The 1.19 A X-ray structure of 2'-O-Me(CGCGCG)(2) duplex shows dehydrated RNA with 2-methyl-2,4-pentanediol in the minor groove

Adenosine modifications impede SARS-CoV-2 RNA-dependent RNA transcription

SARS-CoV-2, the causative virus of the COVID-19 pandemic, follows SARS and MERS as recent zoonotic coronaviruses causing severe respiratory illness and death in humans. The recurrent impact of zoonotic coronaviruses demands a better understanding of their fundamental molecular biochemistry. Nucleoside modifications, which modulate many steps of the RNA life cycle, have been found in SARS-CoV-2 RNA, although whether they confer a pro- or antiviral effect is unknown. Regardless, the viral RNA-dependent RNA polymerase will encounter these modifications as it transcribes through the viral genomic RNA. We investigated the functional consequences of nucleoside modification on the pre-steady state kinetics of SARS-CoV-2 RNA-dependent RNA transcription using an in vitro reconstituted transcription system with modified RNA templates. Our findings show that N 6-methyladenosine and 2'-O-methyladenosine modifications slow the rate of viral transcription at magnitudes specific to each modification, which has the potential to impact SARS-CoV-2 genome maintenance.

Identification and screening of potential inhibitors obtained from Plumeria rubra L. compounds against type 2 diabetes mellitus

Type 2 diabetes mellitus (T2DM) is the inability of the body's cells to retaliate to insulin, which can periodically culminate into absolute insulin deficiency. Hyperinsulinemia can be alleviated by administering oral medications or insulin. Prevailing medicaments engender repercussions with prolonged use, as they transmute to an inefficacious form. Hence, it will be advantageous to design plant-derived antihyperglycemic drugs with remarkable efficacy and safety quotients to address T2DM and associated comorbidities. Based on prior research, we have identified 7 novel phytocompounds from Plumeria rubra L. and 5 co-crystals that serve as an important residence for T2DM. The compounds are assessed for their inhibitory activity and dynamic stability against five major receptors which are responsible for T2DM. Additionally, in silico ADMET assessment followed by GPU-enabled GROMACS was performed on the selected compounds. The results demonstrated that β-d-Hexaglucoside had the highest binding affinity, hydrophobicity and bond length in contrast to all the targeted receptors. β-d-Hexaglucoside was subjected to dynamic simulation to analyze the root mean square deviation and root mean square fluctuation graph rates using the GROMOS force field in GROMACS software. Furthermore, β-d-Hexaglucoside exhibited inhibitory activity against diabetic receptors with a docking score of -9.5 kcal/mol. The current study proposes β-d-Hexaglucoside as a potential candidate for in-vitro or pre-clinical investigations to ameliorate T2DM management.Communicated by Ramaswamy H. Sarma.

Influence of Sugar Modifications on the Nucleoside Conformation and Oligonucleotide Stability: A Critical Review

Ribofuranose sugar conformation plays an important role in the structure and dynamics of functional nucleic acids such as siRNAs, AONs, aptamers, miRNAs, etc. To improve their therapeutic potential, several chemical modifications have been introduced into the sugar moiety over the years. The stability of the oligonucleotide duplexes as well as the formation of stable and functional protein-oligonucleotide complexes are dictated by the conformation and dynamics of the sugar moiety. In this review, we systematically categorise various ribofuranose sugar modifications employed in DNAs and RNAs so far. We discuss different stereoelectronic effects imparted by different substituents on the sugar ring and how these effects control sugar puckering. Using this data, it would be possible to predict the precise use of chemical modifications and design novel sugar-modified nucleosides for therapeutic oligonucleotides that can improve their physicochemical properties.

