The role of electron donors and acceptors in base stacking in DNA and RNA.

The role of donor-acceptor interactions in base pair stacking in DNA and RNA has been minimized because of the perceived low or negative electron affinities of the purines and pyrimidines. The use of the electron capture detector was among the first methods for measuring electron affinities in the gas phase. Recently, the experimental determination of electron affinities has been extended and improved. Now, there are data for similar compounds in the literature which enable us to estimate electron affinities for purines and pyrimidines. These values are significant, and positive, such that donor-acceptor interactions can, and indeed should play a role in the stacking of bases in nucleic acids.     

The role of spin in biological processes: O2, NO,nucleobases, nucleosides,nucleotides and Watson–Crick base pairs

The experimental electron affinities of adenine, guanine, cytosine, thymine and uracil have been determined from reduction potentials and negative ion photoelectron spectra. Updated values for purine, pyrimidine and other nitrogen heterocyclics, which have not been measured in the gas phase, are presented. The electron affinity of Watson–Crick guanine–cytosine is estimated empirically. The experimental values are consistent with quantum mechanical semi-empirical multiconfiguration configuration interaction calculations. The bulk hydration energies of the nucleobase anions, 2.34 eV, determined from the experimental data and sequential anion hydration energy difference of about 0.20(5) eV suggest that 10–15 water molecules complete the hydration shell. The electron affinities for the formation of doublet and quartet anions of the nucleobases, nucleosides, nucleotides and Watson–Crick base pairs are calculated. We postulate that low-lying quartet anion states and their spin distribution can and will participate in electron conduction, radiation damage, oxidation damage and repair, strand breakage and protein synthesis.     

Purine and pyrimidine contents of some desoxypentose nucleic acids

The distribution of purines and pyrimidines in desoxypentose nucleic acids prepared from a variety of animal and plant sources has been studied. 1. The nucleic acids were prepared from calf thymus, calf kidney, sheep spleen, horse spleen, chicken erythrocyte, turtle erythrocyte, trout sperm, shad testes, sea urchin sperm, wheat germ, and Pneumococcus Type III. 2. Separate hydrolyses were carried out for the determination of purines and pyrimidines. These procedures permitted nearly quantitative recovery of nucleic acid phosphorus in many of the preparations examined. 3. In the case of those preparations where a quantitative recovery was obtained it can be concluded that no bases other than adenine, guanine, thymine, and cytosine were present in appreciable amounts. 4. The distribution of purines and pyrimidines in all the nucleic acids studied renders the tetranucleotide hypothesis untenable. 5. The results of the analyses have indicated no great differences in the composition of these nucleic acids with respect to purines and pyrimidines.     

Purine and pyrimidine inhibitors of arginase.

1. Adenosine, inosine, adenine and uric acid are competitive inhibitors and cytidine and cytosine noncompetitive inhibitors of bovine liver arginase (L-arginine amidinohydrolase, EC 3.5.3.1). 2. The affinity of the enzyme for these inhibitors was 10--100 times as great as for substrate in terms of Ki versus Km. 3. These nucleic acid metabolites may thus function in vivo to regulate the urea cycle. 4. Several naturally occuring competitive and noncompetitive inhibitors of arginase of unknown structure have been isolated from plant and animal tissue. From their properties and methods of isolation, they may be the purines and pyrimidines herein described. 5. These purines and pyrimidines have no effect on tryptic hydrolysis.     

Correlation of kinetic parameters of nitroreductase enzymes with redox properties of nitroaromatic compounds

The well-established mechanism of regeneration of the parent nitro compound by the reaction of the nitro anion radical with oxygen in aerobic systems is the basis of the correlation of kinetic parameters of purified flavoenzymes with electron affinities of some selected nitroaryl and nitroheterocyclic compounds. We have found that there is a linear relationship between log Vmax/Km and the one-electron reduction potentials of these compounds and that the measured values of redox dependence for these compounds is similar to that determined by other methods. Our results support the proposal of a rate-determining single electron-transfer as the initial step in the reduction of nitro compounds by purified flavoenzymes and are discussed in terms of the Marcus electron transfer theory.     

Amino acid catalyzed condensation of purines and pyrimidines with 2-deoxyribose.

Mild heating of aqueous mixtures containing 2-deoxyribose, amino compounds, and purines or pyrimidines produces derivatives of the purines and pyrimidines in high yield. Among the major products formed are 2,3-dideoxy-3-(1'-pyrimidino)pentose and 2,3-dideoxy-3-(9'-purino)pentose. The mechanism of the reaction includes amine-catalzyed dehydration of the alpha, beta positions of the sugar followed by addition of the purine or pyrimidine to the double bond. Rapid addition of purines and pyrimidines to alpha, beta-unsaturated carbonyl compounds (such as acrolin) is a general phenomenon which does not require an amine catalyst. While multiple derivatization of the purines will take place, the N-9 derivative is formed first.     

