Origin of informational polymers: differential stability of phosphoester bonds in ribomonomers and ribooligomers

We have measured the stabilities of the bonds that are critical for determining the half-life of ribonucleotides and the beta-glycosidic and 3'- and 5'-phosphoester bonds. Stabilities were measured under a wide range of temperatures and water/formamide ratios. The stability of phosphodiester bonds in oligoribonucleotides was determined in the same environments. The comparison of bond stabilities in the monomer versus the polymer forms of the ribo compounds revealed that physico-chemical conditions exist in which polymerization is thermodynamically favored. These conditions were compared with those determining a similar behavior for 2'-deoxyribonucleosides, deoxyribonucleotides, and deoxyribooligonucleotides and were shown to profoundly differ. The implications of these facts on the origin of informational polymers are discussed.     

Universal sequence replication, reversible polymerization and early functional biopolymers: a model for the initiation of prebiotic sequence evolution

Many models for the origin of life have focused on understanding how evolution can drive the refinement of a preexisting enzyme, such as the evolution of efficient replicase activity. Here we present a model for what was, arguably, an even earlier stage of chemical evolution, when polymer sequence diversity was generated and sustained before, and during, the onset of functional selection. The model includes regular environmental cycles (e.g. hydration-dehydration cycles) that drive polymers between times of replication and functional activity, which coincide with times of different monomer and polymer diffusivity. Template-directed replication of informational polymers, which takes place during the dehydration stage of each cycle, is considered to be sequence-independent. New sequences are generated by spontaneous polymer formation, and all sequences compete for a finite monomer resource that is recycled via reversible polymerization. Kinetic Monte Carlo simulations demonstrate that this proposed prebiotic scenario provides a robust mechanism for the exploration of sequence space. Introduction of a polymer sequence with monomer synthetase activity illustrates that functional sequences can become established in a preexisting pool of otherwise non-functional sequences. Functional selection does not dominate system dynamics and sequence diversity remains high, permitting the emergence and spread of more than one functional sequence. It is also observed that polymers spontaneously form clusters in simulations where polymers diffuse more slowly than monomers, a feature that is reminiscent of a previous proposal that the earliest stages of life could have been defined by the collective evolution of a system-wide cooperation of polymer aggregates. Overall, the results presented demonstrate the merits of considering plausible prebiotic polymer chemistries and environments that would have allowed for the rapid turnover of monomer resources and for regularly varying monomer/polymer diffusivities.     

Formamide chemistry and the origin of informational polymers

Formamide (HCONH2) provides a chemical frame potentially affording all the monomeric components necessary for the formation of nucleic polymers. In the presence of the appropriate catalysts, and by moderate heating, formamide yields a complete set of nucleic bases, acyclonucleosides, and favors both phosphorylations and transphosphorylations. Physico-chemical conditions exist in which formamide favors the stability of the phosphoester bonds in nucleic polymers more than that of the same bonds in monomers. This property establishes 'thermodynamic niches' in which the polymeric forms are favored. The hypothesis that these specific attributes of formamide allowed the onset of prebiotic chemical equilibria capable of Darwinian evolution is discussed.     

Adsorption Behavior of Polydisperse Polymeric Systems

Adsorption behavior of polydisperse polymers at interfaces is studied by the Monte Carlo simulation method based on a lattice model. Effects of temperature and adsorption energies on the polymer density profile, cluster distributions and adsorption layer thickness are evaluated in two different polydisperse systems. It is found that adsorption properties are greatly different in these two systems. In normal distribution polydisperse systems, polymers are more sensitive to the excluded volume effects while in average distribution polymers are more inclined to adsorb on adsorbing interfaces. As higher temperature and lower attraction constrain the polymer adsorption, more clusters are found under these conditions. When temperature approaches the critical temperature of monodisperse systems, stable and large clusters exist in these two polydisperse systems. These results suggest that micro phase transition may exist in polydisperse systems. Polydisperse systems take little change of phase transition temperatures but altered the clusters morphology to some extent. The adsorption layer thickness changes are more sensitive to both temperature and polymer–interface interactions in average distribution systems when the whole polymer concentration increases slightly. This work also suggests significant differences between the polydisperse and the monodisperse systems in adsorption behavior. Therefore, quantitative system errors may exist when the monodisperse system models are used in simulation to evaluate polymer adsorption properties.     

