Sampling of the conformations of the d(CGCTGCGGC) hairpin in solution by two-dimensional nuclear magnetic resonance and theoretical methods

Solution structures of the Huntington's disease DNA triplets, (CAG)n

Highly polymorphic DNA triplet repeats, (CAG)n, are located inside the first exon of the Huntington's disease gene. Inordinate expansion of this repeat is correlated with the onset and progression of the disease. NMR spectroscopy, gel electrophoresis, digestion by single-strand specific P1 enzyme, and in vitro replication assay have been used to investigate the structural basis of (CAG)n expansion. Nondenaturing gel electrophoresis and 1D 1H NMR studies of (CAG)5 and (CAG)6 reveal the presence of hairpins and mismatched duplexes as the major and minor populations respectively. However, at high DNA concentrations (i.e., 1.0-2.0 mM that is typically required for 2D NMR experiments) both (CAG)5 and (CAG)6 exist predominantly in mismatched duplex forms. Mismatched duplex structures of (CAG)5 and (CAG)6 are useful, because they adequately model the stem of the biologically relevant hairpins formed by (CAG)n. We, therefore, performed detailed NMR spectroscopic studies on the duplexes of (CAG)5 and (CAG)6. We also studied a model duplex, (CGCAGCG)2 that contains the underlined building block of the duplex. This duplex shows the following structural characteristics: (i) all the nucleotides are in (C2'-endo, anti) conformations, (ii) mismatched A x A base pairs are flanked by two Watson-Crick G x C base pairs and (iii) A x A base pairs are stably stacked (and intra-helical) and are formed by a single N6-H--N1 hydrogen bond. The nature of A x A pairing is confirmed by temperature-dependent HMQC and HMQC-NOESY experiments on the [(CA*G)5]2 duplex where the adenines are 15N-labeled at N6. Temperature- and pH-dependent imino proton spectra, nondenaturing electrophoresis, and P1 digestion data demonstrate that under a wide range of solution conditions longer (CAG)n repeats (n> or =10) exist exclusively in hairpin conformation with two single-stranded loops. Finally, an in vitro replication assay with (CAG)8,21 inserts in the M13 single-stranded DNA templates shows a replication bypass for the (CAG)21 insert but not for the (CAG)8 insert in the template. This demonstrates that for a sufficiently long insert (n=21 in this case), a hairpin is formed by the (CAG)n even in presence of its complementary strand. This observation implies that the formation of hairpin by the (CAG)n may cause slippage during replication and thus may explain the observed length polymorphism.

Cystosine-rich strands of the insulin minisatellite adopt hairpins with intercalated cytosine+.cytosine pairs

Previously, we reported the high resolution NMR structure of the hairpin G-quartet structure formed by the G-rich strand of the insulin minisatellite of repeat sequence, (ACAG4TGTG4/TGTC4ACAC4) located upstream of the human insulin gene. Here, we report structural studies on the C-rich strand of this insulin minisatellite. First, we show by high resolution NMR that (C4TGTC4) forms a hairpin dimer with intercalated C+.C pairs (referred to as the hairpin i-motif); 340 NOE distance constraints uniquely define the nature of hairpin folding and the pattern of C+.C intercalation. Second, we show by one-dimensional NMR spectroscopy and molecular modeling studies that (C4TGTC4ACA4TGTC4) forms an intramolecularly folded hairpin with intercalated C+.C pairs. Third, we demonstrate by in vitro replication studies that several such hairpin i-motifs are present in long (C4TGTC4ACA)n (n>/=6) sequences, even in the presence of their complementary strands. Finally, we discuss structural and biological significance of the hairpin i-motifs formed by the C-rich strands of the insulin minisatellite.

