Stability Of Nucleic Acids Research Articles

Nucleic Acid Unwinding by Hepatitis C Virus and Bacteriophage T7 Helicases Is Sensitive to Base Pair Stability

Helicases are motor enzymes that convert the chemical energy of NTP hydrolysis into mechanical force for motion and nucleic acid strand separation. Within the cell, helicases process a range of nucleic acid sequences. It is not known whether this composite rate of moving and opening the strands of nucleic acids depends on the base sequence. Our presteady state kinetic studies of helicases from two classes, the ring-shaped T7 helicase and two forms of non-ring-shaped hepatitis C virus (HCV) helicase, show that both the unwinding rate and processivity depend on the sequence and decrease as the nucleic acid stability increases. The DNA unwinding activity of T7 helicase and the RNA unwinding activity of HCV helicases decrease steeply with increasing base pair stability. On the other hand, the DNA unwinding activity of HCV helicases is less sensitive to base pair stability. These results predict that helicases will fall into a spectrum of modest to high sensitivity to base pair stability depending on their biological role in the cell. Modeling of the dependence provided the degree of the active involvement of helicase in base pair destabilization during the unwinding process and distinguished between passive and active mechanisms of unwinding.

A chemical synthesis of LNA-2,6-diaminopurine riboside, and the influence of 2'-O-methyl-2,6-diaminopurine and LNA-2,6-diaminopurine ribosides on the thermodynamic properties of 2'-O-methyl RNA/RNA heteroduplexes.

Modified nucleotides are useful tools to study the structures, biological functions and chemical and thermodynamic stabilities of nucleic acids. Derivatives of 2,6-diaminopurine riboside (D) are one type of modified nucleotide. The presence of an additional amino group at position 2 relative to adenine results in formation of a third hydrogen bond when interacting with uridine. New method for chemical synthesis of protected 3′-O-phosphoramidite of LNA-2,6-diaminopurine riboside is described. The derivatives of 2′-O-methyl-2,6-diaminopurine and LNA-2,6-diaminopurine ribosides were used to prepare complete 2′-O-methyl RNA and LNA-2′-O-methyl RNA chimeric oligonucleotides to pair with RNA oligonucleotides. Thermodynamic stabilities of these duplexes demonstrated that replacement of a single internal 2′-O-methyladenosine with 2′-O-methyl-2,6-diaminopurine riboside (DM) or LNA-2,6-diaminopurine riboside (DL) increases the thermodynamic stability (ΔΔG°37) on average by 0.9 and 2.3 kcal/mol, respectively. Moreover, the results fit a nearest neighbor model for predicting duplex stability at 37°C. D-A and D-G but not D-C mismatches formed by DM or DL generally destabilize 2′-O-methyl RNA/RNA and LNA-2′-O-methyl RNA/RNA duplexes relative to the same type of mismatches formed by 2′-O-methyladenosine and LNA-adenosine, respectively. The enhanced thermodynamic stability of fully complementary duplexes and decreased thermodynamic stability of some mismatched duplexes are useful for many RNA studies, including those involving microarrays.

Synthesis and structure of fluoroindole nucleosides

Chemically modified bases are frequently used to stabilize nucleic acids, to study the driving forces for nucleic acid structure formation, and to tune DNA and RNA hybridization conditions. Nucleoside analogues are chemical means to investigate hydrogen bonds, base stacking, and solvation as the three predominant forces that are responsible for the stability of nucleic acids. To obtain deeper insight into the contributions of these interactions to RNA stability, we decided to synthesize some novel nucleic acid analogues where the nucleobases are replaced by fluoroindoles. Fluorinated indoles can be compared with fluorinated benzimidazoles to determine the role of nitrogen in five-membered ring systems. The synthesis of fluoroindole ribonucleosides as well as the X-ray crystal structures of all synthesized fluoroindole ribonucleosides are reported here. These compounds could also be building blocks for a variety of biologically active RNA analogues.Key words: indoles, nucleosides, crystal structure, glycosilation, indole-synthesis.

