Influence of cationic molecules on the hairpin to duplex equilibria of self-complementary DNA and RNA oligonucleotides

Polycations as Aptamer-Binding Modulators for Sensitive Fluorescence Anisotropy Assay of Aflatoxin B1

Fluorescence induced by the excitation of a fluorophore with plane-polarized light has a different polarization depending on the size of the fluorophore-containing reagent and the rate of its rotation. Based on this effect, many analytical systems have been implemented in which an analyte contained in a sample and labeled with a fluorophore (usually fluorescein) competes to bind to antibodies. Replacing antibodies in such assays with aptamers, low-cost and stable oligonucleotide receptors, is complicated because binding a fluorophore to them causes a less significant change in the polarization of emissions. This work proposes and characterizes the compounds of the reaction medium that improve analyte binding and reduce the mobility of the aptamer-fluorophore complex, providing a higher analytical signal and a lower detection limit. This study was conducted on aflatoxin B1 (AFB1), a ubiquitous toxicant contaminating foods of plant origins. Eight aptamers specific to AFB1 with the same binding site and different regions stabilizing their structures were compared for affinity, based on which the aptamer with 38 nucleotides in length was selected. The polymers that interact reversibly with oligonucleotides, such as poly-L-lysine and polyethylene glycol, were tested. It was found that they provide the desired reduction in the depolarization of emitted light as well as high concentrations of magnesium cations. In the selected optimal medium, AFB1 detection reached a limit of 1 ng/mL, which was 12 times lower than in the tris buffer commonly used for anti-AFB1 aptamers. The assay time was 30 min. This method is suitable for controlling almond samples according to the maximum permissible levels of their contamination by AFB1. The proposed approach could be applied to improve other aptamer-based analytical systems.

Directed Circularization of a Short RNA

Basic research and functional analyses of circular RNA (circRNA) have been limited by challenges in circRNA formation of desired length and sequence in adequate yields. Nowadays, circular RNA can be obtained using enzymatic, "ribozymatic," or modulated splice events. However, there are few records for the directed circularization of RNA. Here, we present a proof of principle for an affordable and efficient RNA-based system for the controlled synthesis of circRNA with a physiological 3',5'-phosphodiester conjunction. The engineered hairpin ribozyme variant circular ribozyme 3 (CRZ-3) performs self-cleavage poorly. We designed an activator-polyamine complex to complete cleavage as a prerequisite for subsequent circularization. The developed protocol allows synthesizing circRNA without external enzymatic assistance and adds a controllable way of circularization to the existing methods.

Template-Assisted Assembly of Hybrid DNA/RNA Nanostructures Using Branched Oligodeoxy- and Oligoribonucleotides

A template-assisted assembly approach to a C24 fullerene-like double-stranded DNA polyhedral shell is proposed. The assembly employed a supramolecular oligonucleotide dendrimer as a 3D template that was obtained via the hybridization of siRNA strands and a single-stranded DNA oligonucleotide joined to three- or four-way branched junctions. A four-way branched oligonucleotide building block (a starlet) was designed for the assembly of the shell composed of three identical self-complementary DNA single strands and a single RNA strand for hybridization to the DNA oligonucleotides of the template. To prevent premature auto-hybridization of the self-complementary oligonucleotides in the starlet, a photolabile protecting group was introduced via the N3-substituted thymidine phosphoramidite. Cleavable linkers such as a disulfide linkage, RNase A sensitive triribonucleotides, and di- and trideoxynucleotides were incorporated into the starlet and template at specific points to guide the post-assembly disconnection of the shell from the template, and enzymatic disassembly of the template and the shell in biological media. At the same time, siRNA strands were modified with 2'-OMe ribonucleotides and phosphorothioate groups in certain positions to stabilize toward enzymatic digestion. We report herein a solid-phase synthesis of branched oligodeoxy and oligoribonucleotide building blocks for the DNA/RNA dendritic template and the branched DNA starlet for a template-assisted construction of a C24 fullerene-like DNA shell after initial molecular modeling, followed by the assembly of the shell around the DNA-coated RNA dendritic template, and visualization of the resulting nanostructure by transmission electron microscopy.

