standards employed in time-correlated single-photon counting. Due to their styryl and pyridinium moieties, DASPMIs have higher peak fluorescence intensity and shorter excited-state lifetimes than iodide ion-quenched fluorophores. The fluorescence lifetimes of o-DASPMI and p-DASPMI were measured to be 6.6 ps and 12.4 ps, respectively. The fluorescence transients of these DASPMIs were used as the IRFs for iterative reconvolution fitting of the time-resolved fluorescence decay profiles of Rhodamine B (RhB), sulforhodamine B (SRB), and the SRB-SRB2m RNA aptamer complex. The quality of the fits employing the DASPMI-derived IRFs are consistently equivalent to those employing IRFs obtained from light scattering. These results indicate that DASPMI-derived IRFs may be suited for a broad range of applications in time-resolved spectroscopy and fluorescence lifetime imaging microscopy (FLIM), especially in the visible emission range.

NMR resonance assignments for the class II GTP binding RNA aptamer in complex with GTP

The structures of RNA-aptamer-ligand complexes solved in the last two decades were instrumental in realizing the amazing potential of RNA for forming complex tertiary structures and for molecular recognition of small molecules. For GTP as ligand the sequences and secondary structures for multiple families of aptamers were reported which differ widely in their structural complexity, ligand affinity and ligand functional groups involved in RNA-binding. However, for only one of these families the structure of the GTP-RNA complex was solved. In order to gain further insights into the variability of ligand recognition modes we are currently determining the structure of another GTP-aptamer--the so-called class II aptamer--bound to GTP using NMR-spectroscopy in solution. As a prerequisite for a full structure determination, we report here (1)H, (13)C, (15)N and partial (31)P-NMR resonance assignments for the class II GTP-aptamer bound to GTP.

Sampling a biomarker of the human immunodeficiency virus across a synthetic nanopore.

One primary goal in nanobiotechnology is designing new methodologies for molecular biomedical diagnosis at stages much earlier than currently possible and without use of expensive reagents and sophisticated equipment. In this work, we show the proof of principle for single-molecule detection of the nucleocapsid protein 7 (NCp7), a protein biomarker of the HIV-1 virus, using synthetic nanopores and the resistive-pulse technique. The biosensing mechanism relied upon specific interactions between NCp7 and aptamers of stem-loop 3 (SL3) in the packaging domain of the retroviral RNA genome. One critical step of this study was the choice of the optimal size of the nanopores for accurate, label-free determinations of the dissociation constant of the NCp7 protein-SL3 RNA aptamer complex. Therefore, we systematically investigated the NCp7 protein-SL3 RNA aptamer complex employing two categories of nanopores in a silicon nitride membrane: (i) small, whose internal diameter was smaller than 6 nm, and (ii) large, whose internal diameter was in the range of 7 to 15 nm. Here, we demonstrate that only the use of nanopores with an internal diameter that is smaller than or comparable with the largest cross-sectional size of the NCp7-SL3 aptamer complex enables accurate measurement of the dissociation constant between the two interacting partners. Notably, this determination can be accomplished without the need for prior nanopore functionalization. Moreover, using small solid-state nanopores, we demonstrate the ability to detect drug candidates that inhibit the binding interactions between NCp7 and SL3 RNA by using a test case of N-ethylmaleimide.

Crystallization and preliminary X-ray diffraction studies of an RNA aptamer in complex with the human IgG Fc fragment.

Aptamers, which are folded DNA or RNA molecules, bind to target molecules with high affinity and specificity. An RNA aptamer specific for the Fc fragment of human immunoglobulin G (IgG) has recently been identified and it has been demonstrated that an optimized 24-nucleotide RNA aptamer binds to the Fc fragment of human IgG and not to other species. In order to clarify the structural basis of the high specificity of the RNA aptamer, it was crystallized in complex with the Fc fragment of human IgG1. Preliminary X-ray diffraction studies revealed that the crystals belonged to the orthorhombic space group P2(1)2(1)2, with unit-cell parameters a = 83.7, b = 107.2, c = 79.0 A. A data set has been collected to 2.2 A resolution.