First High-Resolution Crystal Structures of DNA:2′-O-Methyl-RNA Heteroduplexes

Heteroduplexes composed of all-DNA and all-2′-OMe RNA strands do not occur in nature, but they have found application in the development of molecular beacons and could also be used as aptamers or elements of nucleic acid-based nanostructures that will contain such structural motifs. The crystallization experiments performed have shown that the introduction of overhangs at the ends of the duplex has a great influence on the success of crystallization, as well as on the DNA:2′-OMe-RNA heteroduplex crystal packing. The molecular and crystal structure of the DNA:2′-O-methyl-RNA heteroduplex in its overhanging and blunt-ended versions was determined at 100 K using synchrotron radiation with a resolution of 1.91 and 1.55 Å, respectively. The Zn-SAD method was used to resolve the original duplex structure when molecular replacement by many existing models of duplex structures failed. Both molecules analyzed adopted a conformation close to the A-RNA double helix. The presented structures provide the first insight into this type of heteroduplexes and allowed a comparative analysis with existing nucleic acid homo- and heteroduplex structures. The results of our research expand the knowledge of the structural properties of new heteroduplexes and may be useful for future applications, such as therapies using this class of compounds.

Complexity Reduction in Density Functional Theory Calculations of Large Systems: System Partitioning and Fragment Embedding

With the development of low order scaling methods for performing Kohn-Sham density functional theory, it is now possible to perform fully quantum mechanical calculations of systems containing tens of thousands of atoms. However, with an increase in the size of the system treated comes an increase in complexity, making it challenging to analyze such large systems and determine the cause of emergent properties. To address this issue, in this paper, we present a systematic complexity reduction methodology which can break down large systems into their constituent fragments and quantify interfragment interactions. The methodology proposed here requires no a priori information or user interaction, allowing a single workflow to be automatically applied to any system of interest. We apply this approach to a variety of different systems and show how it allows for the derivation of new system descriptors, the design of QM/MM partitioning schemes, and the novel application of graph metrics to molecules and materials.

Rational design of an XNA ligase through docking of unbound nucleic acids to toroidal proteins

Xenobiotic nucleic acids (XNA) are nucleic acid analogues not present in nature that can be used for the storage of genetic information. In vivo XNA applications could be developed into novel biocontainment strategies, but are currently limited by the challenge of developing XNA processing enzymes such as polymerases, ligases and nucleases. Here, we present a structure-guided modelling-based strategy for the rational design of those enzymes essential for the development of XNA molecular biology. Docking of protein domains to unbound double-stranded nucleic acids is used to generate a first approximation of the extensive interaction of nucleic acid processing enzymes with their substrate. Molecular dynamics is used to optimise that prediction allowing, for the first time, the accurate prediction of how proteins that form toroidal complexes with nucleic acids interact with their substrate. Using the Chlorella virus DNA ligase as a proof of principle, we recapitulate the ligase's substrate specificity and successfully predict how to convert it into an XNA-templated XNA ligase.

RNA Structural Differentiation: Opportunities with Pattern Recognition

Our awareness and appreciation of the many regulatory roles of RNA have dramatically increased in the past decade. This understanding, in addition to the impact of RNA in many disease states, has renewed interest in developing selective RNA-targeted small molecule probes. However, the fundamental guiding principles in RNA molecular recognition that could accelerate these efforts remain elusive. While high-resolution structural characterization can provide invaluable insight, examples of well-characterized RNA structures, not to mention small molecule:RNA complexes, remain limited. This Perspective provides an overview of the current techniques used to understand RNA molecular recognition when high-resolution structural information is unavailable. We will place particular emphasis on a new method, pattern recognition of RNA with small molecules (PRRSM), that provides rapid insight into critical components of RNA recognition and differentiation by small molecules as well as into RNA structural features.