Formation, function, and pathology of RNP granules

Ribonucleoprotein (RNP) granules are diverse membrane-less organelles that form through multivalent RNA-RNA, RNA-protein, and protein-protein interactions between RNPs. RNP granules are implicated in many aspects of RNA physiology, but in most cases their functions are poorly understood. RNP granules can be described through four key principles. First, RNP granules often arise because of the large size, high localized concentrations, and multivalent interactions of RNPs. Second, cells regulate RNP granule formation by multiple mechanisms including posttranslational modifications, protein chaperones, and RNA chaperones. Third, RNP granules impact cell physiology in multiple manners. Finally, dysregulation of RNP granules contributes to human diseases. Outstanding issues in the field remain, including determining the scale and molecular mechanisms of RNP granule function and how granule dysfunction contributes to human disease.

Mono-valent salt corrections for RNA secondary structures in the ViennaRNA package

BACKGROUND

RNA features a highly negatively charged phosphate backbone that attracts a cloud of counter-ions that reduce the electrostatic repulsion in a concentration dependent manner. Ion concentrations thus have a large influence on folding and stability of RNA structures. Despite their well-documented effects, salt effects are not handled consistently by currently available secondary structure prediction algorithms. Combining Debye-Hückel potentials for line charges and Manning's counter-ion condensation theory, Einert et al. (Biophys J 100: 2745-2753, 2011) modeled the energetic contributions of monovalent cations on loops and helices.

RESULTS

The model of Einert et al. is adapted to match the structure of the dynamic programming recursion of RNA secondary structure prediction algorithms. An empirical term describing the salt dependence of the duplex initiation energy is added to improve co-folding predictions for two or more RNA strands. The slightly modified model is implemented in the ViennaRNA package in such way that only the energy parameters but not the algorithmic structure is affected. A comparison with data from the literature show that predicted free energies and melting temperatures are in reasonable agreement with experiments.

CONCLUSION

The new feature in the ViennaRNA package makes it possible to study effects of salt concentrations on RNA folding in a systematic manner. Strictly speaking, the model pertains only to mono-valent cations, and thus covers the most important parameter, i.e., the NaCl concentration. It remains a question for future research to what extent unspecific effects of bi- and tri-valent cations can be approximated in a similar manner.

AVAILABILITY

Corrections for the concentration of monovalent cations are available in the ViennaRNA package starting from version 2.6.0.

DNA Materials Assembled from One DNA Strand

Due to the specific base-pairing recognition, clear nanostructure, programmable sequence and responsiveness of the DNA molecule, DNA materials have attracted extensive attention and been widely used in controlled release, drug delivery and tissue engineering. Generally, the strategies for preparing DNA materials are based on the assembly of multiple DNA strands. The construction of DNA materials using only one DNA strand can not only save time and cost, but also avoid defects in final assemblies generated by the inaccuracy of DNA ratios, which potentially promote the large-scale production and practical application of DNA materials. In order to use one DNA strand to form assemblies, the sequences have to be palindromes with lengths that need to be controlled carefully. In this review, we introduced the development of DNA assembly and mainly summarized current reported materials formed by one DNA strand. We also discussed the principle for the construction of DNA materials using one DNA strand.