An Epistemology on the Nature of Polymers

Liquids have neither a periodic structure nor the completely random character of gases therefore the detailed study of their x-ray scattering diagram encounters many difficulties. The idea of periodic regularity in molecules of liquid polymers has been an attractive proposition for the simple interpretation of liquid polymer x-ray diagrams. The categorisation of polymer substances as being between a crystal phase with a perfect order and an amorphous disordered state is an over simplification of the complex reality. For obtaining structural information, during the early stages of the application of x-ray diffraction, a near crystalline model of the molecular arrangements in liquids was utilised. However, the results from these investigations led to just an approximation of the crystalline state. Our studies have analysed the real image of Fourier space of liquid polymers, for the first time, using anomalous diffractometry. The findings show the precise atomic structure of liquid polymers when transformed, by cooling, to solid polymers. We demonstrate that there is an intermediate ordered structure, characterised by the real full image of Fourier space. This prominent state of matter, an intermediate ordered structure, is defined by a regular unit cell with a five-fold symmetry. These structural atomic studies contribute to a more detailed understanding of the properties of polymers than the traditional studies of the degree of crystallinity.     

Simultaneous purification and polymerization method for bovine serum albumin preparation

Bovine serum albumin (BSA) has various applications in blood group serology and different research purposes. In this study purification of BSA has been compared with human serum albumin (HSA) using modified ethanol precipitation method based on the method of Cohn. The purification process was carried out under controlled conditions, particularly of ethanol concentration, pH, ionic strength and temperature. It was revealed that the produced BSA and HSA have purity more than 95%. It is obvious that HSA can be used, as a drug when the amount of its polymers is less than 5% whereas polymer generation is required in order to enhance the potentiating properties of BSA in agglutination of red cells. We propose here a simple and rapid two-step method for simultaneously purification and polymerization of BSA. By this method simply BSA with desired amount of polymers was obtained by 40% ethanol concentration.     

Poly(2-amino-8-methyladenylic acid). Competing structural and energetic effects of substituents

The ribopolynucleotide poly(2-amino-8-methyladenylic acid), (r2NH2(8)MeA)n, has been synthesized, and its physical and chemical properties have been examined. The study reveals competing effects on these properties of the 2-NH2 and 8-Me substituents. In marked contrast to the analogous (r8MeA)n, the new polymer readily interacts to form double helixes with complementary pyrimidine polynucleotides. Triple helixes are not formed. The 8-Me group is strongly destabilizing for helix formation (delta Tm approximately 65 degrees C), presumably by favoring a syn conformation, which blocks heteroduplex formation with ribohomopolymers. The 2-NH2 substituent stabilizes helixes in the ribo series by about 30 degrees C in Tm by forming a third interbase hydrogen bond. We suggest that the free energy from the 2-NH2 interaction drives the syn-anti equilibrium to the purine polymer to the anti form present in the double helix. CD spectra of the homopolymers (r2NH2A)n and (r2NH2(8)MeA)n are completely different, reflecting major differences of conformation. The double helixes formed by these polymers with (rT)n and (rBrU)n, on the other hand, have closely similar CD spectra, supporting our proposal of a major change in conformation of (2NH2(8)MeA)n on going from single strand to double helix.     

Characterization of degradable polyelectrolyte multilayers fabricated using DNA and a fluorescently-labeled poly(β-amino ester): shedding light on the role of the cationic polymer in promoting surface-mediated gene delivery