2'-O-methyl nucleotide modified DNA substrates influence the cleavage efficiencies of BamHI and BglII

Induction of endonucleolytic DNA cleavage is an essential event that links the initiating stimuli to the final effects of cells. The cleavage efficiency and thus the final yield could be affected by many factors, including structures of DNA substrates, composite structures of enzymes-substrates or enzymes-nucleic analogs and so on. However, it is not clear whether a nucleotide derivative-substituted in DNA substrates can influence the efficiency of enzymatic cleavage. To investigate the effect of sugar pucker conformation on DNA-protein interactions, we used 2'-O-methyl modified nucleotides (OMeN) to modify DNA substrates of isocaudemers BamHI and BglII in this study, and used FRET assay as an efficient method for analysis of enzyme cleavage. Experimental results demonstrated that OMeN-substituted recognition sequences influenced the cleavage rates significantly in a position-dependent manner. OMeN substitutions can reduce the cleavage as expected. Surprisingly, OMeN substitutions can also enhance the cleavage rates. The kinetics parameters of Vmax and Km have been obtained by fitting the Michaelis-Menten kinetic equation. These 2'- OMe nucleotides could behave as a regulatory element to modulate the enzymatic activity in vitro, and this property could enrich our understanding about the endonuclease cleavage mechanism and enhance our ability to regulate the enzymatic cleavage efficiency for applications in synthetic biology.

Interplay of LNA and 2'-O-methyl RNA in the structure and thermodynamics of RNA hybrid systems: a molecular dynamics study using the revised AMBER force field and comparison with experimental results

When used in nucleic acid duplexes, locked nucleic acid (LNA) and 2'-O-methyl RNA residues enhance the duplex stabilities, and this makes it possible to create much better RNA aptamers to target specific molecules in cells. Thus, LNA and 2'-O-methyl RNA residues are finding increasingly widespread use in RNA-based therapeutics. Herein, we utilize molecular dynamics (MD) simulations and UV melting experiments to investigate the structural and thermodynamic properties of 13 nucleic acid duplexes, including full DNA, RNA, LNA, and 2'-O-methyl RNA duplexes as well as hybrid systems such as LNA:RNA, 2'-O-methyl RNA:RNA, LNA/2'-O-methyl RNA:RNA, and RNA/2'-O-methyl RNA:RNA duplexes. The MD simulations are based on a version of the Amber force field revised specifically for RNA and LNA residues. Our results indicate that LNA and 2'-O-methyl RNA residues have two different hybridization mechanisms when included in hybrid duplexes with RNA wherein the former underwinds while the latter overwinds the duplexes. These computational predictions are supported by X-ray structures of LNA and 2'-O-methyl RNA duplexes that were recently presented by different groups, and there is also good agreement with the measured thermal stabilities of the duplexes. We find out that the "underwinding" phenomenon seen in LNA and LNA:RNA hybrid duplexes happens due to expansion of the major groove widths (Mgw) of the duplexes that is associated with decrease in the slide and twist values in base-pair steps. In contrast, 2'-O-methyl RNA residues in RNA duplexes slightly overwind the duplexes while the backbone is forced to stay in C3'-endo. Moreover, base-pair stacking in the LNA and LNA:RNA hybrid systems is gradually reduced with the inclusion of LNA residues in the duplexes while no such effect is seen in the 2'-O-methyl RNA systems. Our results show how competition between base stacking and structural rigidity in these RNA hybrid systems influences structures and stabilities. Even though both LNA and 2'-O-methyl RNA residues have C3'-endo sugar puckering, structurally LNA residues have a frozen sugar backbone which provides entropic enhancement of stabilities while the 2'-O-methyl RNA residues are more flexible and maintain base stacking that is almost untouched compared to RNA. Thus, enhancement of the structural stabilities of RNA duplexes by 2'-O-methyl RNA modifications is smaller than for the corresponding LNA modifications. Indeed, our experimental measurements show that on average each 2'-O-methyl RNA and LNA substitution in a RNA duplex enhances duplex stability by 0.2 and 1.4 kcal/mol, respectively. Our computational binding free energy predictions are qualitatively in line with these results. The only exception is for the full 2'-O-methyl RNA duplex, which is overstabilized, implying that further force field revisions are needed. Collectively, the results presented in this paper explain the atomistic details of the structural and thermodynamic roles of LNA and 2'-O-methyl RNA residues in RNA hybrid duplexes, shedding light on the mechanism behind targeting endogenous micro RNA (miRNA) in order to regulate mRNA activity and inhibit gene expression in the cell.

