Why do nucleic acids have 3'5' phosphodiester bonds?

Evaluating Geometric Definitions of Stacking for RNA Dinucleoside Monophosphates Using Molecular Mechanics Calculations

RNA modulation via small molecules is a novel approach in pharmacotherapies, where the determination of the structural properties of RNA motifs is considered a promising way to develop drugs capable of targeting RNA structures to control diseases. However, due to the complexity and dynamic nature of RNA molecules, the determination of RNA structures using experimental approaches is not always feasible, and computational models employing force fields can provide important insight. The quality of the force field will determine how well the predictions are compared to experimental observables. Stacking in nucleic acids is one such structural property, originating mainly from London dispersion forces, which are quantum mechanical and are included in molecular mechanics force fields through nonbonded interactions. Geometric descriptions are utilized to decide if two residues are stacked and hence to calculate the stacking free energies for RNA dinucleoside monophosphates (DNMPs) through statistical mechanics for comparison with experimental thermodynamics data. Here, we benchmark four different stacking definitions using molecular dynamics (MD) trajectories for 16 RNA DNMPs produced by two different force fields (RNA-IL and ff99OL3) and show that our stacking definition better correlates with the experimental thermodynamics data. While predictions within an accuracy of 0.2 kcal/mol at 300 K were observed in RNA CC, CU, UC, AG, GA, and GG, stacked states of purine-pyrimidine and pyrimidine-purine DNMPs, respectively, were typically underpredicted and overpredicted. Additionally, population distributions of RNA UU DNMPs were poorly predicted by both force fields, implying a requirement for further force field revisions. We further discuss the differences predicted by each RNA force field. Finally, we show that discrete path sampling (DPS) calculations can provide valuable information and complement the MD simulations. We propose the use of experimental thermodynamics data for RNA DNMPs as benchmarks for testing RNA force fields.

2'/3' Regioselectivity of Enzyme-Free Copying of RNA Detected by NMR

The RNA-templated extension of oligoribonucleotides by nucleotides produces either a 3',5' or a 2',5'-phosphodiester. Nature controls the regioselectivity during RNA chain growth with polymerases, but enzyme-free versions of genetic copying have modest specificity. Thus far, enzymatic degradation of products, combined with chromatography or electrophoresis, has been the preferred mode of detecting 2',5'-diesters produced in enzyme-free reactions. This approach hinges on the substrate specificity of nucleases, and is not suitable for in situ monitoring. Here we report how ¹ H NMR spectroscopy can be used to detect the extension of self-templating RNA hairpins and that this reveals the regioisomeric nature of the newly formed phosphodiesters. We studied several modes of activating nucleotides, including imidazolides, a pyridinium phosphate, an active ester, and in situ activation with carbodiimide and organocatalyst. Conversion into the desired extension product ranged from 20 to 90 %, depending on the leaving group. Integration of the resonances of H1' protons of riboses and H5 protons of pyrimidines gave regioselectivities ranging from 40:60 to 85:15 (3',5' to 2',5' diester), but no simple correlation between 3',5' selectivity and yield. Our results show how monitoring with a high-resolution technique sheds a new light on a process that may have played an important role during the emergence of life.

The furanosidic scaffold of d-ribose: a milestone for cell life

The recruitment of the furanosidic scaffold of ribose as the crucial step for nucleotides and then for nucleic acids synthesis is presented. Based on the view that the selection of molecules to be used for relevant metabolic purposes must favor structurally well-defined molecules, the inadequacy of ribose as a preferential precursor for nucleotides synthesis is discussed. The low reliability of ribose in its furanosidic hemiacetal form must have played ab initio against the choice of d-ribose for the generation of d-ribose-5-phosphate, the fundamental precursor of the ribose moiety of nucleotides. The latter, which is instead generated through the 'pentose phosphate pathway' is strictly linked to the affordable and reliable pyranosidic structure of d-glucose.