RNA sequence and structure control assembly and function of RNA condensates

Intracellular condensates formed through liquid-liquid phase separation (LLPS) primarily contain proteins and RNA. Recent evidence points to major contributions of RNA self-assembly in the formation of intracellular condensates. As the majority of previous studies on LLPS have focused on protein biochemistry, effects of biological RNAs on LLPS remain largely unexplored. In this study, we investigate the effects of crowding, metal ions, and RNA structure on formation of RNA condensates lacking proteins. Using bacterial riboswitches as a model system, we first demonstrate that LLPS of RNA is promoted by molecular crowding, as evidenced by formation of RNA droplets in the presence of polyethylene glycol (PEG 8K). Crowders are not essential for LLPS, however. Elevated Mg²⁺ concentrations promote LLPS of specific riboswitches without PEG. Calculations identify key RNA structural and sequence elements that potentiate the formation of PEG-free condensates; these calculations are corroborated by key wet-bench experiments. Based on this, we implement structure-guided design to generate condensates with novel functions including ligand binding. Finally, we show that RNA condensates help protect their RNA components from degradation by nucleases, suggesting potential biological roles for such higher-order RNA assemblies in controlling gene expression through RNA stability. By utilizing both natural and artificial RNAs, our study provides mechanistic insight into the contributions of intrinsic RNA properties and extrinsic environmental conditions to the formation and regulation of condensates comprised of RNAs.

Mass Spectrometry of Nucleic Acid Noncovalent Complexes

Nucleic acids have been among the first targets for antitumor drugs and antibiotics. With the unveiling of new biological roles in regulation of gene expression, specific DNA and RNA structures have become very attractive targets, especially when the corresponding proteins are undruggable. Biophysical assays to assess target structure as well as ligand binding stoichiometry, affinity, specificity, and binding modes are part of the drug development process. Mass spectrometry offers unique advantages as a biophysical method owing to its ability to distinguish each stoichiometry present in a mixture. In addition, advanced mass spectrometry approaches (reactive probing, fragmentation techniques, ion mobility spectrometry, ion spectroscopy) provide more detailed information on the complexes. Here, we review the fundamentals of mass spectrometry and all its particularities when studying noncovalent nucleic acid structures, and then review what has been learned thanks to mass spectrometry on nucleic acid structures, self-assemblies (e.g., duplexes or G-quadruplexes), and their complexes with ligands.

Use of anion-exchange HPLC to study DNA conformational polymorphism

Anion-exchange chromatography carried out under non-denaturing conditions is a versatile tool to differentiate DNA conformations. In this work, the utility of this form of HPLC was demonstrated in four examples. The hairpin and duplex forms of d(CG)₉ were readily resolved, which allowed for the studies of the influence of salt on the equilibrium of these two forms of secondary structures. Similarly, the minimum size of Tn in the loop region required for the sequence 5'-d(CCCAA-(T)n-TTGGG)-3' to form hairpin was established to be two nucleotides using anion-exchange HPLC and fluorescence resonance energy transfer. Furthermore, the efficiency of hybridization of partially self-complementary sequences d[(CG)₆N_x] was readily monitored by non-denaturing anion-exchange HPLC. Finally, different structures adopted by quadruplex-forming sequences were resolved in the same manner.

Single-Molecule Mechanical Unfolding of AT-Rich Chromosomal Fragile Site DNA Hairpins: Resolving the Thermodynamic and Kinetic Effects of a Single G-T Mismatch

Chromosomal fragile sites (CFSs) contain AT-rich sequences that tend to form hairpins on lagging strands in DNA replication, making them hotspots for chromosomal rearrangements in cancers. Here, we investigate the structural stability of the AT-rich CFS DNA hairpins with a single non-AT base pair using magnetic tweezers. Strikingly, a single G-T mismatched base pair in the short CFS DNA hairpin gives a 38.7% reduction of the unfolding Gibbs free energy and a 100-fold increase of the transition kinetics compared to a single G-C matched base pair, which are deviated from the theoretical simulations. Our study reveals the unique features of CFSs to provide profound insights into chromosomal instability and structure-specific genome targeting therapeutics for genetic disorder-related diseases.

