"Phantom" structure of solvents and packing of dual-chain nucleic acid molecules in liquid crystal dispersion particles

The properties of mesomorphic dispersions of double-stranded nucleic acids were studied. A comparison of these properties indicates that their diversity cannot be explained unambiguously in terms of the conception of Van-der-Waals interactions in particles of mesomorphic dispersions without regard for the specific properties of the solvent, water, in the vicinity of adjacent nucleic acid molecules. It was assumed that, with small distances between the molecules of nucleic acids, a specific "phantom" structure of the solvent appears in their vicinity, which acts as an elastic medium that modifies the interactions between nucleic acid molecules and as a medium in which a collective tunneling of protons can occur. The combination of the two effects determines the "recognition" of nucliec acid molecules and the stabilization of the cholesteric structure of mesomorphic dispersions of nucleic acids.     

Thermodynamic model of the formation of bridges between nucleic acid molecules in a liquid crystal]

A thermodynamic model of the formation of bridges consisting of alternating daunomycin molecules and copper ions and connecting neighboring nucleic acid molecules in a particle of a liquid crystalline dispersion was constructed. The model is based on the conception that ligands are adsorbed on lattices of reaction centers which are formed in a liquid crystal at a particular spatial arrangement of adjacent nucleic acid molecules (phasing). Equations were derived that describe typical experimentally obtained S-shaped dependences of bridge concentration on the concentration of copper ions and daunomycin molecules in an initial solution. It was shown that dependences of this kind take place in two variants of the adsorption model: when the binding of daunomycin with adjacent nucleic acid molecules is considered to be independent on the formation of bridges and when bridges compete with single daunomycin molecules for the sites on adjacent nucleic acid molecules.     

Thermodynamic models, describing formation of "bridges" between nucleic acid molecules and liquid crystals

Three variants of the model for the formation of "bridges" between the nucleic acid molecules fixed in the structure of particles of liquid-crystalline dispersions were considered. What the three variants have in common is that the bridges represent polymeric chelate cross-links consisting of alternating molecules of daunomycin and copper ions. The differences between the three variants are that in the first variant, the bridges begin and end with daunomycin molecules that form a complex by the mechanism of external binding with nucleic acids; in the second variant, the bridges begin and end with copper ions coupled with the pairs of bases of nucleic acids; and in the third variant, the bridges begin with the daunomycin molecule and end with the copper ion. For each variant, a mathematical model was constructed, which describes the formation of bridges, and equations of binding were derived. The results of calculations were compared with the experimental data. Within the framework of each variant, the values of the energy of interaction between the daunomycin molecule and the copper ion in the bridge, the energy of interaction of the daunomycin molecule with the nucleic acid, and the length of the bridge were varied. For all variants, those values of the parameters were chosen that fit best the experimental data. The theoretical curves obtained using the three variants of the model agree rather well with the family of experimental curves. The best agreement between the theoretical and experimental data was obtained when the polymeric chelate bridge includes more than two daunomycin molecules.     

Intercalation of water molecules between nucleic acid bases in the crystal structures of 6-azathymine hemihydrate and 5-amino-2-thiocytosine dihydrochloride dihydrate

The crystal structure of 6-azathymine hemihydrate (6AzTH) exhibits a novel intercalation of water molecules interposed half-way between the modified bases 6.3 to 6.7 A apart. The crystal contains four molecules of 6-azathymine (6AzT) and two water molecules as the independent repeating unit. These two water molecules together with the four bases form two separate water sandwiches. In the crystal structure these sandwiches form two sets of local clusters. The anhydrous crystalline form of 6AzT, on the other hand, is stabilized by base stacking interactions. Both the water molecules in 6AzTH that are involved in sandwich formation have trigonal coordination around them. A reexamination of the crystal structure of 5-amino-2-thiocytosine (5A2TC) revealed that one of the water molecules in this structure also forms a water sandwich and has trigonal coordination whereas the other water molecule with tetrahedral coordination does not form a sandwich. The environment and the characteristics of the intercalated water molecule in these structures suggest a possible role for such water intercalations in the dynamics of DNA. Crystals of 6AzTH are monoclinic, space group P21/n, with unit cell parameters a = 8.861 (1), b = 13.177 (3), c = 20.662 (2) A, beta = 93.35 (1) degrees, and Z = 16. From diffractometer data (2503 reflections, greater than or equal to 3 sigma), the crystal structure was solved and refined to an R of 0.056.     