Polyelectrolyte multilayers (PEMs) fabricated from cationic polymers and DNA have been investigated broadly as materials for surface-mediated DNA delivery. One attractive aspect of this "multilayered" approach is the potential to exploit the presence of cationic polymer "layers" in these films to deliver DNA to cells more effectively. Past studies demonstrate that these films can promote transgene expression in vitro and in vivo, but significant questions remain regarding roles that the cationic polymers could play in promoting the internalization and processing of DNA. Here, we report physicochemical and in vitro cell-based characterization of DNA-containing PEMs fabricated using fluorescently end-labeled derivatives of a degradable polycation (polymer 1) used in past studies of surface-mediated transfection. This approach permitted simultaneous characterization of polymer and DNA in solution and in cells using fluorescence-based techniques, and provided information about the locations and behaviors of polymer 1 that could not be obtained using other methods. LSCM and flow cytometry experiments revealed that polymer 1 and DNA released from film-coated objects were both internalized extensively by cells and that they were colocalized to a significant extent inside cells (e.g., ~58% of DNA was colocalized with polymer). Fluorescence anisotropy measurements of solutions containing partially eroded films were also consistent with the presence of aggregates of polymer 1 and DNA in solution (e.g., after release from surfaces, but prior to internalization by cells). Our results support the view that polymer 1, which is incorporated into these materials as "layers" rather than as part of optimized, preformed "polyplexes", can act to promote or enhance surface-mediated DNA delivery. More broadly, our results suggest opportunities to improve the delivery properties of DNA-containing PEMs by incorporation of additional "layers" of other conventional cationic polymers designed to address specific intracellular barriers to transfection, such as endosomal escape, more effectively.     

Copolymerization of tubulin-colchicine complex and unliganded tubulin in a nonmicrotubular polymer

We have shown previously [Saltarelli, D., & Pantaloni, D. (1982) Biochemistry 21, 2996-3006] that the tubulin-colchicine complex is able to polymerize in vitro into peculiar "curly" polymers, under the solution conditions permitting polymerization of unliganded tubulin into microtubules. Here it is further demonstrated that unliganded tubulin can be incorporated into these "curly" polymers. The partial critical concentration of tubulin-colchicine is decreased upon incorporation of unliganded tubulin into the copolymer. GTP hydrolysis occurs on unliganded tubulin upon incorporation in the copolymer. Tubulin-podophyllotoxin does not copolymerize with tubulin-colchicine to form a large polymer but interacts with it, preventing tubulin-colchicine polymerization. The data have been analyzed within a model of random copolymerization of unliganded tubulin and tubulin-colchicine into "curly" polymers. A corollary is that unliganded tubulin is virtually able to self-assemble into curly polymers with a critical concentration 10-fold higher than the critical concentration found for microtubule assembly. Consequently, these peculiar tubulin homopolymers cannot be observed except as transients at high concentrations, or when microtubule assembly is inhibited. Kinetic measurements of the T-TC copolymerization process and associated GTP hydrolysis at different T/TC ratios provide supplementary information about some privileged interactions between tubulin and tubulin-colchicine molecules. A comprehensive phase diagram of the various possible polymers formed in the presence of tubulin and tubulin-colchicine is presented.     

On the Evolution of Neurochemical Transmission

A discussion of the evolution of neurochemical transmission is divided into three main topics: evolution of biochemical signalling devices, evolution of neurotransmitter substances, and evolution of signal meaning. Models of signalling devices are developed from a primitive chemoceptive process through open and closed loop communications to a neuronal commications network and to its development into a symbolic logic exchange. The evolution of neurotransmitter substances is extrapolated from experimental evidence which has been obtained under primitive earth atmosphere conditions. Examples from comparative biology suggest that the evolution of transmitter use was not unidirective and that purine derivatives may well have been the primordial transmitter substances. The classical neurotransmitters, such as acetylcholine and norepinephrine have a limited information content in their molecular structure, whereas inherent message content of peptidergic transmitters is potentially significant. If there are mnemotypic genes, they may be expressed as informational macromolecules which specify behavioral patterns. Such information transfer would represent a second order of neurochemical transmission and its evolution would be closely coupled to that of molecules which contain a universal meaning.     

