Informational symmetry breaking between proteins and nucleic acids.

Anti-symmetry of the information-processing mechanisms between proteins and nucleic acids is generalized to informational symmetry breaking between a genetic polymer and an anti-genetic polymer so as not to depend on particular chemical species. In a genetic polymer, e.g. nucleic acids, any sequence can form a closed double-stranded structure with a specific partner sequence. On the other hand, in an anti-genetic polymer, e.g. proteins, a chain could fold to an open multi-stranded structure and reinterpretation of the genetic information through slides or shifts between stacked strands could be induced by external perturbations. The possibility of the informational symmetry breaking by hierarchical organization of a single chemical species, i.e. polypeptides as a genetic polymer and nucleic acids as an anti-genetic polymer, is examined. The informational functions of genetic polymers and anti-genetic polymers in a complex mixture of macromolecules are characterized.     

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 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).     

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.     

Are there structural analogies between amino acids and nucleic acids?

Space-filling molecular models have been used to examine structural analogies between amino acids and nucleic acids. The three-dimensional structures of amino acidR groups appear to be stereochemically related to cavities formed by removal of single bases in double helical nucleic acids. The common L amino acids may thus be complementary to their codons.Their publications are indicated by an asterisk in the references at the end of this paper.     

Are there structural analogies between amino acids and nucleic acids?

Space-filling molecular models have been used to examine structural analogies between amino acids and nucleic acids. The three-dimensional structures of amino acid R groups appear to be stereochemically related to cavities formed by removal of single bases in double helical nucleic acids. The common L amino acids may thus be complementary to their codons.     

Models of interaction between nucleic acids and proteins. Hydrogen bonding of arginine with nucleic acid bases, phosphate groups and carboxylic acids.

Complex formation between the side chain of arginine and nucleic acid bases has been investigated by proton magnetic resonance in dimethylsulfoxide. Simultaneous formation of two hydrogen bonds leads to a selectivity of arginine interaction towards cytosine and guanine. A comparison is made of the interaction of arginine side chain with nucleic acid bases, phosphate and carboxylate anions. It is shown that interaction between carboxylate and arginine is stronger than between phosphate and arginine. These results are discussed with respect to the selective recognition of nucleic acid bases by arginine side chains and by the arginyl-glutamyl ion pair which could form in proteins interacting with nucleic acids.     

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.     

Difference in conformational diversity between nucleic acids with a six-membered 'sugar' unit and natural 'furanose' nucleic acids

Natural nucleic acids duplexes formed by Watson-Crick base pairing fold into right-handed helices that are classified in two families of secondary structures, i.e. the A- and B-form. For a long time, these A and B allomorphic nucleic acids have been considered as the 'non plus ultra' of double-stranded nucleic acids geometries with the only exception of Z-DNA, a left-handed helix that can be adopted by some DNA sequences. The five-membered furanose ring in the sugar-phosphate backbone of DNA and RNA is the underlying cause of this restriction in conformational diversity. A collection of new Watson-Crick duplexes have joined the 'original' nucleic acid double helixes at the moment the furanose sugar was replaced by different types of six-membered ring systems. The increase in this structural and conformational diversity originates from the rigid chair conformation of a saturated six-membered ring that determines the orientation of the ring substituents with respect to each other. The original A- and B-form oligonucleotide duplexes have expanded into a whole family of new structures with the potential for selective cross-communication in a parallel or antiparallel orientation, opening up a new world for information storage and for molecular recognition-directed self-organization.