Nucleotide deletion and P addition in V(D)J recombination: a determinant role of the coding-end sequence

During V(D)J recombination, the coding ends to be joined are extensively modified. Those modifications, termed coding-end processing, consist of removal and addition of various numbers of nucleotides. We previously showed in vivo that coding-end processing is specific for each coding end, suggesting that specific motifs in a coding-end sequence influence nucleotide deletion and P-region formation. In this study, we created a panel of recombination substrates containing actual immunoglobulin and T-cell receptor coding-end sequences and dissected the role of each motif by comparing its processing pattern with those of variants containing minimal nucleotide changes from the original sequence. Our results demonstrate the determinant role of specific sequence motifs on coding-end processing and also the importance of the context in which they are found. We show that minimal nucleotide changes in key positions of a coding-end sequence can result in dramatic changes in the processing pattern. We propose that each coding-end sequence dictates a unique hairpin structure, the result of a particular energy conformation between nucleotides organizing the loop and the stem, and that the interplay between this structure and specific sequence motifs influences the frequency and location of nicks which open the coding-end hairpin. These findings indicate that the sequences of the coding ends determine their own processing and have a profound impact on the development of the primary B- and T-cell repertoires.

The variable 3' ends of a human cytomegalovirus oriLyt transcript (SRT) overlap an essential, conserved replicator element

The genetically defined human cytomegalovirus (HCMV) lytic-phase replicator, oriLyt, comprises more than 2 kb in a structurally complex region that spans a variety of potential transcription control signals. Several transcripts originate within or cross oriLyt, and we are studying these oriLyt transcription units to determine whether they participate in initiating or regulating lytic-phase DNA synthesis. Results presented here establish the temporal accumulation and structure of the smallest replicator transcript, which we call SRT, and identify a single-sequence element essential to replicator function. SRT was detected as early as 2 h after HCMV infection of human fibroblast cells; transcript levels increased by 24 h and continued to increase thereafter. Consistent with its early appearance, treatment of HCMV-infected cells with the viral DNA polymerase inhibitor phosphonoformic acid had no effect on SRT accumulation; however, no SRT was detected in RNA preparations from cycloheximide-treated infected cells. Additional Northern (RNA) analysis localized the 0.2- to 0.25-kb SRT to an apparently noncoding segment near the center of the oriLyt core region. Reverse transcriptase PCR (rapid amplification of cDNA 5' ends [5'-RACE]) identified a single 5' end. In transient-transfection assays, the sequence immediately upstream of SRT functioned as a promoter responsive to HCMV infection when placed upstream of a reporter gene, suggesting that SRT is the product of a discrete transcription unit. RNA ligase-mediated 3'-RACE showed that SRT is not polyadenylated and has heterogeneous 3' ends within a roughly 45-nucleotide window overlapping an oligopyrimidine sequence having counterparts in the lytic-phase replicators of several herpesviruses. Mutation of the oligopyrimidine element showed that it is essential to oriLyt replicator function; it is the only essential single-sequence HCMV oriLyt replicator element described to date. Collectively, the location of SRT near the center of the oriLyt core region, its early expression, its overlapping relationship with a sequence element essential to replicator function, and its similarities to replicator transcripts in other systems suggest the possibility that SRT plays a role in initiating or regulating HCMV lytic-phase DNA synthesis.

Sodium and potassium ion-promoted formation of supramolecular aggregates of 2'-deoxyguanylyl-(3'-5')-2'-deoxyguanosine

Guanine mono-, oligo-, and polynucleotides, including the guanine-rich telomeric sequences found at the ends of chromosomes, have been shown to form self-associated species which contain cyclic tetramers of hydrogen-bonded guanines (G-tetrads). In this study the effect of the tetramethylammonium (TMA+), Na+, and K+ ions on the self-aggregation of 2'-deoxyguanylyl-(3'-5')-2'-deoxyguanosine, d(GpG), in aqueous solution has been studied by 1H NMR and FTIR spectroscopy. Although just a dinucleotide, it was found that d(GpG) self-associates to form extremely large assemblies in the presence of Na+ or K+ ions, especially the latter. The observed cation order for self-aggregation is TMA+ << Na+ < K+, with TMA+ having only a weak effect. Assuming a two-state model, the Tm for Na[d(GpG)] is 22 degrees C and for K[d(GpG)] is 42 degrees C, as determined by 1H NMR. Below the melting temperatures a large loss in intensity of the NMR signals was observed for these two salts, indicating that very large aggregates are forming in aqueous solution at pD 8. The intensity loss has been estimated to be 85% at 2 degrees C for Na[d(GpG)] and 88% at 24 degrees C for K[d(GpG)]; there is no observable signal for K[d(GpG)] at 2 degrees C. Incremental addition of KCI to 8 mM Na[d(GpG)] shows that at a mole ratio of d(GpG):KCI of 1:1 at 25 degrees C the total intensity loss is 98%. The presence of additional salt, especially a K salt, increases the formation of the supramolecular aggregates. 1H NMR of 9 mM Na[d(GpG)] in 90% H2O/10% D2O at 7 degrees C suggest that there are at least tow different species present, one of which has a G-tetrad structure, or that there are two different environments for the N1H in the G-tetrads. NOESY spectra of Na[d(GpG)] suggest that the glycosidic confomation is anti for both bases and that the dinucleotide units are stacking in a parallel fashion. Variable temperature FTIR spectroscopy in the 1750-1500 cm-1 region corroborates the cation-effect order found by NMR and shows that base-stacking and base-base hydrogen bonding are occurring in the aggregated species.