Some formal consequences of a specific association between double stranded nucleic acid molecules—Properties of multistranded structures

Some possible consequences of a suggested specific association of double stranded nucleic acid to form multistranded, in particular, four stranded structure are discussed in a formal way. A considerable range of isomeric structures and of interactions and transformations between structures seem possible. For example it is possible for one circular nucleic acid chain to exist in several single, double, and quadruple stranded forms, and to form polymers. The suggestion is made that single stranded circles might be involved in some chromosomal material.     

Interactions of molecules with nucleic acids. I. An algorithm to generate nucleic acid structures with an application to the B-DNA structure and a counterclockwise helix.

An algorithm is developed that enables the routine determination of backbone conformations of nucleic acids. All atomic positions including hydrogen are specified in accord with experimental bond lengths and angles but with theoretically determined conformational angles. For two Watson-Crick base pairs at a separation of 3.38 Å, and perpendicular to a common helical axis, minimum energy configurations are found for all 10 combinations at helical angles of α ～ 36°–38°, corresponding to the B-DNA structure with C(2′)-endo sugar puckers. Backbone configurations exist only within the range 35.5° ? α ? 42°, which suggests the origin of the 10-fold helix. Calculated stacking energies for the B-DNA structure increases for each of the clustered groups of base pairs: G·C with G·C, G·C with A·T, and A·T with A·T, and they are in approximate agreement with experimental observations. The counter-clockwise helix is examined, and physically meaningful structures are found only when the helical axes of successive base pairs are disjointed.     

Conformational characteristics and correlations in crystal structures of nucleic acid oligonucleotides: evidence for sub-states

Sugar phosphate backbone conformations are a structural element inextricably involved in a complete understanding of specific recognition nucleic acid ligand interactions, from early stage discrimination of the correct target to complexation per se, including any structural adaptation on binding. The collective results of high resolution DNA, RNA and protein/DNA crystal structures provide an opportunity for an improved and enhanced statistical analysis of standard and unusual sugar-phosphate backbone conformations together with corresponding dinucleotide sequence effects as a basis for further exploration of conformational effects on binding. In this study, we have analyzed the conformations of all relevant crystal structures in the nucleic acids data base, determined the frequency distribution of all possible epsilon, zeta, alpha, beta and gamma backbone angle arrangements within four nucleic acid categories (A-RNA and A-DNA, free and bound B-DNA) and explored the relationships between backbone angles, sugar puckers and selected helical parameters. The trends in the correlations are found to be similar regardless of the nucleic acid category. It is interesting that specific structural effects exhibited by the different unusual backbone sub-states are in some cases contravariant. Certain alpha/gamma changes are accompanied by C3' endo (north) sugars, small twist angles and positive values of base pair roll, and favor a displacement of nucleotide bases towards the minor groove compared to that of canonical B form structures. Unusual epsilon/zeta combinations occur with C2' (south) sugars, high twist angles, negative values of base pair roll, and base displacements towards the major groove. Furthermore, any unusual backbone correlates with a reduced dispersion of equilibrium structural parameters of the whole double helix, as evidenced by the reduced standard deviations of almost all conformational parameters. Finally, a strong sequence effect is displayed in the free oligomers, but reduced somewhat in the ligand bound forms. The most variable steps are GpA and CpA, and, to a lesser extent, their partners TpC and TpG. The results provide a basis for considering if the variable and non-variable steps within a biological active sequence precisely determine morphological structural features as the curvature direction, the groove depth, and the accessibility of base pair for non covalent associations.     

Correlation between occupancy and B factor of water molecules in protein crystal structures

An empirical relationship between occupancy and the atomic displacement parameter of water molecules in protein crystal structures has been found by comparing a set of well refined sperm whale myoglobin crystal structures. The relationship agrees with a series of independent structural features whose impact on water occupancy can easily be predicted as well as with other known data and is independent of the protein fold. The estimation of the water occupancy in protein crystal structures may help in understanding the physico-chemical properties of the protein-solvent interface and can allow the monitoring of the accuracy of the protein crystal structure refinement.     