Influence of Purines and Pyrimidines on Cold Hardiness of Plants. III. Associated Changes in Soluble Protein and Nucleic Acid Content and Tissue pH

When applications of certain purines and pyrimidines enhanced the development or maintenance of cold hardiness, the content of water-soluble, trichloroacetic acid-precipitable protein and nucleic acids and tissue pH were higher in treated plants than in controls. The reverse was generally true when the treated plants were less cold hardy than the controls. In some instances, the purines and pyrimidines increased the content of these nitrogenous constituents in a nonhardy variety to a level equal to that found in untreated plants of a hardy variety.     

Chemical evolution XXIX. Pyrimidines from hydrogen cyanide.

Dilute (0.1 M) solutions of HCN condense to oligomers at pH 8-9. Hydrolysis of these oligomers at pH 8.5 or with 6 N HCl yields 4,5-dihydroxypyrimidine, as the most abundant pyrimidine product along with orotic acid and 5-hydroxyuracil. These results, together with the earlier data, demonstrate that the three major nitrogen-containing classes of biomolecules could have originated from HCN on the primitive earth. The observation of the formation of orotic acid and 4-aminoimidazole-5-carboxamide by the hydrolysis of the HCN oligomers suggests that once the initially formed pyrimidines and purines were consumed, those life forms persisted which evolved enzymes for conversion of these intermediates to the pyrimidines and purines present in contemporary RNA.     

The Ultraviolet Light Inactivation of ΦX174 Bacteriophage at Different wave Lengths and pH's

The bacterial virus, ΦX174, which contains a single strand of DNA has been inactivated by different wave lengths of monochromatic ultraviolet light at pH 7, 2, and 12. The action spectra for inactivation at these three pH's all showed minima at 2400 A rather than at 2300 A, which is the characteristic absorption minimum of DNA. The shapes of the action spectra have been analyzed in terms of the effects of absorbed light on the pyrimidines and purines rather than the effect on nucleoprotein. In this interpretation the pyrimidines are at least 2 to 3 times more sensitive than the purines. The quantum yield for inactivation of the virus at 2650 A and pH 7 is 0.006. The quantum efficiency for quanta absorbed in the pyrimidines is 0.0085 and for the purines 0.0035. It is pointed out that action spectra for single- and double-stranded polynucleotides should have minima at different wave lengths, and that this difference may be used to distinguish between these two configurations in vivo.     

Interaction of nucleic acids and glycans

Spectrophotometric analysis and dot-hybridization have shown that amylose forms complexes with polypyrimidines (poly dC), while polyuronides form complexes with polypurines (poly dA). In addition, the formation of complexes genomic thymus DNA-hyaluronic acid has been observed. A certain role in the mechanism of NA-polysaccharide interactions can be played by the links between purines and the carboxylic group of hexuronic acid residue, as well as between pyrimidines and the hydroxymethyl group of hexose residue. The quantum-chemical calculations showed that, between nitric bases of DNA and the carboxyl groups of hexuronic acids or the hydroxymethyl group of hexose, hydrogen bonds can be formed the energy of which is comparable with that in the complementary AT and CG pairs. The strength of these bonds is unequal: carboxyl groups form stronger hydrogen bonds with purines and weaker bonds with pyrimidines. The hydroxymethyl group, on the contrary, forms stronger hydrogen bonds with pyrimidines and weaker bonds with purines. The quantum-chemical modeling shows that, in the complementary pairs purin-uronic acid and pyrimidine-hexose, hydrogen bonds are produced that form a binary chain nucleic acid-polysaccharide. The data obtained suggest the existence of template synthesis of GAG polysaccharide fragments with the participation of NA.     

Study of the hydration characteristics of nucleic acid bases and their complementary pairs using the Monte-Carlo method

To elucidate the role of certain atomic groups in the formation of the nucleic acid hydrate shell, we simulated the systems involving a base or a complementary pair (the base molecules are methylated in N9 of purines and in N1 of pyrimidines) and 25 water molecules using the Monte-Carlo method. All hydrophilic centers, except for N1 purines and N3 pyrimidines in complementary pairs, form hydrogen bonds (H-bonds) with water molecules. The mean numbers of H-bonds formed by different centers, and distributions of the geometric characteristics of these bonds, which appeared similar to those in crystals, have been calculated. The formation of bridges of one, two of three water molecules between hydrophilic centers was shown. The probabilities of formation of these bridges have been calculated.     