Three-dimensional model of a selective theophylline-binding RNA molecule

A three-dimensional (3D) model for an RNA molecule that selectively binds theophylline but not caffeine is proposed. This RNA, which was found using SELEX (Jenison et al., 1994), is 10,000 times more specific for theophylline (Kn = 320 nM) than for caffeine (KD = 3.5 mM), although the two ligands are identical except for a methyl group substituted at N7 (present only in caffeine). The binding affinity for ten xanthine-based ligands was used to derive a comparative molecular field analysis model (R2 = 0.93 for three components, with cross-validated R2 of 0.73), using the SYBYL and GOLPE programs. A pharmacophoric map was generated to locate steric and electrostatic interactions between theophylline and the RNA binding site. This information was used to identify putative functional groups of the binding pocket and to generate distance constraints. On the basis of a model for the secondary structure (Jenison et al., 1994), the 3D structure of this RNA was then generated using the following method: each helical region of the RNA molecule was treated as a rigid body; single-stranded loops with specific end-to-end distances were generated. The structures of RNA-xanthine complexes were studied using a modified Monte Carlo algorithm. The detailed structure of an RNA-ligand complex model, as well as possible explanations for the theophylline selectivity are discussed.

Structure and dynamics of the DNA hairpins formed by tandemly repeated CTG triplets associated with myotonic dystrophy

Anomalous expansion of the DNA triplet (CTG)n causes myotonic dystrophy. Structural studies have been carried out on (CTG)n repeats in an attempt to better understand the molecular mechanism of repeat expansion. NMR and gel electrophoretic studies demonstrate the presence of hairpin structures for (CTG)5 and (CTG)6 in solution. The monomeric hairpin structure remains invariant over a wide range of salt concentrations (10-200 mM NaCl), DNA concentrations (micromolar to millimolar in DNA strand) and pH (6.0-7.5). The (CTG)n hairpin contains three bases in the loop when n is odd and four bases when n is even. For both odd and even n the stacking and pairing in the stem remain the same, i.e, two hydrogen bond T.T pairs stack with the neighboring G.C pairs. All the nucleotides in (CTG)5 and (CTG)6 adopt C2'-endo, anti conformations. Full-relaxation matrix analysis has been performed to derive the NOE distance constraints from NOESY experiments at seven different mixing times (25, 50, 75, 100, 125, 200 and 500 ms). NOESY-derived distance constraints were subsequently used in restrained molecular dynamics simulations to obtain a family of structures consistent with the NMR data. The theoretical order parameters are computed for H5-H6(cytosines) and H2'-H2" dipolar correlations for both (CTG)5 and (CTG)6 by employing the Lipari-Szabo formalism. Experimental data show that the cytosine in the loop of the (CTG)5 hairpin is slightly more flexible than those in the stem. The cytosine in the loop of the (CTG)6 hairpin is extremely flexible, implying that the dynamics of the four base loop is intrinsically different from that of the three base loop.