Synthetic Delivery Systems for Intravenous Administration of Nucleic Acids

At present, there are no intravenously administered nucleic acid-based therapeutics that have been approved for human use. This reflects the difficulties in applying nucleic acid-based drugs: they are nuclease sensitive and have difficulties in reaching their site of action. Important challenges for intravenously administered nucleic acid formulations are the requirements that they can transport the nucleic acids efficiently in the circulation, have the ability to direct nucleic acids to the desired cell type and are able to steer their intracellular processing. Here, we evaluate nanotechnological strategies that improve the pharmacokinetics and colloidal stability of nucleic acids in the bloodstream, focus biodistribution towards the target tissue and facilitate interactions with and trafficking within the desired cell type.

A Simple Molecular Model for Thermophilic Adaptation of Functional Nucleic Acids

RNA molecules have numerous functions including catalysis and small molecule recognition, which typically arise from a tertiary structure. There is increasing interest in mechanisms for the thermostability of functional RNA molecules. Sosnick, Pan, and co-workers introduced the notion of "functional stability" as the free energy of the tertiary (functional) state relative to the next most stable (nonfunctional) state. We investigated the extent to which secondary structure stability influences the functional stability of nucleic acids. Intramolecularly folding DNA triplexes containing alternating T*AT and C+*GC base triples were used as a three-state model for the folding of nucleic acids with functional tertiary structures. A four-base-pair tunable region was included adjacent to the triplex-forming portion of the helix to allow secondary structure strength to be modulated. The degree of folding cooperativity was controlled by pH, with high cooperativity maintained by lower pH (5.5), and no cooperativity by higher pH (7.0). We find a linear relationship between functional free energy and the free energy of the secondary structure element adjacent to tertiary interactions, but only when folding is cooperative. We translate the definition of functional stability into equations and perform simulations of the thermodynamic data, which lend support to this model. The ability to increase the melting temperature of tertiary structure by strengthening base-pairing interactions separate from tertiary interactions provides a simple means for evolving thermostability in functional RNAs.

Storage stability of nucleic acids in the body louse, Pediculus humanus

Storage stability of nucleic acids in the body louse, Pediculus humanus

Trehalose Click Polymers Inhibit Nanoparticle Aggregation and Promote pDNA Delivery in Serum

Herein, three new glycopolymers have been synthesized via "click polymerization" to promote nucleic acid delivery in the presence of biological media containing serum. These structures were designed to contain a trehalose moiety to promote biocompatibility, water solubility, and stability against aggregation, amide-triazole groups to enhance DNA binding affinity, and an oligoamine unit to facilitate DNA encapsulation, phosphate neutralization, and interactions with cell surfaces. A 2,3,4,2',3',4'-hexa-O-acetyl-6,6'-diazido-6,6'-dideoxy-D-trehalose (4) monomer was polymerized via copper(I)-catalyzed azide-alkyne cycloaddition with a series of dialkyne-amide comonomers that contain either one, two, or three Boc-protected secondary amines (7a, 7b, or 7c, respectively). After deprotection, three water-soluble polycations (9a, 9b, or 9c) were obtained with similar degrees of polymerization (n = 56-61) to elucidate the role of amine number on nucleic acid binding, complex formation, stability, and cellular delivery. Gel electrophoresis and ethidium bromide experiments showed that 9a-9c associated with plasmid DNA (pDNA) and formed complexes (polyplexes) at N/P ratios dependent on the amine number. TEM experiments revealed that 9a-9c polyplexes were small (50-120 nm) and had morphologies (spherical and rodlike) associated with the polymer chain stiffness. Dynamic light scattering studies in the presence of media containing serum demonstrated that 9c polyplexes had a low degree of flocculation, whereas 9a and 9b polyplexesd aggregate rapidly. Further biological studies revealed that these structures were biocompatible and deliver pDNA into HeLa cells. Particularly, 9c polyplexes promoted high delivery efficacy and gene expression profiles in the presence of serum.