Validation of the nearest-neighbor model for Watson-Crick self-complementary DNA duplexes in molecular crowding condition

Recent advancement in nucleic acid techniques inside cells demands the knowledge of the stability of nucleic acid structures in molecular crowding. The nearest-neighbor model has been successfully used to predict thermodynamic parameters for the formation of nucleic acid duplexes, with significant accuracy in a dilute solution. However, knowledge about the applicability of the model in molecular crowding is still limited. To determine and predict the stabilities of DNA duplexes in a cell-like crowded environment, we systematically investigated the validity of the nearest-neighbor model for Watson–Crick self-complementary DNA duplexes in molecular crowding. The thermodynamic parameters for the duplex formation were measured in the presence of 40 wt% poly(ethylene glycol)200 for different self-complementary DNA oligonucleotides consisting of identical nearest-neighbors in a physiological buffer containing 0.1 M NaCl. The thermodynamic parameters as well as the melting temperatures (T_m) obtained from the UV melting studies revealed similar values for the oligonucleotides having identical nearest-neighbors, suggesting the validity of the nearest-neighbor model in the crowding condition. Linear relationships between the measured ΔG°₃₇ and T_m in crowding condition and those predicted in dilute solutions allowed us to predict ΔG°₃₇, T_m and nearest-neighbor parameters in molecular crowding using existing parameters in the dilute condition, which provides useful information about the thermostability of the self-complementary DNA duplexes in molecular crowding.

Control of the polyamine biosynthesis pathway by G2-quadruplexes

G-quadruplexes are naturally-occurring structures found in RNAs and DNAs. Regular RNA G-quadruplexes are highly stable due to stacked planar arrangements connected by short loops. However, reports of irregular quadruplex structures are increasing and recent genome-wide studies suggest that they influence gene expression. We have investigated a grouping of G2-motifs in the UTRs of eight genes involved in polyamine biosynthesis, and concluded that several likely form novel metastable RNA G-quadruplexes. We performed a comprehensive biophysical characterization of their properties, comparing them to a reference G-quadruplex. Using cellular assays, together with polyamine-depleting and quadruplex-stabilizing ligands, we discovered how some of these motifs regulate and sense polyamine levels, creating feedback loops during polyamine biosynthesis. Using high-resolution 1H-NMR spectroscopy, we demonstrated that a long-looped quadruplex in the AZIN1 mRNA co-exists in salt-dependent equilibria with a hairpin structure. This study expands the repertoire of regulatory G-quadruplexes and demonstrates how they act in unison to control metabolite homeostasis.

Trifluoroacetophenone-Linked Nucleotides and DNA for Studying of DNA-Protein Interactions by 19F NMR Spectroscopy

A series of 7-[4-(trifluoroacetyl)phenyl]-7-deazaadenine and -7-deazaguanine as well as 5-substituted uracil and cytosine 2'-deoxyribonucleosides and mono- and triphosphates were synthesized through aqueous Suzuki-Miyaura crosscoupling of halogenated nucleosides or nucleotides with 4-(trifluoroacetyl)phenylboronic acid. The modified nucleoside triphosphates were good substrates for DNA polymerases applicable in primer extension or PCR synthesis of modified oligonucleotides or DNA. Attempted cross-linking with a serine-containing protein did not proceed, however the trifluoroacetophenone group was a sensitive probe for the study of DNA-protein interactions by ¹⁹F NMR.

Use of a Ureido-Substituted Deoxycytidine Module for DNA Assemblies

Ureido-substituted cytosine derivatives are promising for constructing self-assembly structures that can be applied to nanotechnology research. However, conventional cytosine modules achieve assembly in organic solvents. In this study, an N-phenylcarbamoyl deoxycytidine nucleoside was incorporated into a C-rich oligonucleotide to achieve self-assembly in aqueous solution. The results show that the capability of the module to form DNA assemblies varied depending on the number of modules incorporated. The deoxycytidine derivative has a potential application in the development of smart materials based on DNA assembly.