Preparation of solid dispersions of nonsteroidal anti-inflammatory drugs with acrylic polymers and studies on mechanisms of drug-polymer interactions

This work studied the mechanisms of interaction between Eudragit RS100 (RS) and RL100 (RL) polymers with 3 nonsteroidal anti-inflammatory drugs: diflunisal (DIF), flurbiprofen (FLU), and piroxicam (PIR). Solid dispersions of polymers and drugs at different weight ratios were prepared by coevaporation of their ethanol solutions. The resulting coevaporates were characterized in the solid state (Fourier-transformed infrared spectroscopy (FT-IR) IR, differential scanning calorimetry, powder-x-ray diffractometry) as well as by studying the in vitro drug release in a gastroenteric environment. Absorption tests from drug solutions to the solid polymers were also performed to better explain the mechanism of interactions between them. The preparative conditions did not induce changes in the crystalline state of the drugs (amorphization or polymorphic change). Drugs strongly interacted with the ammonium groups present in polymers, giving an electrostatic interaction that reinforced the mere physical dispersion of drug molecules within polymer networks. Such interactions are related to the chemical structure of the drugs and to their dissociated or undissociated state. The dispersion of drugs in the polymer matrices strongly influenced their dissolution rate, which appeared slower and more gradual than those of the pure drugs, when polymer ratios were increased. RL coevaporates usually displayed higher dissolution rates. The kinetic evaluation of the dissolution profile, however, suggested that both the drug solubility in the external medium and its diffusion capacity within the polymer network are involved. In the sorption experiments, RL showed a greater adsorptive capacity than RS, in relation to the greater number of quaternary ammonium functions, which behave as activity sites for the electrostatic interactions. In the presence of Tris-HCl buffer (pH 7.4), drug adsorption was reduced, as a consequence of the competition of the chloride ions with drug anions for the polymer binding sites. In general, DIF and FLU displayed a similar interaction with RS and RL active sites; PIR's was different. The different molecular structures of these agents can justify such findings. The presence of a carboxyl group (instead of another dissociable acidic moiety, like the hydroxy-enolic one in the PIR molecule) could help explain the strong interaction with RS and RL polymers' quaternary ammonium centers. Preliminary studies like ours are important in helping develop better forecasting and increasing the understanding of the incorporation/release behavior of drugs from particulate delivery systems that can be made from these polymers.     

Steric exclusion of cells. A mechanism of glycosaminoglycan-induced cell aggregation.

The mechanism by which chondroitin sulfate enhances both the self-aggregation and the concanavalin A (ConA)-induced agglutination of trypsin-dissociated embryonic chick retina cells was investigated. Studies with fluorescently labeled ConA showed no influence of chondroitin sulfate on patching or capping. When ³H- or ³⁵SO₄-labeled glycosaminoglycans or proteoglycans from retinas were added to freshly dissociated cells, an average of less than 2% of the label became associated with the unwashed cell pellet, and most of this was removed from the cells by a single wash. The presence of ConA did not alter the amount of binding by this criterion. Rapid cell aggregation in the absence of ConA was promoted by a number of natural and synthetic polymers. Aggregation rate bore a direct relationship to polymer viscosity at low viscosities and was inhibited at high viscosities, apparently due to reduced cell collision frequency. For any given polymer, aggregation was directly related to its molecular weight and concentration. Linear polymers were more effective than branched ones. Neutral polymers were as effective as those which were strongly polyanionic. Stable aggregates of formalin-fixed cells were not promoted by polymers. All of these observations are consistent with the hypothesis that enhancement of retina cell aggregation by physiological concentrations of glycosaminoglycans is due largely to steric exclusion of the cells by the polymer mesh. Although others have shown that glycosaminoglycans probably interact specifically with some cells, the evidence presented here suggests that these macromolecules by virtue of their excluded volumes could also have important non-specific influences on cell migration and cell reorganization during morphogenesis.     

IS LIFE IMPOSSIBLE? INFORMATION,SEX, AND THE ORIGIN OF COMPLEX ORGANISMS

The earliest organisms are thought to have had high mutation rates. It has been asserted that these high mutation rates would have severely limited the information content of early genomes. This has led to a well‐known “paradox” because, in contemporary organisms, the mechanisms that suppress mutations are quite complex and a substantial amount of information is required to construct these mechanisms. The paradox arises because it is not clear how efficient error‐suppressing mechanisms could have evolved, and thus allowed the evolution of complex organisms, at a time when mutation rates were too high to permit the maintenance of very substantial amounts of information within genomes. Here, we use concepts from the formal theory of information to calculate the amount of genomic information that can be maintained. We identify conditions under which much higher levels of genomic information can be maintained than previously considered possible among origin‐of‐life researchers. In particular, we find that the highest levels of information are maintained when many genotypes produce identical phenotypes, and when reproduction occasionally involves recombination between multiple parental genomes. There is a good reason to believe that these conditions are relevant for very early organisms, and thus the results presented may provide a solution to a long‐standing logical problem associated with the early evolution of life.     