Role of wobble base pair geometry for codon degeneracy: purine-type bases at the anticodon wobble position

Codon degeneracy is a key feature of the genetic code, explained by Crick (J Mol Biol 19:548-555, 1966) in terms of imprecision of base pairing at the codon third position (the wobble position) of the codon-anticodon duplex. The Crick wobble rules define, but do not explain, which base pairs are allowed/disallowed at the wobble position of this duplex. This work examines whether the H-bonded configurations of solitary RNA base pairs can in themselves help decide which base pairs are allowed at the wobble position during codon-anticodon pairing. Taking the purine-type bases guanine, hypoxanthine, queuine and adenine as anticodon wobble bases, H-bonded pairing energies and optimized configurations of numerous RNA base pairs are calculated in gas and modeled aqueous phase at the B3LYP/6-31 G(d,p) level. Calculated descriptors of alignment of these solitary base pairs are able to screen between allowed and disallowed base pairs for all cases studied here, except two cases which invoke base-sugar interactions in the codon wobble nucleoside. The exclusion of adenine from the anticodon wobble position cannot be explained on the basis of pairing facility or base pair geometry. These DFT results thus account for the specificity and degeneracy of the genetic code for all cases involving guanine, hypoxanthine and queuine as anticodon wobble bases.

Nucleic acid-metal ion interactions in the solid state

Metal ions play a key role in nucleic acid structure and activity. Elucidation of the rules that govern the binding of metal ions is therefore an essential step for better understanding of the nucleic acid functions. This review is as an update to a preceding one (Metal Ions Biol. Syst., 1996, 32, 91-134), in which we offered a general view of metal ion interactions with mono-, di-, tri-, and oligonucleotides in the solid state, based on their crystal structures reported before 1994. In this chapter, we survey all the crystal structures of metal ion complexes with nucleotides involving oligonucleotides reported after 1994 and we have tried to uncover new characteristic metal bonding patterns for mononucleotides and oligonucleotides with A-RNA and A/B/Z-DNA fragments that form duplexes. We do not cover quadruplexes, duplexes with metal-mediated base-pairs, tRNAs, rRNAs in ribosome, ribozymes, and nucleic acid-drug and -protein complexes. Factors that affect metal binding to mononucleotides and oligonucleotide duplexes are also dealt with.

Theoretical study on conformational preferences of ribose in 2-thiouridine--the role of the 2'OH group

Conformational changes in ribose are well-known to play a significant role in biomolecular identification. The mechanism of selectivity towards C3'-endo conformation (conformer b) in ribose of 2-thiouridine has been studied using DFT (B3LYP) and MP2 methodology, together with 6-31+G(d,p) basis set. The polarity of the C2S2 bond is enhanced due to the orientation of H2' towards the S2 atoms, which leads to a difference in the corresponding bond lengths, the atomic charges and the vO2'H2' stretch vibrations in all the conformers. NBO analysis shows that charge transfer mainly occurs in the C2N3 and C2S2 orbitals. The higher stability of conformer b is attributed to its larger orbital interaction energies within the 2-thiouracil base, and total orbital interaction energies of conformer b. Our conclusion is that the distant electrostatic rather than hydrogen bonding effects between 2'OH and the S2 atoms play the dominant role in the orbital interaction, and enhance the selectivity towards the C3'-endo conformation of ribose.