Molecular thermodynamics for charged biomacromolecules

Significant progress has been made over the past 25–30 years toward understanding the molecular basis of stability and biological functions of proteins and nucleic acids. Electrostatic calculations hold a prominent place among most advanced and popular computational methods to describe the influence of solution conditions on and the precise role played by individual amino acids or atoms in stability, folding and molecular recognition. In this article, we present a tutorial overview of coarse-grained and atomistic thermodynamic methods commonly used in modeling electrostatic interactions that are prevalent among biological processes including structural transitions of biomacromolecules and ligand–receptor associations. Illustrative examples are discussed on applications of these thermodynamics models to computational design of proteins with improved function and stability, to charge-transfer equilibria, to structure transitions of nucleic acids and proteins, to protein–ligand interactions, and to ion transport through lipid membranes. Some perspectives are also given on the future trends of computational modeling in biological thermodynamics.

Nucleic Acid Helix Stability: Effects of Salt Concentration, Cation Valence and Size, and Chain Length

Metal ions play crucial roles in thermal stability and folding kinetics of nucleic acids. For ions (especially multivalent ions) in the close vicinity of nucleic acid surface, interion correlations and ion-binding mode fluctuations may be important. Poisson-Boltzmann theory ignores these effects whereas the recently developed tightly bound ion (TBI) theory explicitly accounts for these effects. Extensive experimental data demonstrate that the TBI theory gives improved predictions for multivalent ions (e.g., Mg 2+) than the Poisson-Boltzmann theory. In this study, we use the TBI theory to investigate how the metal ions affect the folding stability of B-DNA helices. We quantitatively evaluate the effects of ion concentration, ion size and valence, and helix length on the helix stability. Moreover, we derive practically useful analytical formulas for the thermodynamic parameters as functions of finite helix length, ion type, and ion concentration. We find that the helix stability is additive for high ion concentration and long helix and nonadditive for low ion concentration and short helix. All these results are tested against and supported by extensive experimental data.

Influence of Thioketo Substitution on the Properties of Uracil and Its Noncovalent Interactions with Alkali Metal Ions: Threshold Collision-Induced Dissociation and Theoretical Studies

Experimental and theoretical studies are carried out to determine the influence of thioketo substitution on the properties of uracil and its noncovalent interactions with alkali metal ions. Bond dissociation energies of alkali metal ion-thiouracil complexes, M(+)(SU), are determined using threshold collision-induced dissociation techniques in a guided ion beam mass spectrometer, where M(+) = Li(+), Na(+), and K(+) and SU = 2-thiouracil, 4-thiouracil, 2,4-dithiouracil, 5-methyl-2-thiouracil, and 6-methyl-2-thiouracil. Ab initio electronic structure calculations are performed to determine the structures and theoretical bond dissociation energies of these complexes and provide molecular constants necessary for thermodynamic analysis of the experimental data. Theoretical calculations are also performed to examine the influence of thioketo substitution on the acidities, proton affinities, and A::SU Watson-Crick base pairing energies. In general, thioketo substitution leads to an increase in both the proton affinity and the acidity of uracil. 2-Thio substitution generally results in an increase in the alkali metal ion binding affinities but has almost no affect on the stability of the A::SU base pair. In contrast, 4-thio substitution results in a decrease in the alkali metal ion binding affinities and a significant decrease in the stability of the A::SU base pair. In addition, alkali metal ion binding is expected to lead to an increase in the stability of both single-stranded and double-stranded nucleic acids by reducing the charge on the nucleic acid in a zwitterion effect as well as through additional noncovalent interactions between the alkali metal ion and the nucleobases.