1.25 Å resolution structure of an RNA 20-mer that binds to the TREX2 complex

The 1.25 Å resolution H32:R crystal structure of a 20 nt ribonucleotide that binds to the TREX-2 complex with high affinity shows a double-stranded RNA duplex arranged along a crystallographic 31 axis in which the antiparallel chains overlap by 18 nucleotides and are related by a crystallographic twofold axis. The duplex shows C-A, U-U and C-C noncanonical base pairings together with canonical Watson-Crick A-U and G-C pairs and a G-U wobble.

Multiple approaches for the investigation of bacterial small regulatory RNAs self-assembly

RNAs are flexible molecules involved in a multitude of roles in the cell. Specifically, noncoding RNAs (i.e., RNAs that do not encode a protein) have important functions in the regulation of biological processes such as RNA decay, translation, or protein translocation. In bacteria, most of those noncoding RNAs have been shown to be critical for posttranscriptional control through their binding to the untranslated regions of target mRNAs. Recent evidence shows that some of these noncoding RNAs have the propensity to self-assemble in prokaryotes. Although the function of this self-assembly is not known and may vary from one RNA to another, it offers new insights into riboregulation pathways. We present here the various approaches that can be used for the detection and analysis of bacterial small noncoding RNA self-assemblies.

Enantioselective recognition mechanism of ofloxacin via Cu(II)-modulated DNA

The specific interactions of Cu(2+) with self-complementary DNA sequences involving d[G4C4(GC)2G4C4], d[(GC)10], and d[(AT)10], as well as the chiral recognition mechanism of ofloxacin enantiomers via the Cu(II)-modulated DNAs, were investigated using characterizations of circular dichroism, gel electrophoresis, FT-IR spectroscopy, UV melting measurement, electron paramagnetic resonance, and HPLC. The Cu(II)-coordinated GC-rich DNAs exhibit amplified enantioselectivity toward the S-enantiomer of ofloxacin. Especially in the case of d[G4C4(GC)2G4C4], ofloxacin enantiomers intercalate into the two adjacent guanine bases through the minor groove mediated by Cu(2+), which leads to a more favorable binding between S-ofloxacin and DNA. The highest ee value of ofloxacin enantiomers in the permeate after being adsorbed by the Cu(II)-DNA complex is obtained as 49.2% in the R-enantiomer at the [Cu(2+)]/[base] molar ratio of 0.25, while at the [Cu(2+)]/[base] molar ratio of 0.05 the highest ee value of ofloxacin enantiomers in the retentate reaches 26.3% in the S-enantiomer. This work illustrates a novel promising route to construct DNA-based chiral selectors toward certain drug enantiomers through the programmable enantioselective recognition on the basis of DNA chirality and the specific binding of transition metal ions.

Master sensors of pathogenic RNA - RIG-I like receptors

Initiating the immune response to invading pathogens, the innate immune system is constituted of immune receptors (pattern recognition receptors, PRR) that sense microbe-associated molecular patterns (MAMPs). Detection of pathogens triggers intracellular defense mechanisms, such as the secretion of cytokines or chemokines to alarm neighboring cells and attract or activate immune cells. The innate immune response to viruses is mostly based on PRRs that detect the unusual structure, modification or location of viral nucleic acids. Most of the highly pathogenic and emerging viruses are RNA genome-based viruses, which can give rise to zoonotic and epidemic diseases or cause viral hemorrhagic fever. As viral RNA is located in the same compartment as host RNA, PRRs in the cytosol have to discriminate between viral and endogenous RNA by virtue of their structure or modification. This challenging task is taken on by the homologous cytosolic DExD/H-box family helicases RIG-I and MDA5, which control the innate immune response to most RNA viruses. This review focuses on the molecular basis for RIG-I like receptor (RLR) activation by synthetic and natural ligands and will discuss controversial ligand definitions.