Sensitivity of mitomycin C and nitrogen mustard crosslinks to extreme alkaline conditions

DNA-DNA crosslinks in cells treated with mitomycin C, nitrogen mustard, or decarbamoyl mitomycin C were measured in alkaline isopycnic gradients as a function of pH. Crosslinks from cells treated with mitomycin C and nitrogen mustard, which react with DNA purines, could be detected at pH 12.5 but not at pH 14. No crosslinks from cells treated with decarbamoyl mitomycin C were detected at either pH. Previous studies with cells exposed to psoralen derivatives plus 360 nm light, which produce DNA-DNA crosslinks with pyrimidines, demonstrated stable crosslinks at pH 14. These studies indicate that DNA-DNA crosslinks involving DNA purines are much less stable at high pH than those involving pyrimidines, and that methods involving exposure to extreme alkaline conditions may give inaccurate information for some agents.     

Chemical detection of Z-DNA within the maize Adh1 promoter

Z-DNA is a left-handed helix which can form within tracts of alternating purines and pyrimidines. Tracts of potential Z-DNA identified by sequence inspection are often noted within regulatory portions of genes, but evidence that these tracts of sequence actually exist as Z-DNA is very limited, and not available for any plant gene. In this study, the chemical probes osmium tetroxide, diethylpyrocarbonate and hydroxylamine were used to show that a tract of alternating purines and pyrimidines in the Adh1 promoter (from -311 to -325) actually assumes a Z-DNA conformation under superhelical stress in vitro.     

The use of multiple alphabets in kappa-gene immunoglobulin DNA sequence comparisons.

Comparisons within and between the human, mouse and rabbit immunoglobulin-kappa gene (J-C region) DNA sequences are carried out in terms of three two-letter nucleotide alphabets: (i) S-W alphabet (W = A or T; S = G or C); (ii) P-Q alphabet which distinguishes purines (P = A or G) from pyrimidines (Q = C or T); and (iii) a 'control' E-F alphabet (E = A or C; F = G or T). All statistically significant direct repeats within each of the three sequences and all significant block identities (a set of consecutive matching letters) shared by two or more sequences are determined for each alphabet. By contrast to the S-W and E-F alphabets, the P-Q alphabet comparisons reveal an abundance of statistically significant block identities not seen at the nucleotide level. Various interpretations of these P-Q structures with respect to control and functional roles are considered.     

Theoretical model of the B-Z transition in DNA with an arbitrary sequence

A statistical-mechanical model is suggested that makes it possible to describe the B-Z transition in DNA with an arbitrary sequence of nucleotides. The key point consists in allowance for the fact that each base pair can assume one of the two states with different energies. One of these states corresponds to the standard Z-form with purines in the syn conformation and pyrimidines in the anti conformation. However, in natural DNA sequences such standard base-pair conformations should be interrupted by energetically unfavorable conformations (syn for pyrimidines and anti for purines). Open regions and cruciform structures are also allowed for in the model. The probabilities of formation of the Z-form stretches, open regions and cruciform structures have been calculated for different values of parameters for pBR322 and pAO3 DNA.     

On the "activation" of cytokinins.

A number of cytokinin analogs containing modifications in the heterocyclic moiety were prepared. These compounds were tested for activity as cytokinins and anticytokinins in the tabacco bioassay and the results were used to determine whether any position(s) of the heterocyclic nucleus of cytokinins may require derivatization as part of an over-all "activation" process. 3-substituted 4-alkylaminopyrazolo [3,4-d]pyrimidines and 4-alkylaminopyrrolo[2,3-d]pyrimidines, for example, have (substituted) carbon rather than nitrogen atoms at positions 3 and 5, respectively (analogous to position 7 in purines) and would be predicted to be metabolically stable at these positions. The finding that these compounds had cytokinin activity suggested that modification at the metabolically stable positions. The finding that these compounds had cytokinin activity suggested that modification at the metabolically stable position, and by extension at position 7 in cytokinin analogues which are purines, is not a prerequisite for the expression of cytokinin activity. Similar consideration of other heterocyclic analogs which have cytokinin activity suggests that the active form of a cytokinin can be the exogenous compound itself. Certain structural analogs of cytokinins were found to inhibit the growth of tobacco callus promoted by 6-(3-methyl-2-butenylamino)purine. These compounds were studied as potential cytokinin antagonists, i.e. having activity analogous to the 7-alkylamino-3-methylpyrazolo[4,3-d]pyrimidines (Hecht, S. M., 2068-2610; Skoog, F., Schmitz, R.Y., Hecht, S.M., and Bock, R. M. (1973) Phytochemistry 12, 25-37). The activity of these compounds is discussed and criteria are proposed to distinguish between those species which are specific anticytokinins and those which otherwise inhibit growth.     