Unfolding of DNA quadruplexes induced by HIV-1 nucleocapsid protein

The human immunodeficiency virus type 1 nucleocapsid protein (NC) is a nucleic acid chaperone that catalyzes the rearrangement of nucleic acids into their thermodynamically most stable structures. In the present study, a combination of optical and thermodynamic techniques were used to characterize the influence of NC on the secondary structure, thermal stability and energetics of monomolecular DNA quadruplexes formed by the sequence d(GGTTGGTGTGGTTGG) in the presence of K+ or Sr2+. Circular dichroism studies demonstrate that NC effectively unfolds the quadruplexes. Studies carried out with NC variants suggest that destabilization is mediated by the zinc fingers of NC. Calorimetric studies reveal that NC destabilization is enthalpic in origin, probably owing to unstacking of the G-quartets upon protein binding. In contrast, parallel studies performed on a related DNA duplex reveal that under conditions where NC readily destabilizes and unfolds the quadruplexes, its effect on the DNA duplex is much less pronounced. The differences in NC's ability to destabilize quadruplex versus duplex is in accordance with the higher ΔG of melting for the latter, and with the inverse correlation between nucleic acid stability and the destabilizing activity of NC.

The FoldX web server: an online force field

FoldX is an empirical force field that was developed for the rapid evaluation of the effect of mutations on the stability, folding and dynamics of proteins and nucleic acids. The core functionality of FoldX, namely the calculation of the free energy of a macromolecule based on its high-resolution 3D structure, is now publicly available through a web server at . The current release allows the calculation of the stability of a protein, calculation of the positions of the protons and the prediction of water bridges, prediction of metal binding sites and the analysis of the free energy of complex formation. Alanine scanning, the systematic truncation of side chains to alanine, is also included. In addition, some reporting functions have been added, and it is now possible to print both the atomic interaction networks that constitute the protein, print the structural and energetic details of the interactions per atom or per residue, as well as generate a general quality report of the pdb structure. This core functionality will be further extended as more FoldX applications are developed.

Essential role for TRPM6 in epithelial magnesium transport and body magnesium homeostasis

Magnesium is an important cofactor for many biological processes such as protein synthesis, nucleic acid stability and neuromuscular excitability. The extracellular magnesium concentration is regulated tightly by the extent of intestinal absorption and renal excretion. Despite their critical role in magnesium handling, the molecular mechanisms mediating transepithelial transport are still not understood completely. Recently, genetic studies in patients with primary hypomagnesaemia and secondary hypocalcaemia (HSH), a combined defect of intestinal magnesium absorption and renal magnesium conservation, have identified "transient receptor potential (melastatin) 6" (TRPM6) as the first component involved directly in epithelial magnesium reabsorption. TRPM7, the closest homologue of TRPM6, has a central role in Mg(2+) uptake in vertebrate cells since TRPM7-deficient cells become Mg(2+) deficient and are not viable. TRPM7 has been characterized functionally as a constitutively active ion channel permeable for a variety of cations including calcium and magnesium and regulated by intracellular concentrations of magnesium and/or magnesium-nucleotide complexes. Both proteins share the unique feature of cation channels fused to serine/threonine kinase domains. This review summarizes recent data that has emerged from molecular genetic, biochemical and electrophysiological studies on these fascinating two new proteins and their involvement in epithelial magnesium transport.

Stabilization of nucleic acids by unusual polyamines produced by an extreme thermophile, Thermus thermophilus

Extreme thermophiles produce two types of unusual polyamine: long linear polyamines such as caldopentamine and caldohexamine, and branched polyamines such as quaternary ammonium compounds [e.g. tetrakis(3-aminopropyl)ammonium]. To clarify the physiological roles of long linear and branched polyamines in thermophiles, we synthesized them chemically and tested their effects on the stability of ds (double-stranded) and ss (single-stranded) DNAs and tRNA in response to thermal denaturation, as measured by differential scanning calorimetry. Linear polyamines stabilized dsDNA in proportion to the number of amino nitrogen atoms within their molecular structure. We used the empirical results to derive formulae that estimate the melting temperature of dsDNA in the presence of polyamines of a particular molecular composition. ssDNA and tRNA were stabilized more effectively by tetrakis(3-aminopropyl)ammonium than any of the other polyamines tested. We propose that long linear polyamines are effective to stabilize DNA, and tetrakis(3-aminopropyl)ammonium plays important roles in stabilizing RNAs in thermophile cells.

