We have used two-dimensional 'H NMR spectroscopy to study the conformation of the thrombin-binding aptamer d (GGTTGGTGTGGTTGG) in solution. This is one of a series of thrombin-binding DNA aptamers with a consensus 15-base sequence that was recently isolated and shown to inhibit thrombin-catalyzed fibrin clot formation in vitro [Bock, L. C., Griffin, L. C., Latham, J. A., Vermaas, E. H. & Toole, J. J. (1992) Nature (London) 355,[564][565][566]. The oligonucleotide forms a unimolecular DNA quadruplex consisting of two G-quartets connected by two TT loops and one TGT loop. A potential T-T bp is formed between the two TT loops across the diagonal of the top G-quartet. Thus, all of the invariant bases in the consensus sequence are base-paired. This aptamer structure was determined by NMR and illustrates that this molecule forms a specific folded structure. Knowledge of this structure may be used in the further development of oligonucleotide-based thrombin inhibitors.The ability of nucleic acids to fold into a variety of different structures has been exploited in the development of techniques for the isolation of aptamers (1) which are DNA or RNA oligonucleotides that have been screened from a randomly generated population of sequences for their ability to bind a desired molecular target (2-4). The isolation process involves repeated cycles of selection for, and enrichment of, oligonucleotides with an affinity to a specific target, followed by amplification of these sequences using the PCR (5). Oligonucleotides with the selected characteristics-i.e., binding to a specific molecule-are finally identified through cloning and sequencing. The potential of these methods for the development of oligonucleotide-based therapeutics has recently been explored by their application in isolating oligonucleotide ligands that selectively inhibit the activity of a target protein. Selection of DNA aptamers that bind to thrombin and inhibit thrombin-catalyzed fibrin-clot formation in vitro (6) and more recently an RNA oligonucleotide that specifically inhibits cDNA synthesis by human immunodeficiency virus reverse transcriptase in vitro (7) have been reported.Here we report two-dimensional NMR studies of the thrombin-binding aptamer d(GGTTGGTGTGGTTGG) (thrombin aptamer) that conforms to the consensus sequence d(GGtTGGN2_5GGtTGG), where an uppercase letter indicates an invariant base, a lowercase letter indicates a base bias at that position, and there are usually three central N nucleotides (6). The oligonucleotide folds into a unimolecular quadruplex containing two G-quartets (8) linked by two TT loops at one end and a TGT loop at the other end. The invariant thymines in the TT loops are potentially basepaired across the top of one G-quartet. This aptamer structure was determined by NMR techniques and illustrates that this molecule forms a specific folded structure. Knowledge of this structure should be useful in the further development of oligonucleotide-based therapeutics or as a starting point for small-molecule drug design...

The telomeres of most eukaryotes contain a repeating G-rich sequence with the consensus d(T/A)1-4G1-8, of which 12-16 bases form a 3' single-strand overhang beyond the telomeric duplex. It has been proposed that these G-rich oligonucleotides associate to form four-stranded structures from one, two or four individual strands and that these structures may be relevant in vivo. The proposed structures contain Hoogsteen base-paired G-quartets, precedent for which has been in the literature for many years. Here we use 1H NMR spectroscopy to study the conformations of the DNA oligonucleotides d(G4T4G4) (Oxy-1.5) and d(G4T4G4T4G4T4G4) (Oxy-3.5) which contain the Oxytricha telomere repeat (T4G4). We find that these molecules fold to form a symmetrical bimolecular and an intramolecular quadruplex, respectively. Both structures have four G-quartets formed from nucleotides that are alternately syn and anti along each strand. This arrangement differs from earlier models in which the strands are alternately all syn or all anti. The T4 loops in Oxy-1.5 are on opposite ends of the quadruplex and loop diagonally across the G-quartet, resulting in adjacent strands being alternately parallel and antiparallel.

Human telomerase contains a 451 nt RNA (hTR) and several proteins, including a specialized reverse transcriptase (hTERT). The 5' half of hTR comprises the pseudoknot (core) domain, which includes the RNA template for telomere synthesis and a highly conserved pseudoknot that is required for telomerase activity. The solution structure of this essential pseudoknot, presented here, reveals an extended triple helix surrounding the helical junction. The network of tertiary interactions explains the phylogenetic sequence conservation and existing human and mouse TR functional studies as well as mutations linked to disease. Thermodynamic stability, dimerization potential, and telomerase activity of mutant RNAs that alter the tertiary contacts were investigated. Telomerase activity is strongly correlated with tertiary structure stability, whereas there is no correlation with dimerization potential of the pseudoknot. These studies reveal that a conserved pseudoknot tertiary structure is required for telomerase activity.

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We have studied the competition between Na+ and K+ for coordination by G quartets using the oligonucleotide d(G3T4G3) as a model system. d(G3T4G3) forms a dimeric foldback structure containing three G quartets in the presence of either NaCl or KCl. Proton chemical shifts, which are particular to the species of coordinated ion, have been used to monitor the conversion between the sodium and potassium forms under equilibrium conditions. Analysis of titration experiments indicates that at least two K+ are coordinated by the three quartets of the dimeric molecule, and perfect fits of the data are obtained for two Na+ being displaced by two K+. Our results also indicate that the conversion of [d(G3T4G3)]2 from the sodium to the potassium form is associated with a net free energy change (delta G degrees) of -1.7 +/- 0.15 kcal/mol. It has long been suggested that the greater thermal stability of DNA quadruplex structures in the presence of K+ is primarily a result of the optimal fit of this ion in the coordination sites formed by G quartets. However, a consideration of the relatively small change in free energy associated with the conversion from the sodium to the potassium form and the relatively large difference between the free energy of hydration for Na+ and K+ indicates that this cannot be correct. Rather, the preferred coordination of K+ over Na+ is actually driven by the greater energetic cost of Na+ dehydration with respect to K+ dehydration.