Solvent interactions in nucleic acid crystal hydrates

A detailed knowledge of structural and energetic aspects of water-nucleic acid interactions is essential for understanding the role of solvent in stabilizing the various helical forms of nucleic acids. In this study, computer simulation techniques have been used to predict structural properties of solvent networks in small nucleic acid crystal hydrates. A detailed comparison of predicted and experimental results on the structure of the solvent networks is presented and includes an analysis of both the local environment and hydrogen bond pattern of each water molecule. A correlation between the environment of each unique water molecule and its energetic properties (such a dipole moment and binding energy) is seen. As in the previous studies on small amino acid hydrate crystals, non-pair additive (cooperative) effects are found to be non-negligible. It is concluded that the potential functions used in this initial study lead to simulated solvent networks in reasonable agreement with experimental data. Thus, it is now feasible to use them in studies of hydration of larger helical fragments of nucleic acids of more direct biological interest.     

Non-canonical base pairs and higher order structures in nucleic acids: crystal structure database analysis

Non-canonical base pairs, mostly present in the RNA, often play a prominent role towards maintaining their structural diversity. Higher order structures like base triples are also important in defining and stabilizing the tertiary folded structure of RNA. We have developed a new program BPFIND to analyze different types of canonical and non-canonical base pairs and base triples involving at least two direct hydrogen bonds formed between polar atoms of the bases or sugar O2' only. We considered 104 possible types of base pairs, out of which examples of 87 base pair types are found to occur in the available RNA crystal structures. Analysis indicates that approximately 32.7% base pairs in the functional RNA structures are non-canonical, which include different types of GA and GU Wobble base pairs apart from a wide range of base pair possibilities. We further noticed that more than 10.4% of these base pairs are involved in triplet formation, most of which play important role in maintaining long-range tertiary contacts in the three-dimensional folded structure of RNA. Apart from detection, the program also gives a quantitative estimate of the conformational deformation of detected base pairs in comparison to an ideal planar base pair. This helps us to gain insight into the extent of their structural variations and thus assists in understanding their specific role towards structural and functional diversity.     

The stabilisation of nucleic acid structures

Summary The difference in stabilisation between DNA and RNA is explained by assuming that the 2 hydrogen of the ribose penetrates into the-electron cloud of the base of the 5 linked nucleotide.     

On the possibilities of error-detecting codes in nucleic acid molecules

Error-detecting codes have been known to mathematicians and to electrical engineers for over ten years. In general, such codes utilize an additional orparity bit for purposes of detecting errors by the addition of all positive binary bits or “1’s” occurring in any code word. However, since the process of addition is required for such code detection, it is not surprising that these codes have not been applied to the nucleic acid molecule. In 1962, P. I. Hershberg (Trans. I.R.E., CS-10, 280–4, 1962) outlined a categorical constraint which permitted the realization of a class of error-detecting codes which did not require parity bits. This class of codes is applied to the nucleic acid molecule in the present paper.     

Interactions of molecules with nucleic acids. XI. Generalization of techniques to generate nucleic acid structures with applications to intercalation sites and kinked structures

A generalized procedure to generate nucleic acid structures is presented. In this procedure, the bases of a base pair are oriented first for characterization of particular DNA receptor sites. The resultant sites are then used in the study of specific molecule–DNA interactions. For example, intercalation sites, kinked DNA, and twisted and tilted bases are envisioned. Alterations of structures via anti → syn orientations of bases, as well as crankshaft motion about collinear bonds, provide additional conformations without disrupting the overall backbone structure. These approaches to the generation of nucleic acid structures are envisioned as required in studies of the intercalation phenomenon, minor adjustments of DNA to accommodate denaturation, binding of carcinogens to DNA, complex formation of transition metals with DNA, and antitumor agents as ligands. For these base-pair and base orientations, backbone orientations are calculated by the AGNAS technique to yield physically meaningful conformations, namely, those conformations for which nonbonded contacts are favourable. A procedure is presented to generate dimer duplex units that are physically meaningful and to assemble these units into a polynucleotide duplex. Double helices that begin with B-DNA, undergo a transition to one of the above-mentioned receptor sites, and return to B-DNA can be assembled from a catalog of dimer duplexes. Stereographic projections of the various receptor sites already being used to model binding to DNA are presented.     