Crystallization and preliminary X-ray analysis of RNA aptamer in complex with human immunoglobulin G

Crystallization and preliminary X-ray analysis of RNA aptamer in complex with human immunoglobulin G

Crystal structure of RNA aptamer in complex with human immunoglobulin G

Crystal structure of RNA aptamer in complex with human immunoglobulin G

2P-119 ヒトIgGに結合するRNAアプタマー複合体の立体構造(核酸・相互作用,複合体,第46回日本生物物理学会年会)

2P-119 ヒトIgGに結合するRNAアプタマー複合体の立体構造(核酸・相互作用,複合体,第46回日本生物物理学会年会)

Retention of Conformational Flexibility in HIV-1 Rev−RNA Complexes

Sequence-specific recognition between HIV-1 Rev and viral RNA mediates the nuclear export of the viral mRNA and thus is important for the viral life cycle. HIV Rev binds to its viral RNA target with high affinity and specificity and also binds to an in vitro selected RNA aptamer that has a significantly different sequence from the viral RNA target with a 6-fold higher affinity than its natural target. The high-resolution structures of HIV Rev Arg-rich motif (ARM) in complexes with the wild-type RNA and the RNA aptamer reveal that, despite the significantly different RNA sequences, the two complexes share similar structural features and the protein-RNA interactions are mediated mostly by the Arg side chains in Rev ARM. To gain further insight into the role of these Arg side chains in the sequence-specific protein-RNA recognition, we have characterized the flexibility of these Arg side chains at the interfaces of the two high-affinity complexes using (15)N R(1), R(2), nuclear Overhauser effect, and chemical-shift anisotropy dipolar cross-correlation relaxation measurements. The ARM peptide contains uniformly (13)C/(15)N-labeled Arg residues, and the RNA samples were unlabeled. Despite the apparently similar roles of Arg side chains in both complexes, most of them display a different dynamic behavior in the context of different RNA molecules, and extensive and highly diverse motions have been observed for all of these side chains that interact with RNA. Most of the differences in side-chain dynamics between the complexes cannot be inferred from the three-dimensional structures. Additionally, more than half of the residues have increased flexibility in the Rev-RNA aptamer complex that has a higher affinity. This study provides new insights into ARM-RNA recognition and indicates that retention of conformational flexibility is likely important in high-affinity ARM-RNA recognition.

Dynamics Studies of a Malachite Green−RNA Complex Revealing the Origin of the Red-Shift and Energetic Contributions of Stacking Interactions

RNA plays a central role in many biological processes and is therefore an important target for drug development. In recent years an increasing wealth of structural and functional information about RNA−ligand complexes has been obtained using in vitro selected RNAs (aptamers). However, all those studies focused on structure and changes of the nucleic acid and mostly considered the ligand as a rigid target. Experimental characterization of the dynamics of a malachite green (MAG)−RNA aptamer complex revealed surprisingly asymmetric changes in the 13C chemical shift of the ligand methyl groups, which indicate that the dye undergoes changes in its conformation and charge distribution upon binding, in addition to the red-shift in its maximum absorption frequency. Earlier computational work explored the electrostatic influence of the highly charged RNA backbone and surrounding counterions for these asymmetrical changes in 13C chemical shift. The work presented here examines the dynamical nature of the MAG molecule inside the RNA ligand-binding site using molecular dynamics with explicit solvent to explore the intermolecular and dynamic influences on the red-shift and to calculate the binding affinity. An induced fit behavior, similar to that caused by the electrostatic field alone, is observed. The binding strength of a series of malachite green derivatives correlates with the structural flatness of the ligand. These findings are important for the rational design of RNA ligands and for understanding the properties of RNA−ligand complexes.

