Interrelationships between polyamines and nucleic acids

Summary The distribution of radioactivity from ³H-putrescine was studied in intact and degenerated sciatic nerves, and spinal ganglia of rats by means of high resolution autoradiography. During the first three days after the administration of the labeled putrescine, the main proportion of radioactive material in the nerves was represented by spermidine and putrescine. Both, in intact and degenerating nerves, developed silver grains were deposited in all cellular components of the nervous tissue, the myelin sheath being markedly tagged. Perineural tissue was also labeled considerably, however, there was no significant amount of label in the extracellular space and in the collagen fibrils. The possible physiological significance of putrescine and spermidine in myelin and in other cellular components of nerves is discussed.Herrn Prof. Dr. W. Krücke zum 60. Geburtstag gewidmet.     

Interaction between polyamines and nucleic acids or phospholipids

The binding of polyamines to DNA, RNA, and phospholipids has been studied by gel filtration and sucrose density gradient centrifugation. Spermine was found to bind more to a GC-rich DNA. Among RNAs containing double-stranded region [poly(AU), poly(GC), and ribosomal RNA], the binding of spermine was nearly equal. Among the single-stranded RNAs, the binding of spermine was in the order poly(U) > poly(C) > poly(A). An increase in K⁺ or Mg²⁺ concentration resulted in a great decrease in spermine binding to DNA and in a slight decrease in spermine binding to RNA. Therefore, in the presence of more than 2 mm Mg²⁺ and 100 mm K⁺, the binding of spermine to RNA was greater than that to DNA. No significant difference in spermine binding was observed between 16 S ribosomal RNA and 30 S ribosomal subunits, suggesting that ribosomal proteins did not affect significantly the binding of spermine to ribosomal RNA. The binding of spermine to microsomes was dependent on phospholipids. The binding strength was in the order phosphatidylinositol > phosphatidylethanolamine > phosphatidylcholine.     

The interactions between nucleic acids and polyamines. III. Microscopic protonation constants of spermidine

Changes in the NMR chemical shifts of protons adjacent to the nitrogen atoms of Spermidine which are undergoing protonation have been measured by two-dimensional heteronuclear coupled NMR. Data thus obtained measure the dependence of the state of protonation of individual nitrogens on the pH, and permit calculation of the microprotonation constants of Spermidine and the concentrations of all of the variously protonated Spermidine species present at any pH.     

Interaction of nucleic acids. VI. Interaction of purine with nucleic acids

The interaction of purine with DNA, tRNA, poly A, poly C, and poly A. poly U complex was investigated. In the presence of purine, the nucleic acids in coil form (such as denatured DNA, poly A and poly C in neutral solutions, or tRNA) have lower optical rotations. In addition, hydrodynamic studies indicate that in purine solutions the denatured DNA has a higher viscosity and a decreased sedimentation coefficient. These findings indicate that through interaction with purine, the bases along the poly-nucleotide chain are unstacked and are separated farther from each other, resulting in increased assymmetry (and possibly volume) of the whole polymer. Thus, the de-naturation effect of purine reported previously can be explained by this preferential interaction of purine with the bases of nucleic acids in coil form through a hydrophobic-costacking mechanism. Results from studies on optical rotation and helix-coil transition show that the interaction of purine is greater with poly A than with poly C. The influence of temperature, Mg⁺⁺ concentration, ionic strength, and purine concentration on the effect of purine on nucleic acid conformation has also been investigated. In all these situations the unraveling of nucleic acid conformation occurs at much lower temperatures (20–40°C lower) in the presence of purine (0.2–0.6M).     

Spin labeled nucleic acids.

Homopolyribonucleotides and E. coli DNA wer spin labeled with an iodoacetamide-nitroxide compound. The extent of labeling is highly dependent upon the nature of the base and the secondary structure of the nucleic acid. This spin label-polymer linkage is unstable at high temperatures and in phosphate buffers. In order to determine the effect of changes in the environment of nucleic acids on the esr signals of their attached spin labels, the polynucleotides were subjected to temperature and viscosity perturbations. An increase in temperature (T) affects a linear decrease in the anisotropy factor of the esr signal. The log tau (tau = correlation time) versus (1/T) profile is linear with a positive slope when the spin label is attached to single stranded polynucleotides but exhibits discontinuities at certain critical temperatures when attached to the duplexes poly (As-U) and poly (I-Cs). These critical temperatures are lower than the optical Tm. Logarithmic increase in viscosity was found to produce a linear increase in tau in aqueous sucrose solutions.     

Iodination of herpesvirus nucleic acids.

A simple method is described for the iodination of herpes simplex virus (HSV) DNA. The procedure involved synthesis of 125-I-labeled 5-iodo-dCTP which was subsequently used as a precursor for the in vitro repair synthesis of HSV DNA. Synthesis of 5-iodo-dCTP and purification from oxidation and reduction reagents, buffer salts, unreacted dCTP and Na125-I was accomplished in a single chromatographic step. It was possible to prepare 125-I-labeled HSV DNA in vitro with specific activities exceeding 10-8 counts/min/mu-g. The DNA prepared by this method reassociated with DNA extracted from HSV-infected HEp-2 cells but not with HEp-2 cell DNA. Iodinated HSV DNA was susceptible to S-1-endonuclease digestion once denatured but was resistant to digestion in the native form. This method was used to synthesize 125-I-labeled ribo-CTP (5-iodo-CTP) which was used to prepare cytomegalovirus-specific complementary RNA. The method should be of value in the preparation of viral probes and for use in autoradiography of viral nucleic acids.     