Both synthetic and natural protegrin-1 form a well-defined structure in solution composed primarily of a two-stranded antiparallel beta sheet, with strands connected by a beta turn. The structure of PG-1 suggests ways in which the peptide may interact with itself or other molecules to form the membrane pores and the large membrane-associated assemblages observed in protegrin-treated, gram-negative bacteria.

An extensive analysis of trans-hydrogen bond 2h J NN and 1h J HN scalar couplings, the covalent 1 J HN couplings, and the imino proton chemical shifts is presented for Hoogsteen−Watson−Crick T•A−T and C+•G−C triplets of an intramolecular DNA triplex. The 2h J NN coupling constants for the Watson−Crick base pairs have values ranging from 6 to 8 Hz, while the Hoogsteen base paired thymines and protonated cytidines have values of approximately 7 and 10 Hz, respectively. Distinct decreases of 2h J NN are observed at the triplex strand ends. Trans-hydrogen bond J correlations (1h J HN) between the donor 1H nucleus and the acceptor 15N nucleus are observed for this triplex by a novel, simple quantitative J-correlation experiment. These one-bond 1h J HN couplings range between 1 and 3 Hz. A strong correlation is found between the chemical shift of the imino proton and the size of 2h J NN, with stronger J couplings corresponding to downfield chemical shifts. A similar, but inverse correlation is found between the proton chemical shift and the (absolute) size of the covalent 1 J HN constant. Methods of density functional theory were used to investigate the structural requirements for scalar J coupling and magnetic shielding associated with hydrogen bonding in nucleic acid base pairs. The dependencies of these NMR parameters on hydrogen bond distances were obtained for a representative base pair fragment. The results reproduce the trans-hydrogen bond coupling effect and the experimental correlations and suggest that the NMR parameters can be used to gain important insight into the nature of the hydrogen bond.

Specific recognition of double-stranded RNA (dsRNA) by dsRNAbinding domains (dsRBDs) is involved in a large number of biological and regulatory processes. Although structures of dsRBDs in complex with dsRNA have revealed how they can bind to dsRNA in general, these do not explain how a dsRBD can recognize specific RNAs. Rnt1p, a member of the RNase III family of dsRNA endonucleases, is a key component of the Saccharomyces cerevisiae RNA-processing machinery. The Rnt1p dsRBD has been implicated in targeting this endonuclease to its RNA substrates, by recognizing hairpins closed by AGNN tetraloops. We report the solution structure of Rnt1p dsRBD complexed to the 5 terminal hairpin of one of its small nucleolar RNA substrates, the snR47 precursor. The conserved AGNN tetraloop fold is retained in the protein-RNA complex. The dsRBD contacts the RNA at successive minor, major, and tetraloop minor grooves on one face of the helix. Surprisingly, neither the universally conserved G nor the highly conserved A are recognized by specific hydrogen bonds to the bases. Rather, the N-terminal helix fits snugly into the minor groove of the RNA tetraloop and top of the stem, interacting in a non-sequencespecific manner with the sugar-phosphate backbone and the two nonconserved tetraloop bases. Mutational analysis of residues that contact the tetraloop region show that they are functionally important for RNA processing in the context of the entire protein in vivo. These results show how a single dsRBD can convey specificity for particular RNA targets, by structure specific recognition of a conserved tetraloop fold.B inding of double-stranded RNA (dsRNA) by proteins is mediated by dsRNA-binding domains (dsRBDs), a 65-to 75-aa domain with a conserved ␣ 1 ␤ 1 ␤ 2 ␤ 3 ␣ 2 fold (1, 2). dsRBD-containing proteins play essential roles in a wide variety of biological and regulatory processes (3, 4). dsRBDs are found in dsRNAdependent protein kinases, in proteins involved in dsRNA editing, developmental regulation through RNA localization and translational regulation, as well as dsRNA endonucleases of the RNase III family (3). The latter include the Dicer and Drosha proteins that play key roles in RNA interference and in the processing of microRNAs (5, 6) which bind to and cleave dsRNA (7-9).The identification of the mechanism by which dsRBDs bind dsRNA would provide a structural framework to study a number of regulatory processes based on dsRBD-dsRNA interactions. Two structures of dsRBDs, from Xenopus laevis RNA-binding protein A (Xlrbpa) and Drosophila melanogaster Staufen, in complex with model dsRNA have been described (10,11). In these complexes, the conformation of the bound protein is essentially the same as that of the free protein, and the helix ␣1, the ␤3-␣2 loop, and the ␤1-␤2 loop (Fig. 1A) interact primarily with the sugar-phosphate backbone of successive minor, major, and minor grooves, respectively, on one face of the RNA. These complex structures explain how dsRBDs can recognize and bind dsRNA vs. ds or single-stranded (ss)...