Investigating the structural basis of purine specificity in the structures of MS2 coat protein RNA translational operator hairpins

We have determined the structures of complexes between the phage MS2 coat protein and variants of the replicase translational operator in order to explore the sequence specificity of the RNA–protein interaction. The 19-nt RNA hairpins studied have substitutions at two positions that have been shown to be important for specific binding. At one of these positions, –10, which is a bulged adenosine (A) in the stem of the wild-type operator hairpin, substitutions were made with guanosine (G), cytidine (C) and two non-native bases, 2-aminopurine (2AP) and inosine (I). At the other position, –7 in the hairpin loop, the native adenine was substituted with a cytidine. Of these, only the G-10, C-10 and C-7 variants showed interpretable density for the RNA hairpin. In spite of large differences in binding affinities, the structures of the variant complexes are very similar to the wild-type operator complex. For G-10 substitutions in hairpin variants that can form bulges at alternative places in the stem, the binding affinity is low and a partly disordered conformation is seen in the electron density maps. The affinity is similar to that of wild-type when the base pairs adjacent to the bulged nucleotide are selected to avoid alternative conformations. Both purines bind in a very similar way in a pocket in the protein. In the C-10 variant, which has very low affinity, the cytidine is partly inserted in the protein pocket rather than intercalated in the RNA stem. Substitution of the wild-type adenosine at position –7 by pyrimidines gives strongly reduced affinities, but the structure of the C-7 complex shows that the base occupies the same position as the A-7 in the wild-type RNA. It is stacked in the RNA and makes no direct contact with the protein.     

Origin of life: Consideration of alternatives to proteins and nucleic acids

Summary Starting with relatively simple, non-hydrolyzable compounds in aqueous solution, entirely spontaneous condensations give rise to polymers that contain purines, pyrimidines, amino acids, coenzymes, lipid components and even phosphate. The presence of certain lipid micelles allows significant product formation at millimolar substrate concentrations. The first step involves formation of a Michael adduct from--unsaturated carbonyl compounds and various nucleophiles. Polymerization of these adducts occurs via sequential Knoevenagel condensations. All reactions take place readily at temperatures below 45°. The polymers can act as macromolecular catalysts as evidenced by hydrolytic activity. The purines and pyrimidines in the polymers appear to be capable of both base pairing and stacking interactions with ribonucleic acids. Specific examples of potential alternatives to base pairing are presented. These results are discussed from the standpoint of the spontaneous development of reproducing molecules. Proteins and nucleic acids may be evolutionary developments which have displaced earlier biopolymers.     

Intramolecular electron transfer in [4Fe-4S] proteins: estimates of the reorganization energy and electronic coupling in Chromatium vinosum ferredoxin

The semi-classical electron transfer theory has been very successful in describing reactions occurring in biological systems, but the relevant parameters in the case of iron-sulfur proteins remain unknown. The recent discovery that 2[4Fe-4S] proteins homologous to Chromatium vinosum ferredoxin contain clusters with different reduction potentials now gives the opportunity to study the dependence of the intramolecular electron transfer rate between these clusters as a function of the driving force. This work shows how decreasing the reduction potential difference between the clusters by site-directed mutagenesis of C. vinosum ferredoxin modifies the rate of electron hopping between the two redox sites of the protein by measuring the line broadening of selected 1H NMR signals. Beside the shifts of the reduction potentials, no signs of large structural changes or of significant alterations of the intrinsic kinetic parameters among the different variants of C. vinosum ferredoxin have been found. A reorganization energy of less than 0.5 eV was deduced from the dependence of the electron transfer rates with the reduction potential difference. This small value is associated with a weak electronic coupling between the two closely spaced clusters. This set of parameters, determined for the first time in an iron-sulfur protein, may help to explain how efficient vectorial electron transfer occurs with a small driving force in the many enzymatic systems containing a 2[4Fe-4S] domain.     

Five-membered heteroaromatic ring fused-pyrimidine derivatives: Design,synthesis, and hedgehog signaling pathway inhibition study

A series of novel five-membered heteroaromatic ring fused-pyrimidine derivatives including purines, pyrrolo[2,3-d]pyrimidines, pyrrolo[3,2-d]pyrimidines, thieno[2,3-d]pyrimidines, thieno[3,2-d]pyrimidines and furo[3,2-d]pyrimidines have been identified to be potent inhibitors of hedgehog signaling pathway. The synthesis and SAR of these compounds are described. Among this new series of hedgehog signaling pathway inhibitors, most compounds exhibited significant inhibitory activity compared to vismodegib, indicating that the five-membered heteroaromatic ring fused-pyrimidines stand out as encouraging scaffolds among the currently reported structural skeletons for hedgehog signaling pathway inhibitors, deserving more exploration and further investigation.