Structural insights into RNA duplexes with multiple 2΄-5΄-linkages

2΄-5΄-linked RNAs play important roles in many biological systems. In addition, the mixture of 2΄-5΄ and 3΄-5΄ phosphodiester bonds have emerged as a plausible structural element in prebiotic RNAs. Toward our mechanistic studies of RNA folding and structures with heterogeneous backbones, we recently reported two crystal structures of a decamer RNA duplex containing two and six 2΄-5΄-linkages, showing how RNA duplexes adjust the structures to accommodate these non-canonical linkages (Proc. Natl. Acad. Sci. USA, 2014, 111, 3050-3055). Herein, we present two additional high-resolution crystal structures of the same RNA duplex containing four and eight 2΄-5΄-linkages at different positions, providing new insights into the effects of these modifications and a dynamic view of RNA structure changes with increased numbers of 2΄-5΄-linkages in the same duplex. Our results show that the local structural perturbations caused by 2΄-5΄ linkages can be distributed to nearly all the nucleotides with big ranges of changes in different geometry parameters. In addition, hydration pattern and solvation energy analysis indicate less favorable solvent interactions of 2΄-5΄-linkages comparing to the native 3΄-5΄-linkages. This study not only promotes our understanding of RNA backbone flexibility, but also provides a knowledge base for studying the biochemical and prebiotic significance of RNA 2΄-5΄-linkages.

Structural insights into the effects of 2'-5' linkages on the RNA duplex

The mixture of 2'-5' and 3'-5' linkages generated during the nonenzymatic replication of RNA has long been regarded as a central problem for the origin of the RNA world. However, we recently observed that both a ribozyme and an RNA aptamer retain considerable functionality in the presence of prebiotically plausible levels of linkage heterogeneity. To better understand the RNA structure and function in the presence of backbone linkage heterogeneity, we obtained high-resolution X-ray crystal structures of a native 10-mer RNA duplex (1.32 Å) and two variants: one containing one 2'-5' linkage per strand (1.55 Å) and one containing three such linkages per strand (1.20 Å). We found that RNA duplexes adjust their local structures to accommodate the perturbation caused by 2'-5' linkages, with the flanking nucleotides buffering the disruptive effects of the isomeric linkage and resulting in a minimally altered global structure. Although most 2'-linked sugars were in the expected 2'-endo conformation, some were partially or fully in the 3'-endo conformation, suggesting that the energy difference between these conformations was relatively small. Our structural and molecular dynamic studies also provide insight into the diminished thermal and chemical stability of the duplex state associated with the presence of 2'-5' linkages. Our results contribute to the view that a low level of 2'-5' substitution would not have been fatal in an early RNA world and may in contrast have been helpful for both the emergence of nonenzymatic RNA replication and the early evolution of functional RNAs.

Promotion of stable triplex formation by partial incorporation of 2',5'-phosphodiester linkages into triplex-forming oligonucleotides

Pentadecamer homopyrimidine oligonucleotides containing three or more 2',5'-phosphodiester linkages in different modes were prepared and used to evaluate the ability as a triplex-forming oligonucleotide (TFO), and it was found that discontinuous replacement of the 3',5'-phosphodiester linkages in TFO by 2',5'-linkages significantly stabilizes parallel-motif triplexes.

Primer on medical genomics part II: Background principles and methods in molecular genetics

The nucleus of every human cell contains the full complement of the human genome, which consists of approximately 30,000 to 70,000 named and unnamed genes and many intergenic DNA sequences. The double-helical DNA molecule in a human cell, associated with special proteins, is highly compacted into 22 pairs of autosomal chromosomes and an additional pair of sex chromosomes. The entire cellular DNA consists of approximately 3 billion base pairs, of which only 1% is thought to encode a functional protein or a polypeptide. Genetic information is expressed and regulated through a complex system of DNA transcription, RNA processing, RNA translation, and posttranslational and cotranslational modification of proteins. Advances in molecular biology techniques have allowed accurate and rapid characterization of DNA sequences as well as identification and quantification of cellular RNA and protein. Global analytic methods and human genetic mapping are expected to accelerate the process of identification and localization of disease genes. In this second part of an educational series in medical genomics, selected principles and methods in molecular biology are recapped, with the intent to prepare the reader for forthcoming articles with a more direct focus on aspects of the subject matter.

Structural basis for the unusual properties of 2',5' nucleic acids and their complexes with RNA and DNA