On the origin of genomic adaptation at high temperature for prokaryotic organisms

For a long time, the central issue of evolutionary genomics was to find out the adaptive strategy of nucleic acid molecules of various microorganisms having different optimal growth temperatures ( T opt). Long-standing controversies exist regarding the correlations between genomic G + C content and T opt, and this debate has not been yet settled. We address this problem by considering the fact that adaptation to growth at high temperature requires a coordinated set of evolutionary changes affecting: (i) nucleic acid thermostability and (ii) stability of codon–anticodon interactions. In the present study, we analyzed 16 prokaryotic genomes having intermediate G + C content and widely varying optimal growth temperatures. Results show that elevated growth temperature imposes selective constraints not only on nucleic acid level but also affects the stability of codon–anticodon interaction. We observed a decrease in the frequency of SSC and SSG codons with the increase in T opt to avoid the formation of side-by-side GC base pairs in the codon–anticodon interaction, thereby making it impossible for a genome to increase GC composition uniformly through the whole coding sequence. Thus, we suggest that any attempt to obtain a generalized relation between genomic GC composition and optimal growth temperature would hardly evolve any satisfactory result.

Stability of HCV, HIV-1 and HBV nucleic acids in plasma samples under long-term storage

The implementation of nucleic acid amplification technology (NAT) for detection of HCV, HIV-1 and HBV has undoubtedly contributed to the viral safety of blood, reducing the window period. One important matter related to the stability of RNA/DNA is the effect of the storage conditions on samples. In a previous work, we studied the stability of HCV RNA in plasma samples after storage at different temperatures. This work is an update on the follow-up of a sample containing 100 IU/ml HCV RNA for 5 years at −20 °C, showing no decrease in the initial titre. The nucleic acid stability of other viruses, such as HIV-1 and HBV, has also been studied. At −20 °C, samples containing HIV-1 were followed up for approximately 3 years and the results obtained show no decay in HIV-1 RNA detectability. Regardless of the HIV-1 RNA concentration, samples stored at 5 °C maintain their titre for at least 14 days. At 25 °C, the HIV-1 RNA half-life was determined at nearly 7 days. The HBV DNA, at 5 °C and 25 °C, is stable for at least 28 days, regardless of the initial titre.

Influence of methylation on the properties of uracil and its noncovalent interactions with alkali metal ions: Threshold collision-induced dissociation and theoretical studies

The influence of methylation on the properties of uracil and its noncovalent interactions with alkali metal ions is investigated both experimentally and theoretically. Threshold collision-induced dissociation (CID) of M +( xMeU) with Xe is studied in a guided ion beam mass spectrometer. M + include the following alkali metal ions: Li +, Na +, and K +. Five methylated uracils are examined, xMeU = 1-methyluracil, 3-methyluracil, 6-methyluracil, 1,3-dimethyluracil, and 5,6-dimethyluracil. In all cases endothermic loss of the intact nucleobase is the dominant reaction pathway, while ligand exchange to produce MXe + is observed as a minor reaction pathway. The threshold regions of the cross sections are interpreted to extract 0 and 298 K bond dissociation energies (BDEs) for M + xMeU after accounting for the effects of multiple ion-neutral collisions, kinetic and internal energies of the reactants, and dissociation lifetimes. Ab initio calculations at the MP2(full)/6–31 G* level of theory are used to determine the structures of these complexes and provide molecular constants required for the thermochemical analysis of the experimental data. Theoretical bond dissociation energies are determined from single point energy calculations at the MP2(full)/6–311 + G(2d,2p) level using the MP2(full)/6–31 G* geometries. Excellent agreement between theory and experiment is found for the Na + and K + systems, while theory systematically underestimates the strength of binding in the Li + systems. Theoretical calculations are also performed to examine the influence of methylation on the acidities, proton affinities, and Watson–Crick base pairing energies. The present results are compared to earlier studies of uracil and 5-methyluracil to more fully elucidate the influence of methylation on the properties of uracil, its noncovalent interactions with alkali metal ions, and nucleic acid stability.