Noncanonical G(syn)-G(anti) base pairs stabilized by sulphate anions in two X-ray structures of the (GUGGUCUGAUGAGGCC) RNA duplex

The structures of two crystal forms of the RNA 16-mer with the sequence GUGGUCUGAUGAGGCC, grown in the presence of a high concentration of sulphate ions, have been determined using synchrotron radiation at 1.4- and 2.0-A resolution. RNA with this sequence is known as one of the two strands of the noncleavable form of the hammerhead ribozyme. In both crystal structures, two G(syn)-G(anti) noncanonical base pairs are observed in the middle of a 14 base-pair (bp) duplex having 5'-dangling GU residues. Both structures contain sulphate anions interacting with the G-G bp stabilizing G in its syn conformation and bridging the two RNA strands. In both cases the interactions take place in the major groove, although the anions are accommodated within different helix geometries, most pronounced in the changing width of the major groove. In one structure, where a single sulphate spans both G-G pairs, the major groove is closed around the anion, while in the other structure, where each of the two G-G pairs is associated with a separate sulphate, the groove is open. This work provides the first examples of a G-G pair in syn-anti conformation, which minimizes the purine-purine clash in the center of the duplex, while utilizing its residual hydrogen bonding potential in specific interactions with sulphate anions.

Isoenergetic penta- and hexanucleotide microarray probing and chemical mapping provide a secondary structure model for an RNA element orchestrating R2 retrotransposon protein function

LNA (locked nucleic acids, i.e. oligonucleotides with a methyl bridge between the 2′ oxygen and 4′ carbon of ribose) and 2,6-diaminopurine were incorporated into 2′-O-methyl RNA pentamer and hexamer probes to make a microarray that binds unpaired RNA approximately isoenergetically. That is, binding is roughly independent of target sequence if target is unfolded. The isoenergetic binding and short probe length simplify interpretation of binding to a structured RNA to provide insight into target RNA secondary structure. Microarray binding and chemical mapping were used to probe the secondary structure of a 323 nt segment of the 5′ coding region of the R2 retrotransposon from Bombyx mori (R2Bm 5′ RNA). This R2Bm 5′ RNA orchestrates functioning of the R2 protein responsible for cleaving the second strand of DNA during insertion of the R2 sequence into the genome. The experimental results were used as constraints in a free energy minimization algorithm to provide an initial model for the secondary structure of the R2Bm 5′ RNA.

Effect of a water molecule on the sugar puckering of uridine, 2'-deoxyuridine, and 2'-O-methyl uridine inserted in duplexes

We used high-level quantum mechanical calculations to determine the pucker (north type or south type) of various compounds: uridine, 2'-deoxyuridine, and 2'-O-methyl uridine. Although the dihedrals of the backbone are set close to their experimental values in double-stranded nucleic acids, calculations using density functional theory show that, in vacuo or in a continuum mimicking the dielectric properties of water, the south puckering conformations of uridine is favored. This contrasts with experimental data: most ribonucleosides inserted into a duplex have the north puckering. We show here that the north puckering is favored when an explicit water molecule is introduced into the calculation. The orientations of the 2' group and of the water molecule have implications for the prevalence of the north puckering. We studied several orientations of the water molecule binding uracil O2 and the 2' group and estimated the energy barriers in the path between the north-to-south conformations. The north puckering is more favored in 2'-OH than in 2'-OCH3 compounds in the presence of the explicit water molecule.

Selective quenching of fluorescence from unbound oligonucleotides by gold nanoparticles as a probe of RNA structure

Binding of small oligonucleotides to the periphery of folded RNA can provide insight into the secondary structure of complex RNA in solution. To discriminate between bound and unbound fluorescein-labeled 2'-O-methyl RNA probes, we use ionically coated gold nanoparticles to selectively adsorb unbound probes and quench their fluorescence. The target is the 3' untranslated region of Bombyx mori R2 RNA. Fluorescence indicates that R2 sequences complementary to some of the probes are accessible for binding in the three-dimensional structure. Hybridization occurs under homogeneous conditions in the absence of the gold nanoparticles so that steric issues associated with chip-based assays are avoided. The assay is compatible with well plate formats, takes less than 5 min, and requires only 2 pmol or less of unlabeled target RNA per probe sequence tested.