To provide insights into the unusual properties of 2',5' nucleic acids (iso nucleic acids), that includes their rejection by Nature as information molecules, modeling studies have been carried out to examine if they indeed possess the stereochemical ability to form helical duplexes and triplexes, just as their 3',5' linked constitutional isomers. The results show that the formation of helical duplexes with 2',5' linkages demands a mandatory displacement of the Watson and Crick base pairs from the helical axis, as a direct consequence of the lateral shift of the sugar-phosphate backbone from the periphery towards the interior of the helix. Thus, both duplexes and triplexes formed with a 2',5'-sugar-phosphate backbone possess this intrinsic trait, manifested normally only in A type duplexes of DNA and RNA. It was found that only a 10-fold symmetric parallel triplex with isomorphous T.AT triplets is stereochemically favorable for isoDNA with 'extended' nucleotide repeats, unlike the 12-fold symmetric triplex favored by DNA. The wider nature of a 12-fold triplex, concomitant with mandatory slide requirement for helix formation in isoDNA, demands even larger displacement, especially with 'extended' nucleotide structural repeats, thereby violating symmetry. However, a symmetric triplex possessing higher twist, can be naturally formed for isoDNA with a 'compact' nucleotide repeat. Two nanosecond molecular dynamics simulation of a 2',5'-B DNA duplex, formed with an intrinsic base pair displacement of -3.3 A, does not seem to favor a total transition to a typical A type duplex, although enhanced slide, X-displacement, decrease in helical rise and narrowing of the major groove during simulation seem to indicate a trend. Modeling of the interaction between the chimeric isoDNA.RNA duplex and E. coli RNase H has provided a structural basis for the inhibitory action of the enzyme. Interaction of residues Gln 80, Trp 81, Asn 16 and Lys 99, of E. coli RNase H with DNA of the DNA.RNA hybrid, are lost when the DNA backbone is replaced by isoDNA. Based on modeling and experimental observations, it is argued that 2',5' nucleic acids possess restricted conformational flexibility for helical polymorphism. The inability of isoDNA to favor the biologically relevant B form duplex and the associated topological inadequacies related to nucleic acid compaction and interactions with regulatory proteins may be some of the factors that might have led to the rejection of 2',5' links.

Conformational rigidity introduced by 2',5'-phosphodiester links in DNA

Conformational properties of 2',5'-linked 3'-deoxyribonucleotides have been compared with their natural isomer using CD spectroscopy. It is inferred from the salt induced titration curves that the 2',5'-linked-3'deoxyribonucleotides have rigid phosphodiester backbone.

Chemical etiology of nucleic acid structure

Systematic chemical studies indicate that the capability of Watson-Crick base-pairing is widespread among potentially natural nucleic acid alternatives taken from RNA's close structural neighborhood. A comparison of RNA and such alternatives with regard to chemical properties that are fundamental to the biological function of RNA provides chemical facts that may contain clues to RNA's origin.

Stereochemistry of 2',5' nucleic acids and their constituents

Shape and dimension of the preferred nucleotide repeats in nucleic acids are found to depend on whether the sugar-phosphate linkage is of 2',5' or 3',5' type. It is shown that a nucleotide which is "compact" in 3',5' nucleic acids is rendered "extended" and vice versa for a given sugar pucker. It is interesting that this feature is accompanied by a switch in the preferred sugar ring conformation in 3',5' and 2',5' nucleic acids. 3' ribose and 3' deoxyribose rings (in 2',5' linkages) tend to favour C2' endo and C3' endo puckers respectively in contrast to C3' endo and C2' endo puckers favored by 2' ribose and 2' deoxyribose sugars (in 3',5' linkages). The distinguishable features between the nucleotide repeats of 3',5' and 2',5' nucleic acids need to be recognised while discussing their structural properties, as well as those of a variety of complexes that could be formed involving 2',5' and 3',5' strands of DNA and RNA. Ability and stability, or lack of them, for formation of a specific combination of these complexes may be directly related to the stereochemical constraints imposed as a consequence of conformationally homogeneous or heterogeneous nature of the repeating nucleotides of the complexing chains. As a first step towards delineating stereochemical features that distinguish 2',5' nucleic acids from their naturally occurring isomer A and B type helices have been modelled using the new concept of "compact" and "extended" nucleotide repeat that seemingly unifies helix generation of both types of linkages. Helical models for 2',5' RNA with "dinucleotide" repeat based on the crystal structure of 2',5' ApU have also been obtained.

The 2-5A system: modulation of viral and cellular processes through acceleration of RNA degradation