A water channel in the core of the vitamin B 12 RNA aptamer

Background: The 3.0 Å crystal structure of the vitamin B 12 RNA aptamer revealed an unusual tertiary structure that is rich in novel RNA structural motifs. Important details of the interactions that stabilize noncanonical base pairing and the role of solvent in the structure were not apparent owing to the limited resolution. Results: The structure of the vitamin B 12 RNA aptamer in complex with its ligand has been determined at 2.3 Å resolution by X-ray crystallography. The crystallographic asymmetric unit contains five independent copies of the aptamer—vitamin B 12 complex, making it possible to accurately define well-conserved features. The core of the aptamer contains an unusual water-filled channel that is buried between the three strands of an RNA triplex. Well-ordered water molecules positioned within this channel form bridging hydrogen bonds and stabilize planar base triples that otherwise lack significant direct base—base contacts. The water channel terminates at the interface between the RNA and the bound ligand, leaving a pair of water molecules appropriately positioned to hydrogen bond with the highly polarized cyanide nitrogen of vitamin B 12. Analysis of the general solvation patterns for each nucleotide suggests that water molecules are not precisely positioned, as observed in previous RNA duplex structures, but instead might adjust in response to the varying local environment. Unusual intermolecular base pairing contributes to the formation of three different dimerization contacts that drive formation of the crystal lattice. Conclusions: The structure demonstrates the important role of water molecules and noncanonical base pairing in driving the formation of RNA tertiary structure and facilitating specific interactions of RNAs with other molecules.

A molecular dynamics simulation of the flavin mononucleotide–RNA aptamer complex

We report on an unrestrained molecular dynamics simulation of the flavin mononucleotide (FMN)–RNA aptamer. The simulated average structure maintains both cross-strand and intermolecular FMN–RNA nuclear Overhauser effects from the nmr experiments and has all qualitative features of the nmr structure including the G10–U12–A25 base triple and the A13–G24, A8–G28, and G9–G27 mismatches. However, the relative orientation of the hairpin loop to the remaining part of the molecule differs from the nmr structure. The simulation predicts that the flexible phosphoglycerol part of FMN moves toward G27 and forms hydrogen bonds. There are structurally long-lived water molecules in the FMN binding pocket forming hydrogen bonds within FMN and between FMN and RNA. In addition, long-lived water is found bridging primarily RNA backbone atoms. A general feature of the environment of long-lived “structural” water is at least two and in most cases three or four potential acceptor atoms. The 2′-OH group of RNA usually acts as an acceptor in interactions with the solvent. There are almost no intrastrand O2′H(n)⋮O4′(n + 1) hydrogen bonds within the RNA backbone. In the standard case the preferred orientation of the 2′-OH hydrogen atoms is approximately toward O3′ of the same nucleotide. However, a relatively large number of conformations with the backbone torsional angle γ in the trans orientation is found. A survey of all experimental RNA x-ray structures shows that this backbone conformation occurs but is less frequent than found in the simulation. Experimental nmr RNA aptamer structures have a higher fraction of this conformation as compared to the x-ray structures. The backbone conformation of nucleotide n + 1 with the torsional angle γ in the trans orientation leads to a relatively short distance between 2′-OH(n) and O5′(n + 1), enabling hydrogen-bond formation. In this case the preferred orientation of the 2′-OH hydrogen atom is approximately toward O5′(n + 1). We find two relatively short and dynamically stable types of backbone–backbone next-neighbor contacts, namely C2′(H)(n)⋮O4′(n + 1) and C5′(H)(n + 1)⋮O2′(n). These interactions may affect both backbone rigidity and thermodynamic stability of RNA helical structures. © 1999 John Wiley & Sons, Inc. Biopoly 50: 287–302, 1999