Structure-property studies on carbohydrate-derived polymers for use as protein-resistant biomaterials

Here we describe structure-property studies on our carbohydrate-derived side-chain ether polymers as protein-resistant biomaterials. A series of side-chain ether polymers, including two polyesters and two polyamides, were prepared by condensation polymerization of monomers derived from simple carbohydrates. The two side-chain permethoxylated polyesters having different stereochemical repeating units demonstrate excellent resistance toward nonspecific protein adsorption as shown by surface plasmon resonance, indicating that the polymer stereochemistry does not have much effect on its protein-resistant properties. The introduction of amide bonds to polymer backbones leads to more pronounced effects. While the polymer degradation stability is significantly enhanced by replacing ester with amide linkages, the protein resistance for the polymer is greatly reduced by introduction of amide bonds. Finally, our results suggest that free hydroxyl and amide groups, while both are hydrogen-bond donors, seem to have different effects on protein resistant properties for polymers. It appears that free amide groups have more detrimental effect on protein resistance than free hydroxyl groups. These results show that the protein-resistant properties of this family of polymers can be tailored by modifying the backbone and side chain functionalities. In combination with the biodegradability and functionalizability, this family of carbohydrate-derived polymers shows promise as versatile biomaterials for biomedical applications.     

Macromolecule-small molecule interactions; introduction of additional binding sites in polyethyleneimine by disulfide cross-linkages

Polyethyleneimine and its acyl derivatives have been thiolated with thiobutyrolactone and the SH groups introduced have been crosslinked in the presence of and in the absence of methyl orange, respectively. After crosslinking of the polymers, the bound methyl orange was removed. The resultant two kinds of crosslinked polymers have been examined for their ability to bind methyl orange. The polymer crosslinked in the presence of methyl orange shows more binding sites and stronger binding than does the polymer crosslinked in the absence of methyl orange. It seems, therefore, that the conformation of the polymer may be molded to provide sites that can accommodate a specific small molecule.     

Energetics of the cooperative assembly of cell division protein FtsZ and the nucleotide hydrolysis switch

FtsZ is the first protein recruited to the bacterial division site, where it forms the cytokinetic Z ring. We have determined the functional energetics of FtsZ assembly, employing FtsZ from the thermophilic Archaea Methanococcus jannaschii bound to GTP, GMPCPP, GDP, or GMPCP, under different solution conditions. FtsZ oligomerizes in a magnesium-insensitive manner. FtsZ cooperatively assembles with magnesium and GTP or GMPCPP into large polymers, following a nucleated condensation polymerization mechanism, under nucleotide hydrolyzing and non-hydrolyzing conditions. The effect of temperature on the critical concentration indicates polymer elongation with an apparent heat capacity change of -800 +/- 100 cal mol-1 K-1 and positive enthalpy and entropy changes, compatible with axial hydrophobic contacts of each FtsZ in the polymer, and predicts optimal polymer stability near 75 degrees C. Assembly entails the binding of one medium affinity magnesium ion and the uptake of one proton per FtsZ. Interestingly, GDP- or GMPCP-liganded FtsZ cooperatively form helically curved polymers, with an elongation only 1-2 kcal mol-1 more unfavorable than the straight polymers formed with nucleotide triphosphate, suggesting a physiological requirement for FtsZ polymerization inhibitors. This GTP hydrolysis switch should provide the basic properties for FtsZ polymer disassembly and its functional dynamics.     

Effect of polyanionic polymers on haemoglobin oxygen-binding properties: application to the synthesis of covalent conjugates with low oxygen affinity

Polyanionic water-soluble polymers containing sulphate, phosphate and polycarboxylate groups were synthesized. These compounds, when simply added to haemoglobin solutions, were shown to lower the affinity of the protein for oxygen. Their influence on oxygen affinity was regarded as the result of a specific interaction of the polymer anionic groups inside the 2,3-diphosphoglycerate-binding site of deoxyhaemoglobin. On the other hand, these polymers were linked to deoxyhaemoglobin to give covalent conjugates also exhibiting an oxygen affinity lower than that of free haemoglobin in the presence of 2,3-diphosphoglycerate, its natural effector, which means that after fixation, the polyanionic polymers are still acting as effectors.     