The 2-5A system is an RNA degradation pathway that can be induced by the interferons (IFNs). Treatment of cells with IFN activates genes encoding several double-stranded RNA (dsRNA)-dependent synthetases. These enzymes generate 5'-triphosphorylated, 2',5'-phosphodiester-linked oligoadenylates (2-5A) from ATP. The effects of 2-5A in cells are transient since 2-5A is unstable in cells due to the activities of phosphodiesterase and phosphatase. 2-5A activates the endoribonuclease 2-5A-dependent RNase L, causing degradation of single-stranded RNA with moderate specificity. The human 2-5A-dependent RNase is an 83.5 kDa polypeptide that has little, if any, RNase activity, unless 2-5A is present. 2-5A binding to RNase L switches the enzyme from its off-state to its on-state. At least three 2',5'-linked oligoadenylates and a single 5'-phosphoryl group are required for maximal activation of the RNase. Even though the constitutive presence of 2-5A-dependent RNase is observed in nearly all mammalian cell types, cellular amounts of 2-5A-dependent mRNA and activity can increase after IFN treatment. One well-established role of the 2-5A system is as a host defense against some types of viruses. Since virus infection of cells results in the production and secretion of IFNs, and since dsRNA is both a frequent product of virus infection and an activator of 2-5A synthesis, the replication of encephalomyocarditis virus, which produces dsRNA during its life cycle, is greatly suppressed in IFN-treated cells as a direct result of RNA decay by the activated 2-5A-dependent RNase. This review covers the organic chemistry, enzymology, and molecular biology of 2-5A and its associated enzymes. Additional possible biological roles of the 2-5A system, such as in cell growth and differentiation, human immunodeficiency virus replication, heat shock, atherosclerotic plaque, pathogenesis of Type I diabetes, and apoptosis, are presented.

Conformational and stacking properties of 3'-5' and 2'-5' linked oligoribonucleotides studied by CD

Comparative CD studies have been carried out to characterize the properties of 2'-5' and 3'-5' oligoriboadenylates and oligoribouridylates from dimer to decamer. The CD band of the 3'-5' oligoribonucleotides was larger than that of the 2'-5' oligoribonucleotides and increased with the increase in chain length, while the CD band of the 2'-5' oligoribonucleotides increased little beyond the dimer level. The CD analysis of the chain length dependency revealed that the 3'-5' oligoribonucleotides adopt mainly the base-base stacking interaction, while the base-sugar interaction is predominant in the 2'-5' oligoribonucleotides. The CD intensity of 3'-5' oligoribonucleotides decreased to a larger extent at elevated temperatures or in the presence of ethanol compared to that of the 2'-5' counterparts. Mg2+ or Mn2+ ion enhanced the magnitude of the CD of 3'-5' octariboadenylate, while a small decrease in the CD was observed by the presence of Mg2+ or Mn2+ ion to the 2'-5' octariboadenylate. The 3'-5' oligoribonucleotide is likely conformationally flexible and can form helical ordered structure with strong base-base stacking depending on changes in the environment such as temperature the presence of Mg2+ ion, or hydrophobicity of the solution.

Comparative studies of duplex and triplex formation of 2'-5' and 3'-5' linked oligoribonucleotides

We have studied double and triple helix formation between 2'-5' or 3'-5' linked oligoriboadenylates and oligoribouridylates with chain length 7 or 10 by CD spectrometry. The complex formation depends on the type of linkage of oligoribonucleotides, chain length, concentration and molar ratio of the strands, temperature and the cationic concentration. Mixture of any linkage isomers of oligo(rA) and oligo(rU) in 1:1 molar ratio form duplex at 0.1 M NaCl. The duplex stability largely depends on the type of the linkages and is in the following order, [3'-5'] oligo(rA)-[3'-5'] oligo(rU) > [2'-5'] oligo(rA)-[3'-5'] oligo(rU) > [3'-5'] oligo(rA)-[2'-5'] oligo(rU) > [2'-5'] oligo(rA)-[2'-5'] oligo(rU). The higher cationic concentrations, 0.5 M MgCl2, stabilize the complex and either duplex or triplex is formed depending on the input strand ratio and the type of linkage. Thermodynamic parameters, DH and DS, for the complex formation between linkage isomers of oligo(rA) and oligo(rU) showed a linear relationship indicating an enthalpy-entropy compensation phenomena. The duplex and triplex composed of [2'-5'] oligo(rA) and [2'-5'] oligo(rU) exhibit different CD spectra compared to those of any others containing 3'-5' linkage, suggesting that the fully 2'-5' duplex and triplex may possess a unique conformation. We describe prebiological significance of the linkage isomers of RNA and selection of the 3'-5' linkage against 2'-5 linkage.