Oligoribonucleotide analogues containing a mixed backbone of phosphodiester and formacetal internucleoside linkages, together with vicinal 2'-O-methyl groups

Oligoribonucleotides containing formacetal internucleoside linkages have been prepared and studied by UV melting experiments. In RNA duplexes, the formacetal substitution is stabilizing (Deltat(m)=0 to +0.9 degrees C per modification) at physiological salt concentrations (0.1 M) but destabilizing (Deltat(m)=-0.4 to -0.8 degrees C per modification) at high salt concentrations (1 M); this suggests that reduction of electrostatic repulsion contributes substantially to the stabilization. The presence of 2'-O-Me substituents increases the stabilities of the duplexes (Deltat(m)=+0.5 to +1.1 degrees C per modification). The positive effects of formacetals and 2'-O-Me groups were independent and additive. (1)H NMR studies on monomeric model compounds containing 3'-(ethyl phosphate) or 3'-O-ethoxymethyl groups showed that the formacetal and 2'-O-Me substitutions shift the conformational equilibria of the ribose residues towards the North conformers by 5 to 12 %. Although the preference for the North conformers qualitatively correlates with increased duplex stabilities, changes in thermodynamic parameters (DeltaH degrees and TDeltaS degrees ) for formation of oligonucleotide duplexes and differences in dependence on concentrations of sodium acetate, sodium chloride and sodium perchlorate suggest that solvation effects are also important for the duplex stabilities. Overall the formacetal linkages fit well in A-type RNA duplexes, making them potentially interesting modifications for RNA-based gene-control strategies (e.g., antisense and RNA interference).

In silico prediction of SARS protease inhibitors by virtual high throughput screening

A structure‐based in silico virtual drug discovery procedure was assessed with severe acute respiratory syndrome coronavirus main protease serving as a case study. First, potential compounds were extracted from protein–ligand complexes selected from Protein Data Bank database based on structural similarity to the target protein. Later, the set of compounds was ranked by docking scores using a Electronic High‐Throughput Screening flexible docking procedure to select the most promising molecules. The set of best performing compounds was then used for similarity search over the 1 million entries in the Ligand.Info Meta‐Database. Selected molecules having close structural relationship to a 2‐methyl‐2,4‐pentanediol may provide candidate lead compounds toward the development of novel allosteric severe acute respiratory syndrome protease inhibitors.

The chemical and biochemical properties of methylphosphotriester DNA and RNA in comparison with their corresponding methylphosphonates. A dynamic model description

Methylphosphotriester DNA and RNA are of great interest to investigate their hybridization affinity with natural DNA and RNA with respect to their physical and biological properties. The results are compared with related modified oligonucleotides. Specific attention will be given to the development of recent antiretroviral nucleosides focused on their molecular conformation and the mechanistic aspects based on the physical properties of phosphorus in a trigonal bipyramidal configuration corresponding with in vitro and in vivo kinetics.

Thermodynamics and kinetics for base-pair opening in the P1 duplex of the Tetrahymena group I ribozyme

The thermodynamics and kinetics for base-pair opening of the P1 duplex of the Tetrahymena group I ribozyme were studied by NMR hydrogen exchange experiments. The apparent equilibrium constants for base pair opening were measured for most of the imino protons in the P1 duplex using the base catalysts NH₃, HPO42− or TRIS. These equilibrium constants were also measured for several modified P1 duplexes, and the C-2·G23 base pair was the most stable base pair in all the duplexes. The conserved U-1·G22 base pair is required for activity of the ribozyme and the data here show that this wobble base pair destabilizes neighboring base pairs on only one side of the wobble. A 2′-OMe modification on the U-3 residue stabilized its own base pair but had little effect on the neighboring base pairs. Three base pairs, U-1·G22, C-2·G23 and A2·U21 showed unusual equilibrium constants for opening and possible implications of the opening thermodynamics of these base pairs on the undocking rates of the P1 helix with catalytic core are discussed.