Influence of Halogenation on the Properties of Uracil and Its Noncovalent Interactions with Alkali Metal Ions. Threshold Collision-Induced Dissociation and Theoretical Studies

The influence of halogenation on the properties of uracil and its noncovalent interactions with alkali metal ions is investigated both experimentally and theoretically. Bond dissociation energies of alkali metal ion-halouracil complexes, M+(XU), are determined using threshold collision-induced dissociation techniques in a guided ion beam mass spectrometer, where M+ = Li+, Na+, and K+ and XU = 5-fluorouracil, 5-chlorouracil, 6-chlorouracil, 5-bromouracil, and 5-iodouracil. The structures and theoretical bond dissociation energies of these complexes are determined from ab initio calculations. Theoretical calculations are also performed to examine the influence of halogenation on the acidities, proton affinities, and Watson-Crick base pairing energies. Halogenation of uracil is found to produce a decrease in the proton affinity, an increase in the alkali metal ion binding affinities, an increase in the acidity, and stabilization of the A::U base pair. In addition, alkali metal ion binding is expected to lead to an increase in the stability of nucleic acids by reducing the charge on the nucleic acid in a zwitterion effect as well as through additional noncovalent interactions between the alkali metal ion and the nucleobases.

Alteration of Nucleic Acid Structure and Stability Modulates the Efficiency of Minus-Strand Transfer Mediated by the HIV-1 Nucleocapsid Protein

During human immunodeficiency virus type 1 minus-strand transfer, the nucleocapsid protein (NC) facilitates annealing of the complementary repeat regions at the 3'-ends of acceptor RNA and minus-strand strong-stop DNA ((-) SSDNA). In addition, NC destabilizes the highly structured complementary trans-activation response element (TAR) stem-loop (TAR DNA) at the 3'-end of (-) SSDNA and inhibits TAR-induced self-priming, a dead-end reaction that competes with minus-strand transfer. To investigate the relationship between nucleic acid secondary structure and NC function, a series of truncated (-) SSDNA and acceptor RNA constructs were used to assay minus-strand transfer and self-priming in vitro. The results were correlated with extensive enzymatic probing and mFold analysis. As the length of (-) SSDNA was decreased, self-priming increased and was highest when the DNA contained little more than TAR DNA, even if NC and acceptor were both present; in contrast, truncations within TAR DNA led to a striking reduction or elimination of self-priming. However, destabilization of TAR DNA was not sufficient for successful strand transfer: the stability of acceptor RNA was also crucial, and little or no strand transfer occurred if the RNA was highly stable. Significantly, NC may not be required for in vitro strand transfer if (-) SSDNA and acceptor RNA are small, relatively unstructured molecules with low thermodynamic stabilities. Collectively, these findings demonstrate that for efficient NC-mediated minus-strand transfer, a delicate thermodynamic balance between the RNA and DNA reactants must be maintained.

Accurate interaction energies of hydrogen-bonded nucleic acid base pairs.

Hydrogen-bonded nucleic acids base pairs substantially contribute to the structure and stability of nucleic acids. The study presents reference ab initio structures and interaction energies of selected base pairs with binding energies ranging from -5 to -47 kcal/mol. The molecular structures are obtained using the RI-MP2 (resolution of identity MP2) method with extended cc-pVTZ basis set of atomic orbitals. The RI-MP2 method provides results essentially identical with the standard MP2 method. The interaction energies are calculated using the Complete Basis Set (CBS) extrapolation at the RI-MP2 level. For some base pairs, Coupled-Cluster corrections with inclusion of noniterative triple contributions (CCSD(T)) are given. The calculations are compared with selected medium quality methods. The PW91 DFT functional with the 6-31G basis set matches well the RI-MP2/CBS absolute interaction energies and reproduces the relative values of base pairing energies with a maximum relative error of 2.6 kcal/mol when applied with Becke3LYP-optimized geometries. The Becke3LYP DFT functional underestimates the interaction energies by few kcal/mol with relative error of 2.2 kcal/mol. Very good performance of nonpolarizable Cornell et al. force field is confirmed and this indirectly supports the view that H-bonded base pairs are primarily stabilized by electrostatic interactions.