Comparative spectroscopic, calorimetric, and computational studies of nucleic acid complexes with 2',5"-versus 3',5"-phosphodiester linkages

We have used a combination of spectroscopic, calorimetric, and computational techniques to characterize the properties of nucleic acid complexes with 2',5''- and 3',5''-phosphodiester linkages. Specifically, we have compared the properties of complexes formed by the association of 3',5'' single-stranded 16-mers of adenylic acid (A16) and thymidylic acid (T16) with the complexes formed by the corresponding single-stranded 16-mers with 2',5''-phosphodiester linkages (A*16 and T*16). Our results reveal the following differential features: (i) the 3',5'' strands form either a duplex or a triplex, depending on the sodium ion concentration, whereas the 2',5'' strands form either a triplex or no complex at all; (ii) the 2',5'' and 3',5'' triplexes exhibit significantly different CD spectra, suggesting that the two triplex states are conformationally nonequivalent; (iii) the 2',5'' triplex has a lower charge density than the 3',5'' triplex; (iv) the thermal stability of the 3',5'' triplex, as expected, is concentration dependent, whereas the thermal stability of the 2',5'' triplex is concentration independent; (v) relative to their component single strands, the 2',5'' triplex is thermodynamically much less stable than the 3',5'' triplex, despite being thermally more stable; (vi) the reduced thermodynamic stability of the 2',5'' triplex relative to the 3',5'' triplex is overwhelmingly enthalpic in origin. In the aggregate, our results reveal and characterize significant differences in the properties of complexes formed by the association of strands with identical base sequences but different phosphodiester linkages. We describe a structural model that is consistent with many of the differential properties observed. We also speculate on how these differential properties may have provided an evolutionary advantage for 3',5'' linkages and how the properties of 2',5'' complexes might be exploited in antisense strategies.

Recognition and catalysis in nucleic acid chemistry

The enzyme ribonuclease A catalyzes the cleavage of RNA, using the imidazole groups of histidine-12 and histidine-119 as its principal catalytic groups. Model studies show that RNA can be cleaved by imidazole buffer itself and that, as in the enzyme, a bell-shaped pH vs. rate profile is seen. This indicates that one imidazole functions as a base, while the other, as the imidazolium ion, functions as an acid. However, in contrast to the enzymatic case, the simple model uses the imidazoles in sequential, rather than simultaneous, bifunctional catalysis. Mechanistic studies on this reaction and on the reactions of simple dinucleotides catalyzed by imidazole and other buffers establish the details of the process. The results let us propose a mechanism for the enzymatic process different from the standard one; they also stimulated us to design an improved mimic of the enzyme that uses a mechanism like that proposed for the enzyme. Critical to the mechanistic studies is observation of the rearrangement of normal 3',5'' RNA nucleotides to the 2',5'' isomers. This led us to investigate the properties of DNA isomers in which a 2',5'' link also replaces the normal 3',5'' one. The results indicate that poor base stacking in a double helix with such links makes them less suitable as genetic units.

Stereochemistry of 2'-5' linked nucleic acids: crystal and molecular structure of ammonium adenylyl-2',5'-adenosine tetrahydrate: a core fragment of 2'-5' oligo A's produced by interferon induced adenylate synthetase

The preponderance of 3'-5' phosphodiester links in nucleic acids is well known. Albeit less prevalent, the 2'-5' links are specifically utilised in the formation of 'lariat' in group II introns and in the msDNA-RNA junction in myxobacterium. As a sequel to our earlier study on cytidylyl-2',5'-adenosine we have now obtained the crystal structure of adenylyl-2',5'-adenosine (A2'p5'A) at atomic resolution. This dinucleoside monophosphate crystallizes in the orthorhombic space group P2(1)2(1)2(1) with a = 7.956(3) A, b = 12.212(3) A and c = 36.654(3) A. CuK alpha intensity data were collected on a diffractometer. The structure was sloved by direct methods and refined by full matrix least squares methods to R = 10.8%. The 2' terminal adenine is in the commonly observed anti (chi 2 = 161 degrees) conformation and the 5' terminal base has a syn (chi 1 = 55 degrees) conformation more often seen in purine nucleotides. A noteworthy feature of A2'p5'A is the intranucleotide hydrogen bond between N3 and O5' atoms of the 5' adenine base. The two furanose rings in A2'p5'A show different conformations - C2' endo, C3' endo puckering for the 5' and 2' ends respectively. In this structure too there is a stacking of the purine base on the ribose O4' just as in other 2'-5' dinucleoside structures, a feature characteristically seen in the left handed Z DNA. In having syn, anti conformation about the glycosyl bonds, C2' endo, C3' endo mixed sugar puckering and N3-O5' intramolecular hydrogen bond A2'p5'A resembles its 3'-5' analogue and several other 2'-5' dinucleoside monophosphate structures solved so far. Striking similarities between the 2'-5' dinucleoside monophosphate structures suggest that the conformation of the 5'-end nucleoside dictates the conformation of the 2' end nucleoside. Also, the 2'-5' dimers do not favour formation of miniature classical double helical structures like the 3'-5' dimers. It is conceivable, 2-5(A) could be using the stereochemical features of A2'p5'A which accounts for its higher activity.