Position-specific chemical modification of siRNAs reduces "off-target" transcript silencing

Transfected siRNAs regulate numerous transcripts sharing limited complementarity to the RNA duplex. This unintended ("off-target") silencing can hinder the use of RNAi to define gene function. Here we describe position-specific, sequence-independent chemical modifications that reduced silencing of partially complementary transcripts by all siRNAs tested. Silencing of perfectly matched targets was unaffected by these modifications. The chemical modification also reduced off-target phenotypes in growth inhibition studies. Key to the modification was 2'-O-methyl ribosyl substitution at position 2 in the guide strand, which reduced silencing of most off-target transcripts with complementarity to the seed region of the siRNA guide strand. The sharp position dependence of 2'-O-methyl ribosyl modification contrasts with the broader position dependence of base-pair substitutions within the seed region, suggesting a role for position 2 of the guide strand distinct from its effects on pairing to target transcripts.

The influence of locked nucleic acid residues on the thermodynamic properties of 2'-O-methyl RNA/RNA heteroduplexes

The influence of locked nucleic acid (LNA) residues on the thermodynamic properties of 2'-O-methyl RNA/RNA heteroduplexes is reported. Optical melting studies indicate that LNA incorporated into an otherwise 2'-O-methyl RNA oligonucleotide usually, but not always, enhances the stabilities of complementary duplexes formed with RNA. Several trends are apparent, including: (i) a 3' terminal U LNA and 5' terminal LNAs are less stabilizing than interior and other 3' terminal LNAs; (ii) most of the stability enhancement is achieved when LNA nucleotides are separated by at least one 2'-O-methyl nucleotide; and (iii) the effects of LNA substitutions are approximately additive when the LNA nucleotides are separated by at least one 2'-O-methyl nucleotide. An equation is proposed to approximate the stabilities of complementary duplexes formed with RNA when at least one 2'-O-methyl nucleotide separates LNA nucleotides. The sequence dependence of 2'-O-methyl RNA/RNA duplexes appears to be similar to that of RNA/RNA duplexes, and preliminary nearest-neighbor free energy increments at 37 degrees C are presented for 2'-O-methyl RNA/RNA duplexes. Internal mismatches with LNA nucleotides significantly destabilize duplexes with RNA.

Induced coalescence of cations through low-temperature Poisson-Boltzmann calculations

The computational determination of preferred binding regions of divalent counterions to nucleic acids is either inaccurate (standard Poisson-Boltzmann approaches) or extremely time-consuming (Monte Carlo or molecular dynamics simulations). A novel "selective low-temperature" Poisson-Boltzmann method is introduced that, although approximate in nature, qualitatively accounts for ion correlation and charge-transfer effects and allows for the rapid determination of such regions through an "induced coalescence" of divalent ions. The method is illustrated here for the binding of Mg(2+) to a double-helical sequence of B-form DNA (CGCGAATTCGCG) but the technique is readily applicable to locating divalent cations in other systems such as DNA-endonuclease complexes and ribozymes.

High salt solution structure of a left-handed RNA double helix

Right-handed RNA duplexes of (CG)n sequence undergo salt-induced helicity reversal, forming left-handed RNA double helices (Z-RNA). In contrast to the thoroughly studied Z-DNA, no Z-RNA structure of natural origin is known. Here we report the NMR structure of a half-turn, left-handed RNA helix (CGCGCG)2 determined in 6 M NaClO4. This is the first nucleic acid motif determined at such high salt. Sequential assignments of non-exchangeable proton resonances of the Z-form were based on the hitherto unreported NOE connectivity path [H6(n)-H5'/H5''(n)-H8(n+1)-H1'(n+1)-H6(n+2)] found for left-handed helices. Z-RNA structure shows several conformational features significantly different from Z-DNA. Intra-strand but no inter-strand base stacking was observed for both CpG and GpC steps. Helical twist angles for CpG steps have small positive values (4-7 degrees), whereas GpC steps have large negative values (-61 degrees). In the full-turn model of Z-RNA (12.4 bp per turn), base pairs are much closer to the helix axis than in Z-DNA, thus both the very deep, narrow minor groove with buried cytidine 2'-OH groups, and the major groove are well defined. The 2'-OH group of cytidines plays a crucial role in the Z-RNA structure and its formation; 2'-O-methylation of cytidine, but not of guanosine residues prohibits A to Z helicity reversal.

