Single macromolecular assemblies

Hydrophobic associations in random copolymers of sodium 2-(acrylamido)-2-methylpropanesulfonate and some methacrylamides and methacrylates substituted with bulky hydrophobes are described with a focus on preferential intrapolymer self-association which leads to the formation of single-macromolecular assemblies (i.e., unimolecular micelles). Structural parameters that critically determine the type of the macromolecular association (i.e., intra- vs. interpolymer associations) are discussed, which include the type of hydrophobes, their content in a polymer, sequence distribution of electrolyte and hydrophobic monomer units, and the type of spacer bonding. Functionalization of single-macromolecular assemblies with some photoactive chromophores is also presented. 

This chapter will discuss hydrophobic associations in random copolymers of AMPS and some hydrophobic methacrylamide and methacrylate comonomers with a focus on the intra- versus interpolymer self-association in connection witih the type of hydrophobes, their content in the polymers, and spacer bonding. A particular emphasis will be placed on intrapolymer association of hydrophobes which leads to single-molecular self-assemblies. Functionalization of the single-macromolecular assemblies with some photoactive chromophores will also be presented briefly. 

It is worth to mention that this definition is not always consistent with the nature of the macromolecular assembly when applying to nucleic acids. For example, from all different types of quadruplex nucleic acids only quadruplex monomers are covered by lUPAC definition of tertiary structure being a single chain of DNA or RNA. However, also the quadruplexes with higher molecularity of the formed structures (dimers, tetramers) belong to this important tertiary structure family. 

Paul, D., Patwardhan, A., Squire, J. M., and Morris, E. P. (2004). Single particle analysis of filamentous and highly elongated macromolecular assemblies. /. Struct. Biol. 148, 236-250. 

International Union of Pure and Applied Chemistry, Nomenclature of Regular Double-Strand (Ladder and Spiro) Organic Polymers (Recommendations 1993), PureAppL Chem., 65,1561-1580 (1993). International Union of Pure and Applied Chemistry, Structure-Based Nomenclature for Irregular Single-Strand Organic Polymers (Recommendations 1994), PureAppL Chem., 66,873-889 (1994). International Union of Pure and Applied Chemistry, Source-Based Nomenclature for Non-Linear Macromolecules and Macromolecular Assemblies (Recommendations 1997). PureAppL Chem., 69, 2511— 2521 (1997). 

This impossibility of reducing a complex process to single macromolecules explains the co-existence of different levels of explanation in biologists molecular descriptions. This does not mean that the nature of the molecular components is of no importance, nor that the complex functions originate only from the rules of assembly of the different macromolecular components. The organization of living beings is based both on the precise nature of the molecular components and on the way that these molecular components are assembled. 

Another complex macromolecular aggregate that can reassemble from its components is the bacterial ribosome. These ribosomes are composed of 55 different proteins and by 3 different RNA molecules, and if the individual components are incubated under appropriate conditions in a test tube, they spontaneously form the original structure (Alberts et al., 1989). It is also known that even certain viruses, e.g., tobacco mosaic virus, can reassemble from the components this virus consists of a single RNA molecule contained in a protein coat composed by an array of identical protein subunits. Infective virus particles can self-assemble in a test tube from the purified components. 

Recommendations on additional aspects of macromolecular nomenclature such as that of regular double-strand (ladder and spiro) and irregular single-strand organic polymers continue to be published in Pure and Applied Chemistry. Recommendations on naming nonlinear polymers and polymer assemblies (networks, blends, complexes, etc) are expected to be issued in the near future. 

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