Association of 2'-5' oligoribonucleotides

Oligoribonucleotides with 2'-5' linkages have been synthesized on solid support. UV melting and CD experiments indicate complementary strands associate to give complexes with melting temperatures 30 to 40 degrees C lower than for duplexes formed by 3'-5' oligoribonucleotides with the same sequence. UV melting and imino proton NMR spectra and NOEs for (2'-5') CGGCGCCG are consistent with formation of an antiparallel duplex. The results suggest greater duplex stability was one factor favoring 3'-5' over 2'-5' linkages in evolution.

Influence of internucleotide phosphate linkage on relative base stacking in 3'-5' and 2'-5' RNA: a circular dichroic spectroscopic study of RNA hexamer AACCUU

The variations in base stacking interactions of two isomeric RNA hexamers, 3'-5'r (AACCUU) and 2'-5'r' (AACCUU), have been studied using temperature dependent CD spectroscopy. Both RNA hexamers, in single strand form, exhibited a right handed helical sense. Van't Hoff analysis of the CD spectral results, derived from a two state model, gave a higher enthalpy of stacking for 3'-5' RNA than for 2'-5'RNA. The results suggest that 3'-5' linkage in RNA facilitates formation of better helical stacks in relation to an isomeric 2'-5' linkage.

Visualisation of a 2'-5' parallel stranded double helix at atomic resolution: crystal structure of cytidylyl-2',5'-adenosine

X-ray crystallographic studies on 3'-5' oligomers have provided a great deal of information on the stereochemistry and conformational flexibility of nucleic acids and polynucleotides. In contrast, there is very little information available on 2'-5' polynucleotides. We have now obtained the crystal structure of Cytidylyl-2',5'-Adenosine (C2'p5'A) at atomic resolution to establish the conformational differences between these two classes of polymers. The dinucleoside phosphate crystallises in the monoclinic space group C2, with a = 33.912(4)A, b = 16.824(4)A, c = 12.898(2)A and beta = 112.35(1) with two molecules in the asymmetric unit. Spectacularly, the two independent C2'p5'A molecules in the asymmetric unit form right handed miniature parallel stranded double helices with their respective crystallographic two fold (b axis) symmetry mates. Remarkably, the two mini duplexes are almost indistinguishable. The cytosines and adenines form self-pairs with three and two hydrogen bonds respectively. The conformation of the C and A residues about the glycosyl bond is anti same as in the 3'-5' analog but contrasts the anti and syn geometry of C and A residues in A2'p5'C. The furanose ring conformation is C3' endo, C2' endo mixed puckering as in the C3'p5'A-proflavine complex. A comparison of the backbone torsion angles with other 2'-5' dinucleoside structures reveals that the major deviations occur in the torsion angles about the C3'-C2' and C4'-C3' bonds. A right-handed 2'-5' parallel stranded double helix having eight base pairs per turn and 45 degrees turn angle between them has been constructed using this dinucleoside phosphate as repeat unit. A discussion on 2'-5' parallel stranded double helix and its relevance to biological systems is presented.

Why do all lariat RNA introns have adenosine as the branch-point nucleotide? Conformational study of naturally-occurring branched trinucleotides and its eleven analogues by 1H-, 31P-NMR and CD spectroscopy

1H-NMR conformational studies of six branched triribonucleotides where the branch-point nucleotide was either U, C or G (4-9) have been carried out by assigning 1H resonances through 2D NMR and then observing the temperature-dependent (i) chemical shifts of the aromatic and the anomeric protons, and (ii) shifts of the equilibrium of N and S pseudorotamer populations of each sugar moiety. The data have been compared with those of 2'----5' dimers (1-3) and other branched trimers (10-16). It emerged that all the branched trimers (4-16) adopt a conformational state closer to the corresponding 2'----5' dimers than the corresponding 3'----5' dimers. A temperature-dependent 31P chemical shift study confirmed that the conformational constraint is mainly associated with the 2'----5' phosphate linkage. Although, it appeared with the CD data that when C or especially when U is at the branch-point the overall constraint is weak. This suggests that even if these trimers adopt a 2'----5' dimer geometry, there is a lack of stabilization by strong stackings within the molecule. This is in sharp contrast with the results found for A (10-16) and to a smaller extent for G (8, 9) at the branch-point.