Dimerization of nucleic acid hairpins in the conditions caused by neutral cosolutes

Characterization of metal ion binding to RNA and DNA base pairs is important for understanding their energy contribution to the folding and conformational changes of nucleic acid structures. In this study, we examine the equilibrium shift from the hairpin toward the dimer formation, induced by nonspecifically bound metal ions. The hairpin dimerization is markedly enhanced in the presence of high background concentrations of poly(ethylene glycol) (PEG) and several small organic molecules. The simple volume exclusion effect and the base pair stability cannot entirely account for this increase. We find that the dielectric constant correlates well with the dimerization efficiency in the conditions caused by small alcohol molecules and amide compounds as well as PEG. The hairpin dimerization experiments reveal the potential of PEG for enhancing the binding affinity between nucleic acids and metal ions, by reducing the solution dielectric constant without decreasing the thermodynamic stability of nucleic acid structures. The results presented here contribute to the understanding of nucleic acid folding and its ability to switch between alternative conformations under the condition of limited cation availability and cellular physiology.

Complexity in the binding of minor groove agents: netropsin has two thermodynamically different DNA binding modes at a single site

Structural results with minor groove binding agents, such as netropsin, have provided detailed, atomic level views of DNA molecular recognition. Solution studies, however, indicate that there is complexity in the binding of minor groove agents to a single site. Netropsin, for example, has two DNA binding enthalpies in isothermal titration calorimetry (ITC) experiments that indicate the compound simultaneously forms two thermodynamically different complexes at a single AATT site. Two proposals for the origin of this unusual observation have been developed: (i) two different bound species of netropsin at single binding sites and (ii) a netropsin induced DNA hairpin to duplex transition. To develop a better understanding of DNA recognition complexity, the two proposals have been tested with several DNAs and the methods of mass spectrometry (MS), polyacrylamide gel electrophoresis (PAGE) and nuclear magnetic resonance spectroscopy in addition to ITC. All of the methods with all of the DNAs investigated clearly shows that netropsin forms two different complexes at AATT sites, and that the proposal for an induced hairpin to duplex transition in this system is incorrect.

RNA dimerization monitored by fluorescence correlation spectroscopy

Fluorescence correlation spectroscopy (FCS) provides a versatile tool to investigate molecular interaction under native conditions, approximating infinite dilution. One precondition for its application is a sufficient difference between the molecular weights of the fluorescence-labelled unbound and bound ligand. In previous studies, an 8-fold difference in molecular weights or correspondingly a 1.6-fold difference in diffusion coefficients was required to accurately distinguish between two diffusion species by FCS. In the presented work, the hybridization of two complementary equally sized RNA single strands was investigated at an excellent signal-to-noise ratio enabled by the highly photostable fluorophore Atto647N. The fractions of ssRNA and dsRNA were quantified by applying multicomponent model analysis of single autocorrelation functions and globally fitting several autocorrelation functions. By introducing a priori knowledge into the fitting procedure, 1.3- to 1.4-fold differences in diffusion coefficients of single- and double-stranded RNA of 26, 41, and 54 nucleotides could be accurately resolved. Global fits of autocorrelation functions of all titration steps enabled a highly accurate quantification of diffusion species fractions and mobilities. At a high signal-to-noise ratio, the median of individually fitted autocorrelation functions allowed a robust representation of heterogeneous data. These findings point out the possibility of studying molecular interaction of equally sized molecules based on their diffusional behavior, which significantly broadens the application spectrum of FCS.

Cationic modified nucleic acids for use in DNA hairpins and parallel triplexes

Non-nucleosidic DNA monomers comprising partially protonated amines at low pH have been designed and synthesized. The modifications were incorporated into DNA oligonucleotides via standard DNA phosphoramidite synthesis. The ability of cationic modifications to stabilize palindromic DNA hairpins and parallel triplexes were evaluated using gel electrophoresis, circular dichroism and thermal denaturation measurements. The non-nucleosidic modifications were found to increase the thermal stability of palindromic hairpins at pH 8.0 as compared with a nucleosidic tetraloop (TCTC). Incorporation of modifications at the 5'-end of a triplex forming oligonucleotide resulted in a significant increase in thermal stability at low pH when the modifications were placed as the 5'-dangling end.