Ring-closing metathesis reactions in nucleic acid chemistry-cyclic dinucleotides for targeting secondary nucleic acid structures

Cyclic dinucleotides are synthesized using a ring-closing metathesis protocol and incorporated into oligonucleotides. A stabilization of a three-way junction is observed by an oligodeoxynucleotide containing a central 2'-C to 3'-phosphate connection.     

Development of a novel pretargeting system with bifunctional nucleic acid molecules

This study was aimed at exploring a novel pretargeting system based upon bifunctional nucleic acid molecules that are comprised of a nucleic acid aptamer and a nucleic acid tail. The properties of bifunctional molecules were investigated by both theoretical prediction and experimental determination. Different from the algorithm-based structure prediction, the experimental data showed that some nucleic acid tails could significantly decrease the binding capability of the aptamer. It was also found that the effectiveness of bifunctional molecules in labeling cells was dependent on the hybridization length. Based on these understandings, one bifunctional molecule was selected to study pretargeting. The results demonstrated that the bifunctional molecule could not only bind to target cells, but also hybridize with its complementary oligonucleotide on the cell surface. Thus, bifunctional nucleic acid molecules hold great potential for pretargeting applications.     

Quantitative analysis of nucleic acid three-dimensional structures

A new computer program to annotate DNA and RNA three-dimensional structures, MC-Annotate, is introduced. The goals of annotation are to efficiently extract and manipulate structural information, to simplify further structural analyses and searches, and to objectively represent structural knowledge. The input of MC-Annotate is a PDB formatted DNA or RNA three-dimensional structure. The output of MC-Annotate is composed of a structural graph that contains the annotations, and a series of HTML documents, one for each nucleotide conformation and base-base interaction present in the input structure. The atomic coordinates of all nucleotides and the homogeneous transformation matrices of all base-base interactions are stored in the structural graph. Symbolic classifications of nucleotide conformations, using sugar puckering modes and nitrogen base orientations around the glycosyl bond, and base-base interactions, using stacking and hydrogen bonding information, are introduced. Peculiarity factors of nucleotide conformations and base-base interactions are defined to indicate their marginalities with all other examples. The peculiarity factors allow us to identify irregular regions and possible stereochemical errors in 3-D structures without interactive visualization. The annotations attached to each nucleotide conformation include its class, its torsion angles, a distribution of the root-mean-square deviations with examples of the same class, the list of examples of the same class, and its peculiarity value. The annotations attached to each base-base interaction include its class, a distribution of distances with examples of the same class, the list of examples of the same class, and its peculiarity value. The distance between two homogeneous transformation matrices is evaluated using a new metric that distinguishes between the rotation and the translation of a transformation matrix in the context of nitrogen bases. MC-Annotate was used to build databases of nucleotide conformations and base-base interactions. It was applied to the ribosomal RNA fragment that binds to protein L11, which annotations revealed peculiar nucleotide conformations and base-base interactions in the regions where the RNA contacts the protein. The question of whether the current database of RNA three-dimensional structures is complete is addressed.     

On loop folding in nucleic acid hairpin-type structures

In a series of studies, combining NMR, optical melting and T-jump experiments, it was found that DNA hairpins display a maximum stability when the loop part of the molecule comprises four or five nucleotide residues. This is in contrast with the current notion based on RNA hairpin studies, from which it had been established that a maximum hairpin stability is obtained for six or seven residues in the loop. Here we present a structural model to rationalize these observations. This model is based on the notion that to a major extent base stacking interactions determine the stability of nucleic acid conformations. The model predicts that loop folding in RNA is characterized by an extension of the base stacking at the 5'-side of the double helix by five or six bases; the remaining gap can then easily be closed by two nucleotides. Conversely, loop folding in DNA is characterized by extending base stacking at the 3'-side of the double helical stem by two or three residues; again bridging of the remaining gap can then be achieved by one or two nucleotides. As an example of loop folding in RNA the anticodon loop of yeast tRNAPhe is discussed. For the DNA hairpin formed by d(ATCCTAT4TAGGAT) it is shown that the loop structure obtained from molecular mechanics calculations obeys the above worded loop folding principles.