Conformational properties of branched RNA fragments in aqueous solution

The conformational properties of branched trinucleoside diphosphates ACC, ACG, AGC, AGG, AUU, AGU, AUG, ATT, GUU, and aAUU [XYZ = X(2'p5'Y)3'p5'Z] have been studied in aqueous solution by nuclear magnetic resonance (1H, 13C), ultraviolet absorption, and circular dichroism. It is concluded from these studies that the purine ring of the central residue (X; e.g., adenosine) forms a base-base stack exclusively with the purine or pyrimidine ring of the 2'-nucleotidyl unit (Y; 2'-residue). The residue attached to the central nucleoside via the 3'-5'-linkage (Z; 3'-residue) is "free" from the influence of the other two heterocyclic rings. The ribose rings of the central nucleoside and the 2'- and 3'-residues exist as equilibrium mixtures of C2'-endo (2E)-C3'-endo (3E) conformers. The furanose ring of the central nucleoside (e.g., A) when linked to a pyrimidine nucleoside via the 2'-5'-linkage shows a higher preference for the 2E pucker conformation (e.g., AUG, AUU, ACG, ca. 80%) than those linked to a guanosine nucleoside through the same type of bond (AGU, AGG, AGC, ca. 70%). This indicates some correlation between nucleotide sequence and ribose conformational equilibrium. The 2E-3E equilibrium of 2'-pyrimidines (Y) shows significant, sometimes exclusive, preference (70-100%) for the 3E conformation; 3'-pyrimidines and 2'-guanosines have nearly equal 2E and 3E rotamer populations; and the ribose conformational equilibrium of 3'-guanosines shows a preference (60-65%) for the 2E pucker. Conformational properties were quantitatively evaluated for most of the bonds (C4'-C5', C5'-O5', C2'-O2', and C3'-O3') in the branched "trinucleotides" AUU and AGG by analysis of 1H-1H, 1H-31P, and 13C-31P coupling constants. The C4'-C5' bond of the adenosine units shows a significant preference for the gamma + conformation. The dominant conformation about C4'-C5' and C5'-O5' for the 2'-and 3'-nucleotidyl units is gamma + and beta t, respectively, with larger gamma + and beta t rotamer populations for the 2'-unit. The increased conformational purity in the 2'-residue, compared to the 3'-residue, is ascribed to the presence of an ordered (adenine----2'-residue) stacked state. The favored rotamers about C3'-O3' and C2'-O2' are epsilon- and epsilon'-, respectively. The conformational features of AUU and AGG were compared to those of their constitutive dimers A3'p5'G, A2'p5'G, A3'p5'U, and A2'p5'U and monomers 5'pG and 5'pU.

Conformational studies of (2'-5') polynucleotides: theoretical computations of energy, base morphology, helical structure, and duplex formation

A detailed theoretical analysis has been carried out to probe the conformational characteristics of (2'-5') polynucleotide chains. Semi-empirical energy calculations are used to estimate the preferred torsional combinations of the monomeric repeating unit. The resulting morphology of adjacent bases and the tendency to form regular single-stranded structures are determined by standard computational procedures. The torsional preferences are in agreement with available nmr measurements on model compounds. The tendencies to adopt base stacked and intercalative geometries are markedly depressed compared to those in (3'-5') chains. Very limited families of regular monomerically repeating single-stranded (2'-5') helices are found. Base stacking, however, can be enhanced (but helix formation is at the same time depressed) in mixed puckered chains. Constrained (2'-5') duplex structures have been constructed from a search of all intervening glycosyl and sugar conformations that form geometrically feasible phosphodiester linkages. Both A- and B-type base stacking are found to generate non-standard backbone torsions and mixed glycosyl/sugar combinations. The 2'- and 5'-residues are locked in totally different arrangements and are thereby prevented from generating long helical structures.

X-ray structure of a dinucleoside monophosphate A2'p5'C that contains a 2'-5' link found in (2'-5')oligo(A)s induced by interferons: single-stranded helical conformation of 2'-5'-linked oligonucleotides

In order to understand why DNA and RNA have the 3'-5' and not the 2'-5' link and to delineate the stereochemistry of the 2'-5' phosphodiester links, we crystallized and carried out a very accurate x-ray diffraction analysis of A2 p5'C, an analog of A2' p5'A. Contrary to numerous reports in the literature that conclude that the tendency for 2'-5' nucleotides to stack intramolecularly is stronger than for 3'-5' counterparts, we find hardly any intramolecular base stacking for this molecule but find an intramolecular "stacking" of the ribose oxygen-4' of cytidine on top of the adenine ring. Although A2' p5'C shows the standard conformational features usually found for 3'-5' nucleotides, the overall stereochemistry of 2'-5' nucleotides is quite different because the 2' link orients the backbone inwards to the bases unlike the 3' and 5' links that orient it away from the bases. With the conformational features found for A2' p5'C, it is possible to build a very compact right-handed single-stranded helix but not a double helix. Such a preference for single-stranded helices may be the reason for the absence of 2'-5' bonds in DNA and RNA even though the 2'-5' bonds are formed more readily then 3'-5' bonds.