Solution structures of the individual single strands of the fragile X DNA triplets (GCC)n.(GGC)n

Three-dimensional structures of the fragile X triplet repeats (GCC)n and (GGC)n are derived by using one- dimensional/two-dimensional NMR. Under a wide range of solution conditions (10-150 mM NaCl,pH6-7)(GCC)5-7 strands form exclusively slipped hairpins with a 3' overhanging C. The slipped hairpins of (GCC)n strands show the following structural characteristics: (i) maximization of Watson-Crick G.C pairs; (ii) formation of C.C mispairs at the CpG steps in the stem; (iii) C2'-endo, anti conformations for all the nucleotides. The ability of (GCC)n strands to form hairpin structures more readily than complementary (GGC)n strands suggests preferential slippage during replication and subsequent expansion of the (GCC)n strands. In addition, the C.C. mispairs at the CpG site of (GCC)n hairpins account for their exceptional substrate efficiencies for human methyltransferase. Gel electrophoresis data show that (GGC)n strands form both hairpin and mismatched duplex structures in 10-150 mM NaCl (ph 6-7) for n < 10, but for n > or + 11 hairpin structures are exclusively present. However, (GGC)n strands remain predominantly in the duplex state for n=4-11 under NMR solution conditions, which require DNA concentrations 100- to 1000-fold higher than in gel electrophoresis. NMR analyses of [(GGC)n]2 duplexes for n=4-6 show the presence of Watson-Crick G.C and mismatched G anti G syn pairs. The mismatches adjacent to the CpG step introduce local structural flexibility in these duplexes. Similar structural properties are also expected in the stem of the hairpins formed by (GGC)n strands.

Hairpin opening by single-strand-specific nucleases

DNA molecules with covalently sealed (hairpin) ends are probable intermediates in V(D)J recombination. According to current models hairpin ends are opened to produce short single-stranded extensions that are thought to be precursors of a particular type of extra nucleotides, termed P nucleotides, which are frequently present at recombination junctions. Nothing is known about the activities responsible for hairpin opening. We have used two single-strand-specific nucleases to explore the effects of loop sequence on the hairpin opening reaction. Here we show that a variety of hairpin ends are opened by P1 nuclease and mung bean nuclease (MBN) to leave short, 1-2 nt single-stranded extensions. Analysis of 22 different hairpin sequences demonstrates that the terminal 4 nt of the hairpin loop strongly influence the sites of cleavage. Correlation of the nuclease digestion patterns with structural (NMR) data for some of the hairpin loops studied here provides new insights into the structural features recognized by these enzymes.

Hairpins are formed by the single DNA strands of the fragile X triplet repeats: structure and biological implications

Inordinate expansion and hypermethylation of the fragile X DNA triplet repeat, (GGC)n.(GCC)n, are correlated with the ability of the individual G- and C-rich single strands to form hairpin structures. Two-dimensional NMR and gel electrophoresis studies show that both the G- and C-rich single strands form hairpins under physiological conditions. This propensity of hairpin formation is more pronounced for the C-rich strand than for the G-rich strand. This observation suggests that the C-rich strand is more likely to form hairpin or "slippage" structure and show asymmetric strand expansion during replication. NMR data also show that the hairpins formed by the C-rich strands fold in such a way that the cytosine at the CpG step of the stem is C.C paired. The presence of a C.C mismatch at the CpG site generates local flexibility, thereby providing analogs of the transition to the methyltransferase. In other words, the hairpins of the C-rich strand act as better substrates for the human methyltransferase than the Watson-Crick duplex or the G-rich strand. Therefore, hairpin formation could account for the specific methylation of the CpG island in the fragile X repeat that occurs during inactivation of the FMR1 gene during the onset of the disease.

Thermodynamic and structural properties of r(ACC) as revealed by ultraviolet electronic absorption, circular dichroism, 1H-NMR spectroscopy and Monte Carlo simulations