Hexamer oligonucleotide topology and assembly under solution phase NMR and theoretical modeling scrutiny

The entire family of noncomplementary hexamer oligodeoxyribonucleotides d(GCXYGC) (X and Y = A, G, C, or T) were assessed for topological indicators and equilibrium thermodynamics using a priori molecular modeling and solution phase NMR spectroscopy. Feasible modeled hairpin structures formed a basis from which solution structure and equilibria for each oligonucleotide were considered. ¹H and ³¹P variable temperature-dependent (VT) and concentration-dependent NMR data, NMR signal assignments, and diffusion parameters led to d(GCGAGC) and d(GCGGGC) being understood as exceptions within the family in terms of self-association and topological character. A mean diffusion coefficient D(298 K) = (2.0 ± 0.07) × 10⁻¹⁰ m² s⁻¹ was evaluated across all hexamers except for d(GCGAGC) (D(298 K) = 1.7 × 10⁻¹⁰ m² s⁻¹) and d(GCGGGC) (D(298 K) = 1.2 × 10⁻¹⁰ m² s⁻¹). Melting under VT analysis (T(m) = 323 K) combined with supporting NMR evidence confirmed d(GCGAGC) as the shortest tandem sheared GA mismatched duplex. Diffusion measurements were used to conclude that d(GCGGGC) preferentially exists as the shortest stable quadruplex structure. Thermodynamic analysis of all data led to the assertion that, with the exception of XY = GA and GG, the remaining noncomplementary oligonucleotides adopt equilibria between monomer and duplex, contributed largely by monomer random-coil forms. Contrastingly, d(GCGAGC) showed preference for tandem sheared GA mismatch duplex formation with an association constant K = 3.9 × 10⁵M⁻¹. No direct evidence was acquired for hairpin formation in any instance although its potential existence is considered possible for d(GCGAGC) on the basis of molecular modeling studies.

Crystallization and preliminary X-ray diffraction analysis of a self-complementary DNA heptacosamer with a 20-base-pair duplex flanked by seven-nucleotide overhangs at the 3'-terminus

The self-complementary DNA heptacosamer (a 27-mer oligonucleotide) with sequence d(CGAGCACTGCGCAGTGCTCGTTGTTAT) forms a 20-base-pair duplex flanked by seven-nucleotide overhangs at the 3'-terminus. Crystals of the oligonucleotide were obtained by sitting-drop vapour diffusion and diffracted to 2.8 A resolution. The oligonucleotide was crystallized at 277 K using polyethylene glycol as a precipitant in the presence of magnesium chloride. The crystals belonged to the triclinic space group, with unit-cell parameters a = 48.74, b = 64.23, c = 79.34 A, alpha = 91.37, beta = 93.21, gamma = 92.35 degrees .

Synthesis and hybridization properties of modified oligodeoxynucleotides carrying non-natural bases

The impact of the presence of nonnatural bases on the properties of oligodeoxynucleotides has been studied. First, oligodeoxynucleotides carrying 2'-deoxyzebularine were prepared, and the stability of duplexes carrying this analogue was determined by DNA melting experiments. Melting temperatures and thermodynamic data indicated the preference of 2'-deoxyzebularine for 2'-deoxyguanosine, which behaves as a 2'-deoxycytidine analogue, forming a less stable base pair due to the absence of the amino group at position 4. Moreover, the duplex-hairpin equilibrium of a self-complementary oligodeoxynucleotide carrying several natural and nonnatural bases including 2'-deoxyzebularine as a central mispair, was studied. Depending on the base present in the middle of the sequence, it is possible to affect the stability of the bimolecular duplex modulating the duplex-hairpin equilibrium. Magnesium ions were shown to stabilize preferentially the bimolecular duplex form. The results indicate the importance of the modifications and the role of cations in shifting the structural equilibrium.