RNA architecture dictates the conformations of a bound peptide

The biological function of several viral and bacteriophage proteins, and their arginine-rich subdomains, involves RNA-mediated interactions. It has been shown recently that bound peptides adopt either beta-hairpin or alpha-helical conformations in viral and phage peptide-RNA complexes. We have compared the structures of the arginine-rich peptide domain of HIV-1 Rev bound to two RNA aptamers to determine whether RNA architecture can dictate the conformations of a bound peptide. The core-binding segment of the HIV-1 Rev peptide class II RNA aptamer complex spans the two-base bulge and hairpin loop of the bound RNA and the carboxy-terminal segment of the bound peptide. The bound peptide is anchored in place by backbone and sidechain intermolecular hydrogen bonding and van der Waals stacking interactions. One of the bulge bases participates in U*(A*U) base triple formation, whereas the other is looped out and flaps over the bound peptide in the complex. The seven-residue hairpin loop is closed by a sheared G*A mismatch pair with several pyrimidines looped out of the hairpin fold. Our structural studies establish that RNA architecture dictates whether the same HIV-1 Rev peptide folds into an extended or alpha-helical conformation on complex formation. Arginine-rich peptides can therefore adapt distinct secondary folds to complement the tertiary folds of their RNA targets. This contrasts with protein-RNA complexes in which elements of RNA secondary structure adapt to fit within the tertiary folds of their protein targets.

Solution structure of the tobramycin-RNA aptamer complex.

We have solved the solution structure of the aminoglycoside antibiotic tobramycin complexed with a stem-loop RNA aptamer. The 14 base loop of the RNA aptamer 'zippers up' alongside the attached stem through alignment of four mismatches and one Watson-Crick pair on complex formation. The tobramycin inserts into the deep groove centered about the mismatch pairs and is partially encapsulated between its floor and a looped out guanine base that flaps over the bound antibiotic. Several potential intermolecular hydrogen bonds between the charged NH3 groups of tobramycin and acceptor atoms on base pair edges and backbone phosphates anchor the aminoglycoside antibiotic within its sequence/structure specific RNA binding pocket.

Selective inhibition of cell-free translation by oligonucleotides targeted to a mRNA hairpin structure.

Using an in vitro selection approach we have previously isolated oligodeoxy aptamers that can bind to a DNA hairpin structure without disrupting the double-stranded stem. We report here that these oligomers can bind to the RNA version of this hairpin, mostly through pairing with a designed 6 nt anchor. The part of the aptamer selected against the DNA hairpin did not increase stability of the RNA-aptamer complex. However, it contributed to the binding site for Escherichia coli RNase H, leading to very efficient cleavage of the target RNA. In addition, a 2'- O -methyloligoribonucleotide analogue of one selected sequence selectively blocked in vitro translation of luciferase in wheat germ extract by binding to the hairpin region inserted upstream of the initiation codon of the reporter gene. Therefore, non-complementary oligomers can exhibit antisense properties following hybridization with the target RNA. Our study also suggests that in vitro selection might provide a means to extend the repertoire of sequences that can be targetted by antisense oligonucleotides to structured RNA motifs of biological importance.

Assignment methodology for larger RNA oligonucleotides: application to an ATP-binding RNA aptamer.

The use of uniform 13C, 15N labeling in the NMR spectroscopic study of RNA structures has greatly facilitated the assignment process in small RNA oligonucleotides. For ribose spin system assignments, exploitation of these labels has followed previously developed methods for the study of proteins. However, for sequential assignment of the exchangeable and nonexchangeable protons of the nucleotides, it has been necessary to develop a variety of new NMR experiments. Even these are of limited utility in the unambiguous assignment of larger RNAs due to the short carbon relaxation times and extensive spectral overlap for all nuclei. These problems can largely be overcome by the additional use of basetype selectively 13C, 15N-labeled RNA in combination with a judicious use of related RNAs with base substitutions. We report the application of this approach to a 36-nucleotide ATP-binding RNA aptamer in complex with AMP. Complete sequential 1H assignments, as well as the majority of 13C and 15N assignments, were obtained.

Specific labeling approaches to guanine and adenine imino and amino proton assignments in the AMP-RNA aptamer complex.