Synthesis and properties of CpG analogues containing an 8-bromoguanosine residue. Evidence for Z-RNA duplex formation

Three dinucleoside monophosphates containing 8-bromoguanosine (br8G), (2'-5')C-br8G, (3'-5')C-br8G, and dC-br8G, were synthesized and characterized by UV absorption, CD, and 1H NMR spectroscopy. The 1H NMR data show that all the br8G residues in these dimers take a syn glycosidic conformation. At low dimer strand concentration (5 X 10(-5) M), the UV hypochromicity data suggest that the degree of base stacking decreases in the following order, (2'-5')C-br8G greater than C-G approximately equal to dC-br8G greater than (3'-5')C-br8G. The CD data also suggest little stacking in (3'-5')C-br8G. At high dimer strand concentration (5 X 10(-3) M), only (3'-5')C-br8G shows duplex formation in 0.1 M NaCl. The duplex is assumed to take a left-handed helical structure similar to that of Z-DNA. The Tm of this duplex is surprisingly high for a dimer (about 35 and 45 degrees C at 5 X 10(-3) and 10(-2) M dimer strand concentration, respectively). The above results and the similarity between the CD spectra of (3'-5')C-br8G and poly(G-C) suggest the possible existence of Z-form structure in ribooligo- and ribopolynucleotides with alternating purine-pyrimidine sequences.

Conformational analysis of the nucleotides A2'-5'A, A2'-5'A2'-5'A and A2'-5'U from nuclear magnetic resonance and circular dichroism studies

In recent publications A2'-5'A2'-5'A was found to be an inhibitor of protein synthesis. In this research conformational analysis of the 2'-5'-linked nucleotides A2'-5'A, A2'-5'A2'-5'A and A2'-5'U is reported. The complete 1H-NMR assignment of the three compounds is given. The degree and mode of base-base stacking is extracted from coupling constant data and circular dichroic (CD) spectra at various temperatures. The 2'-5' nucleotides surprisingly show a much stronger tendency to stack than the 3'-5' compounds. At 85 degrees C A2'-5'A occurs for about 50% in stacked states. The mode of stacking is different from 3'-5'ribonucleotides where the sugar rings predominantly adopt an N conformation. A2'-5'U displays an A(S)2'-5'U(N) stacked state. In A2'-5'A 'mixed' modes of stacking, i.e. NN, NS, SN and SS, are proposed to account for the CD and NMR observations.

Stacking properties of a highly hydrophobic dinucleotide sequence, N6, N6-dimethyladenylyl(3' leads to 5')N6, N6-dimethyladenosine, occurring in 16--18-S ribosomal RNA

The thermal denaturation ultraviolet absorption spectra of N6,N6-dimethyladenylyl(3' leads to 5')-N6,N6-dimethyladenosine (m2(6)Apm2(6)A), which is a common sequence in 16--18-S ribosomal RNA, in aqueous buffer at pH 7 have been measured over the temperature range 3-90 degrees C. These data have been used to determine the thermodynamic quantitites associated with the intramolecular stacking equilibria. At 25 degrees C in neutral aqueous solution m2(6)Apmw(6)A exists mainly (about 81%) as a stacked form, so that the stacking interactions are stronger than those in the parent unmethylated adenylyl-(3'-5')adenosine (ApA), where about 52% is stacked. From the parameters of delta H and delta S, it is concluded that 'hidden' hydrophobic inteactions are of prime importance in the enhanced stability of m2(6)Apm2(6)A. Transphosphorylation reaction of ApA and m2(6)Apm2(6)A to form the corresponding cyclic 2',3'-phosphates has been studied. First-order rate constants at 25 degrees C for the reactions, which are base-catalyzed, have been obtained. Insertion of two methyl groups at N-6 of ApA reduces the rate of transphosphorylation. Effects of stacking on rates are discussed in the light of reaction mechanisms.