UV absorption, circular dichroism (CD) and 1H NMR, associated with Monte Carlo (MC) molecular structure simulations have been applied to the study of the trinucleoside diphosphate: r(ACC). The MC study which has been conducted as a function of temperature, is based on random variations of the nucleotide conformational angles, i.e. phosphodiester chain torsional angles and sugar pucker pseudorotational angles. All of the chemical bond lengths and valence angles remained fixed during the structural simulation, except those of the sugar pucker. Six different initial structures have been selected in order to explore the molecular conformational space as completely as possible. This simulation procedure led to distinct families of equilibrium conformations at 283, 298 and 318 K. The thermodynamical parameters such as variations in entropy, enthalpy and also melting temperature (delta SX0, delta HX0 and Tm) of the stacking (X) equilibrium were obtained from UV absorption and circular dichroism (CD) spectra recorded over a 80K temperature range. Chemical shifts (delta), vicinal coupling constants (3Jk,l), and cross-relaxation rate (sigma k,l) of trimers were measured at 400.13 MHz over a range of concentrations (2-13 mM) and temperatures (283-333K). Least-squares fitting of the experimental chemical shifts to simple models of association (A) and stacking equilibria allowed separation of the variations in the delta values (delta delta X and delta delta A) due to either phenomenon. The three NMR data sets (delta delta X, 3Jk,l, and sigma k,l) were then evaluated for the minima conformers obtained with the MC stimulations. Theoretical values of delta delta X were estimated using the results of an ab initio study while the coupling constant data were simulated with Karplus-type equations. Finally, the relaxation data were simulated from the distance matrices using treatment for cases of both slow conformational exchange accompanied by rapid small-amplitude fluctuations about the minima structures. A consistent picture of the large amplitude deformations (torsional angle variation) of these trimers has emerged from the present study. Optimized conformational blends at 283,296 and 318K were obtained by least-squares fitting of the experimental data to the theoretical ones, while considering the populations as adjustable parameters. As it would be expected, the right-handed helical conformation (A-RNA type) is found to be the major stacked species, in the temperature range of 283 to 318K. Limited evidence for bulged structures has been obtained, whereas novel reverse-stacked and half-stacked conformers also presented theoretical data compatible with the NMR observables of aqueous r(ACC).

Structure of hydrated oligonucleotides studied by in situ scanning tunneling microscopy

We have used the scanning tunneling microscope (STM) to image several synthetic oligonucleotides adsorbed onto a positively charged Au(111) electrode. The molecules were deposited and imaged in aqueous electrolyte under potential control, a procedure that eliminated the problem of the substrate artifacts that had limited some previous STM studies. Experiments were carried out with two types of single-stranded molecules (11 and 20 bases long) and three types of double-stranded molecules (20 and 61 base pairs and 31 bases with 25 bases paired and 6-base "sticky" ends). The molecules lie along symmetry directions on the reconstructed (23 x square root of 3) gold surface, and length measurements indicate that they adopt simple base-stacked structures. The base stacking distances are, within experimental uncertainty, equal to the 0.33 nm measured for polymeric aggregates of stacked purines by direct imaging in identical conditions. The images show features consistent with helical structures. Double helices have a major-groove periodicity that is consistent with a 36 degrees twist. The single helices appear to be more tightly twisted. A simple tunneling model of STM contrast generates good agreement between measured and calculated images.

Structural influence of RNA incorporation in DNA: quantitative nuclear magnetic resonance refinement of d(CG)r(CG)d(CG) and d(CG)r(C)d(TAGCG)

RNA and DNA adopt different types of conformations, i.e., A-type with C3'-endo sugar pucker for RNA and B-type with C2'-endo sugar pucker for DNA, respectively. The structural influence of the incorporation of RNA nucleotides into DNA is less understood. In this paper, we present the three-dimensional structures of two RNA-containing oligonucleotides, d(CG)r(CG)d(CG) and d(CG)r(C)d-(TAGCG), as determined by the NMR refinement procedure, and assess the possible structural perturbation of DNA induced by RNA. With a single RNA insertion into an octamer DNA, its overall conformation remains as the canonical B-DNA, except that the sugar pucker of the rC3 residue is C3'-endo (pseudorotation angle P = 3.6 degrees). In contrast, the hybrid hexamer is neither the pure B-DNA nor the pure A-DNA conformation. Instead, we propose a model in which the DNA parts adopt B conformation, whereas the RNA part adopts A conformation, with the overall conformation closer to A-DNA. To ensure an exhaustive search of the conformational space, the model was subjected to 100-ps simulated annealing with slow cooling or 100-ps molecular dynamics with subsequent quenching. Models obtained at different time points of the trajectories were further subjected to the SPEDREF NOE refinement [Robinson & Wang (1992) Biochemistry 31, 3524] and they appeared to arrive at a convergent model (< 0.5 A RMSD for the central four base pairs). The consensus hexamer structure contains a significant discontinuity at the (rG4)p(dC5) step with a base pair tilt angle of 6.7 degrees and roll angle of 11.5 degrees.(ABSTRACT TRUNCATED AT 250 WORDS)