The secondary structure of a recently identified ATP-binding RNA aptamer consists of a purine-rich 11-residue internal loop positioned opposite a single guanine bulge flanked on either side by helical stem segments. The ATP ligand targets the internal loop and bulge domains, inducing a structural transition in this RNA segment on complex formation. Specifically, 10 new slowly exchanging proton resonances in the imino, amino and sugar hydroxyl chemical shift range are observed on AMP-RNA aptamer complex formation. This paper outlines site-specific labeling approaches to identify slowly exchanging imino (guanine) and amino (guanine and adenine) protons in internal loop and bulge segments of compact RNA folds such as found in the AMP-RNA aptamer complex. One approach incorporates 15N-labeled guanine (N1 imino and N2 amino positions) and 15N-labeled adenine (N6 amino position), one residue at a time, in the AMP-binding RNA aptamer, with labeling incorporation through chemical synthesis facilitated by generating the aptamer from two separate strands. The unambiguous assignments deduced from the 15N labeling studies have been verified from an independent labeling strategy where individual guanines in the internal loop have been replaced, one at a time, by inosines and assignments were made on the basis of the large 2 ppm downfield shift of the guanine imino protons on inosine substitution. The strengths and limitations of the inosine-for-guanine substitution approach emerge from our studies on the AMP-RNA aptamer complex. The assignment of the internal loop and bulge imino and amino protons was critical in our efforts to define the solution structure of the AMP-RNA aptamer complex since these slowly exchanging protons exhibit a large number of long-range intramolecular NOEs within the RNA, as well as intermolecular NOEs to the AMP in the complex. The current application of specific 15N and inosine labeling approaches for exchangeable imino and imino proton assignments in the nonhelical segments of an RNA aptamer complex in our laboratory complements selective 2H and 13C approaches to assign nonexchangeable base and sugar protons in RNA and ligand-RNA complexes reported in the literature.

Structural basis of RNA folding and recognition in an AMP-RNA aptamer complex.

The catalytic properties of RNA and its well known role in gene expression and regulation are the consequence of its unique solution structures. Identification of the structural determinants of ligand recognition by RNA molecules is of fundamental importance for understanding the biological functions of RNA, as well as for the rational design of RNA Sequences with specific catalytic activities. Towards this latter end, Szostak et al. used in vitro selection techniques to isolate RNA sequences ('aptamers') containing a high-affinity binding site for ATP, the universal currency of cellular energy, and then used this motif to engineer ribozymes with polynucleotide kinase activity. Here we present the solution structure, as determined by multidimensional NMR spectroscopy and molecular dynamics calculations, of both uniformly and specifically 13C-, 15N-labelled 40-mer RNA containing the ATP-binding motif complexed with AMP. The aptamer adopts an L-shaped structure with two nearly orthogonal stems, each capped proximally by a G x G mismatch pair, binding the AMP ligand at their junction in a GNRA-like motif.

Molecular Recognition in the FMN – RNA Aptamer Complex

We report on a combined NMR – molecular dynamics calculation approach that has solved the solution structure of the complex of flavin mononucleotide (FMN) bound to the conserved internal loop segment of a 35 nucleotide RNA aptamer identified through in vitro selection. The FMN – RNA aptamer complex exhibits exceptionally well-resolved NMR spectra that have been assigned following application of two, three and four-dimensional heteronuclear NMR techniques on samples containing uniformly 13C, 15N-labeled RNA aptamer in the complex. The assignments were aided by a new through-bond NMR technique for assignment of guanine imino and adenine amino protons in RNA loop segments. The conserved internal loop zippers up through the formation of base-pair mismatches and a base-triple on complex formation with the isoalloxazine ring of FMN intercalating into the helix between a G·G mismatch and a G·U·A base-triple. The recognition specificity is associated with hydrogen bonding of the uracil like edge of the isoalloxazine ring of FMN to the Hoogsteen edge of an adenine at the intercalation site. There is significant overlap between the intercalated isoalloxazine ring and its adjacent base-triple platform in the complex. The remaining conserved residues in the internal loop participate in two G·A mismatches in the complex. The zippered-up internal loop and flanking stem regions form a continuous helix with a regular sugar – phosphate backbone except at a non-conserved adenine, which loops out of the helix to facilitate base-triple formation. Our solution structure of the FMN – RNA aptamer complex is to our knowledge the first structure of an RNA aptamer complex and outlines folding principles that are common to other RNA internal and hairpin loops, and molecular recognition principles common to model self-replication systems in chemical biology.