Hydration of short DNA, RNA and 2'-OMe oligonucleotides determined by osmotic stressing

Studies on hydration are important for better understanding of structure and function of nucleic acids. We compared the hydration of self-complementary DNA, RNA and 2'-O-methyl (2'-OMe) oligonucleotides GCGAAUUCGC, (UA)6 and (CG)3 using the osmotic stressing method. The number of water molecules released upon melting of oligonucleotide duplexes, Delta(n)W, was calculated from the dependence of melting temperature on water activity and the enthalpy, both measured with UV thermal melting experiments. The water activity was changed by addition of ethylene glycol, glycerol and acetamide as small organic co-solutes. The Delta(n)W was 3-4 for RNA duplexes and 2-3 for DNA and 2'-OMe duplexes. Thus, the RNA duplexes were hydrated more than the DNA and the 2'-OMe oligonucleotide duplexes by approximately one to two water molecules depending on the sequence. Consistent with previous studies, GC base pairs were hydrated more than AU pairs in RNA, whereas in DNA and 2'-OMe oligonucleotides the difference in hydration between these two base pairs was relatively small. Our data suggest that the better hydration of RNA contributes to the increased enthalpic stability of RNA duplexes compared with DNA duplexes.

Covalent incorporation of selenium into oligonucleotides for X-ray crystal structure determination via MAD: proof of principle. Multiwavelength anomalous dispersion

Selenium was incorporated into an oligodeoxynucleotide in the form of 2'-methylseleno-uridine (U(Se)). The X-ray crystal structure of the duplex left open bracket d(GCGTA)U(Se)d(ACGC) right open bracket (2) was determined by the multiwavelength anomalous dispersion (MAD) technique and refined to a resolution of 1.3 A, demonstrating that selenium can selectively substitute oxygen in DNA and that the resulting compounds are chemically stable. Since derivatization at the 2'-alpha-position with selenium does not affect the preference of the sugar for the C3'-endo conformation, this strategy is suitable for incorporating selenium into RNA. The availability of selenium-containing nucleic acids for crystallographic phasing offers an attractive alternative to the commonly used halogenated pyrimidines.

alpha-L-ribo-configured locked nucleic acid (alpha-L-LNA): synthesis and properties

The syntheses of monomeric nucleosides and 3'-O-phosphoramidite building blocks en route to alpha-L-ribo-configured locked nucleic acids (alpha-L-LNA), composed entirely of alpha-L-LNA monomers (alpha-L-ribo configuration) or of a mixture of alpha-L-LNA and DNA monomers (beta-D-ribo configuration), are described and the alpha-L-LNA oligomers are studied. Bicyclic 5-methylcytosin-1-yl and adenine-9-yl nucleoside derivatives have been prepared and the phosphoramidite approach has been used for the automated oligomerization leading to alpha-L-LNA oligomers. Binding studies revealed very efficient recognition of single-stranded DNA and RNA target oligonucleotide strands. Thus, stereoirregular alpha-L-LNA 11-mers containing a mixture of alpha-L-LNA monomers and DNA monomers ("mix-mer alpha-L-LNA") were shown to display DeltaT(m) values of +1 to +3 degrees C per modification toward DNA and +4 to +5 degrees C toward RNA when compared with the corresponding unmodified DNA x DNA and DNA x RNA reference duplexes. The corresponding DeltaT(m) values per modification for the stereoregular fully modified alpha-L-LNA were determined to be +4 degrees C (against DNA) and +5 degrees C (against RNA). 11-Mer alpha-L-LNAs (mix-mer alpha- L-LNA or fully modified alpha- L-LNA) were shown in vitro to be significantly stabilized toward 3'-exonucleolytic degradation. A duplex formed between RNA and either mix-mer alpha-L-LNA or fully modified alpha-L-LNA induced in vitro Escherichia coli RNase H-mediated cleavage, albeit very slow, of the RNA targets at high enzyme concentrations.