Capture of cationic ligands bound diffusely to base pairs during DNA refolding

We obtained the intrinsic binding affinity for metal ions, polyamines, and oligolysine peptides diffusely bound to base-paired sites in DNA by monitoring the shift of the hairpin-duplex equilibrium of the self-complementary DNA sequences, which can be widely used for capturing cationic ligands bound diffusely to nucleotide base pairs.

Conformation and the sodium ion condensation on DNA and RNA structures in the presence of a neutral cosolute as a mimic of the intracellular media

Water-soluble neutral cosolutes can be used to quantify biomolecular properties in the particular molecular environment occurring in a cell. We studied the conformation and the thermal stability of DNA and RNA structures in the presence of PEG [poly(ethylene glycol)] and smaller cosolutes of glycerol, ethylene glycol, 1,3-propanediol, 2-methoxyethanol, and 1,2-dimethoxyethane. Although the neutral cosolutes destabilized the oligonucleotide duplex and the hairpin structures, the left-handed Z-form duplex was more energetically favored in the cosolute-containing solutions. These observations were due to the contribution of water molecule on the nucleotide structure formations because the cosolutes act as an osmolyte to reduce the water activity of a solution. Moreover, the sodium ion condensation for the duplex and the hairpin formations was reduced in the presence of PEG, while that for the transition from the B-form to the Z-form was unaltered. The CD (circular dichroism) and EPR (electron paramagnetic resonance) spectra demonstrated that the cosolutes changed the helical conformation of the unstructured oligonucleotides, but not those of the ordered structures. The results of the favorable formation of the noncanonical nucleotide structures, and minimized conformational and thermal perturbations of the ordered nucleotide structures in the cosolute-containing solutions implicate the significance of the intracellular environment on DNA and RNA structures in a cell.

Database resources of the National Center for Biotechnology Information

In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data available through NCBI's web site. NCBI resources include Entrez, the Entrez Programming Utilities, My NCBI, PubMed, PubMed Central, Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link, Electronic PCR, OrfFinder, Spidey, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosomes, Entrez Genome, Genome Project and related tools, the Trace, Assembly, and Short Read Archives, the Map Viewer, Model Maker, Evidence Viewer, Clusters of Orthologous Groups, Influenza Viral Resources, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus, Entrez Probe, GENSAT, Database of Genotype and Phenotype, Online Mendelian Inheritance in Man, Online Mendelian Inheritance in Animals, the Molecular Modeling Database, the Conserved Domain Database, the Conserved Domain Architecture Retrieval Tool and the PubChem suite of small molecule databases. Augmenting the web applications are custom implementations of the BLAST program optimized to search specialized data sets. These resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.

What drives the binding of minor groove-directed ligands to DNA hairpins?

Understanding the molecular basis of ligand-DNA-binding events, and its application to the rational design of novel drugs, requires knowledge of the structural features and forces that drive the corresponding recognition processes. Existing structural evidence on DNA complexation with classical minor groove-directed ligands and the corresponding studies of binding energetics have suggested that this type of binding can be described as a rigid-body association. In contrast, we show here that the binding-coupled conformational changes may be crucial for the interpretation of DNA (hairpin) association with a classical minor groove binder (netropsin). We found that, although the hairpin form is the only accessible state of ligand-free DNA, its association with the ligand may lead to its transition into a duplex conformation. It appears that formation of the fully ligated duplex from the ligand-free hairpin, occurring via two pathways, is enthalpically driven and accompanied by a significant contribution of the hydrophobic effect. Our thermodynamic and structure-based analysis, together with corresponding theoretical studies, shows that none of the predicted binding steps can be considered as a rigid-body association. In this light we anticipate our thermodynamic approach to be the basis of more sophisticated nucleic acid recognition mechanisms, which take into account the dynamic nature of both the nucleic acid and the ligand molecule.