Synthesis of poly(beta-amino ester)s optimized for highly effective gene delivery

Several families of synthetic polymers, including degradable poly(beta-amino ester)s, have been previously shown to effectively mediate gene transfer. However, the combined impact of potentially significant factors-such as polymer molecular weight, polymer chain end-group, and polymer/DNA ratio-on different gene transfer properties has yet to be systematically investigated. The elucidation of these relationships may aid in the design of nonviral vectors with greatly enhanced transfection properties. To examine these factors, two distinct poly(beta-amino ester) structures, Poly-1 and Poly-2, were generated by adding 1,4-butanediol diacrylate and 1,6-hexanediol diacrylate, respectively, to 1-aminobutanol. Twelve unique versions of each structure were synthesized by varying amine/diacrylate stoichiometric ratios, resulting in polymers with either amine or acrylate end-groups and with molecular weights ranging from 3350 to 18000. Using high throughput methods, all polymers were tested in quadruplicate at nine different polymer/DNA ratios ranging from 10:1 w/w to 150:1 w/w. Through the optimization of molecular weight, polymer chain end-group, and polymer/DNA ratio, these polymers successfully mediated gene transfer at levels that surpassed both PEI and Lipofectamine 2000 in vitro.     

Higher frequency of social learning in China than in the West shows cultural variation in the dynamics of cultural evolution

Cultural evolutionary models have identified a range of conditions under which social learning (copying others) is predicted to be adaptive relative to asocial learning (learning on one''s own), particularly in humans where socially learned information can accumulate over successive generations. However, cultural evolution and behavioural economics experiments have consistently shown apparently maladaptive under-utilization of social information in Western populations. Here we provide experimental evidence of cultural variation in people''s use of social learning, potentially explaining this mismatch. People in mainland China showed significantly more social learning than British people in an artefact-design task designed to assess the adaptiveness of social information use. People in Hong Kong, and Chinese immigrants in the UK, resembled British people in their social information use, suggesting a recent shift in these groups from social to asocial learning due to exposure to Western culture. Finally, Chinese mainland participants responded less than other participants to increased environmental change within the task. Our results suggest that learning strategies in humans are culturally variable and not genetically fixed, necessitating the study of the ‘social learning of social learning strategies'' whereby the dynamics of cultural evolution are responsive to social processes, such as migration, education and globalization.     

Universal metastability of sickle hemoglobin polymerization

Sickle hemoglobin (HbS) polymerization occurs when the concentration of deoxyHbS exceeds a well-defined solubility. In experiments using sickle hemoglobin droplets suspended in oil, it has been shown that when polymerization ceases the monomer concentration is above equilibrium solubility. We find that the final concentration in uniform bulk solutions (i.e., with negligible boundaries) agrees with the droplet measurements, and both exceed the expected solubility. To measure hemoglobin in uniform solutions, we used modulated excitation of trace amounts of CO in gels of HbS. In this method, a small amount of CO is introduced to a spatially uniform deoxyHb sample, so that less than 2% of the sample is liganded. The liganded fraction is photolyzed repeatedly and the rate of recombination allows the concentration of deoxyHbS in the solution phase to be determined, even if polymers have formed. Both uniform and droplet samples exhibit the same quantitative behavior, exceeding solubility by an amount that depends on the initial concentration of the sample, as well as conditions under which the gel was formed. We hypothesize that the early termination of polymerization is due to the obstruction in polymer growth, which is consistent with the observation that pressing on slides lowers the final monomer concentration, making it closer to solubility. The thermodynamic solubility in free solution is thus achieved only in conditions with low polymer density or under external forces (such as found in sedimentation) that disrupt polymers. Since we find that only about 67% of the expected polymer mass forms, this result will impact any analysis predicated on predicting the polymer fraction in a given experiment.