Quadruplex structures in nucleic acids.

DNA oligonucleotides that have repetitive tracts of guanine bases can form G-quadruplex structures that display an amazing polymorphism. Structures of several new G-quadruplexes have been solved recently that greatly expand the known structural motifs observed in nucleic acid quadruplexes. Base triads, base hexads, and quartets that contain cytosine have recently been identified stacked over the familiar G-quartets. The current status of the diverse array of structural features in quadruplexes is described and used to provide insight into the polymorphism and folding pathways. This review also summarizes recent progress in the techniques used to probe the structures of G-quadruplexes and discusses the role of ion binding in quadruplex formation. Several of the quadruplex structures featured in this review can be accessed in the online version of this review as CHIME representations.     

Trinitrophenylation of nucleic acids and their constituents.

1. Under relatively mild conditions, nucleic acids and their constituents were trinitrophenylated with 2,4,6-trinitrobenzenesulfonate (TNBS) in aqueous solution (pH 8-11), yielding reddish-orange trinitrophenyl (TNP) derivatives. Guanine residues were trinitrophenylated on the base residues at the 2-amino group (N2-TNP derivatives), and in addition, 2'- and 3'-hydroxyl groups of the ribose moieties of nucleosides or nucleotides were trinitrophenylated to form Meisenheimer complexes. 2. The preparation of TNP derivatives (N2-TNP-guanine, -guanosine, N2, O-bis-TNP-guanosine, O-TNP-guanosine, -adenosine, -cytidine , and -uridine), their rates of formation, absorption spectra (UV, visible, and infrared), molar extinction coefficients, Rf value, electrophoretic mobilities, and stability in acid or alkaline solution, are presented. 3. Trinitrophenylation of several kinds of nucleic acid was investigated. Calf thymus DNA and yeast transfer RNA showed a resistance to trinitrophenylation compared to guanosine 3'(2')-phosphate, yeast RNA or denatured calf thymus DNA. TNP-RNA showed resistance to the action of ribonucleases T1 and T2 [EC 3.1.4.8 and 3.1.4.23]. 4. Trinitrophenylation reactions using 2,4,6-trinitrochlorobenzene and 2,4,6-trinitrofluorobenzene were compared with that using TNBS as regards specificity and reaction rate.     

The interactions between nucleic acids and polyamines. II. Protonation constants and 13C-NMR chemical shift assignments of spermidine, spermine, and homologs

Macroscopic protonation constants have been determined by pulentiometric titration for spermidine, spermine and for the four pulyamines. 3,5-Spd, 4,4-Spd, 4,3,4-Spm and 4,4,4-Spm. which are homologs of spermidine and spermine. A method for calculation of microscopic protonation constants of polyamines based on data for mono- and diamines gives results for spermidine that agree well with the experimental macroscopic protonation constants and the protonation sequence of Kimberly and Goldstein. ¹³C-NMR spectra of spermidine, spermine and six homologs have been obtained and used to assign specific resonances, correcting some ambiguity in the assignments for spermidine and some errors in the assignments for spermine.     

Conformational classification of functional nucleic acids.

The kink parameters would provide the tolerant aspect for irregular helical structure of nucleic acid. Using these kink parameters, the classification of conformation space was carried for the functional nucleic acid molecules. The kink parameters could afford us the simple structural aspects about the constructive parts of functional molecules. Local elastic kink phenomena can be classified by rod like models with the combination of kink parameters. The constructive parts, such as the stable tetra nucleotides loop, U-turn conformation and adenosine platform, were selected and the statistical analyses were carried on the parameters calculated by program BIOCON.     

Nucleotide composition of nucleic acids of fungi. II. Deoxyribonucleic acids

Storck, Roger (The University of Texas, Austin). Nucleotide composition of nucleic acids from fungi. II. Deoxyribonucleic acids. J. Bacteriol. 91:227-230. 1966.-The nucleotide composition of the deoxyribonucleic acids (DNA) present in extracts of 30 species of fungi was determined. The results were analyzed, together with those in the literature. It was found that the content, in moles per cent of guanine plus cytosine (GC content), varied from 38 to 63% in a distribution composed of 9 species of zygomycetes, 14 of ascomycetes, and 9 each of deuteromycetes and basidiomycetes. The GC content ranges were: 38 to 48% for the zygomycetes, 38 to 54% for the ascomycetes, 47 to 62% for the deuteromycetes, and 44 to 63% for the basidiomycetes. The GC content ranged from 38 to 40% for four Mucor species. The base composition of fungal DNA appears, therefore, to have a taxonomic and phylogenetic significance.