Nucleic acids Macromolecules with sequencing

The concept of the similarity of molecules has important ramifications for physical, chemical, and biological systems. Grunwald (7) has recently pointed out the constraints of molecular similarity on linear free energy relations and observed that Their accuracy depends upon the quality of the molecular similarity. The use of quantitative structure-activity relationships (2-6) is based on the assumption that similar molecules have similar properties. Herein we present a general and rigorous definition of molecular structural similarity. Previous research in this field has usually been concerned with sequence comparisons of macromolecules, primarily proteins and nucleic acids (7-9). In addition, there have appeared a number of ad hoc definitions of molecular similarity (10-15), many of which are subsumed in the present work. Difficulties associated with attempting to obtain precise numerical indices for qualitative molecular structural concepts have already been extensively discussed in the literature and will not be reviewed here. 

Proteins and nucleic acids are informational macromolecules each protein and each nucleic acid has a characteristic information-rich subunit sequence. Some oligosaccharides, with six or more different sug-... 

A major theme running through these chapters is the added complexity inherent in the biosynthesis of macromolecules that contain information. Assembling nucleic acids and proteins with particular sequences of nucleotides and amino acids represents nothing less than preserving the faithful expression of the template... 

Bioactive macromolecules like peptides, proteins, and nucleic acids have been successfully embedded in planar LbL films. An important question is the retention of the bioactivity of the film-embedded biomolecules. The structural properties and stability of the LbL films formed from synthesized polypeptides of various amino acid sequences were recently reported [50]. The authors showed that control over the amino acid sequence enables control over non-covalent interpolypeptide interaction in the film, which determines the film properties. Haynie and coworkers showed by circular dichroism spectroscopy that the extent of adsorption of poly(L-glutamic acid) (PGA) and poly(L-lysine) (PLL) in the LbL films scales with the extent of secondary structure of the polypeptides in solution [51]. Boulmedais demonstrated that the secondary structure of the film composed of these polypeptides is the same as the peptide structure in the complex formed in solution [52], as found by Fourier transform IR spectroscopy (FUR). 

In fact, a tremendous amount of information is available on the structures of biological macromolecules descriptions of structures of proteins and nucleic acids make up major portions of modern textbooks in biochemistry and molecular biology. The Protein Data Bank and the Nucleic Acid Database are online archives that contain sequence and structural data on thousands of specific molecules and complexes of molecules. This structural information comes from in vitro experiments, with structures inferred from the x-ray diffraction patterns of crystallized molecules, spectroscopic measurements using multi-dimensional nuclear magnetic resonance, and a host of other methodologies. 

Over the past 30 years, most of the important discoveries in the biological sciences have been associated with proteins and nucleic acids, and thus chemists have been most active in conducting their research to address the relationship between the structure and function of these macromolecules as well as to develop small molecules as mechanistic probes or drug candidates to target these two types of biopolymers. This rapid progress of development is undoubtedly due to—other than the importance of proteins and nucleic acids in biological functions—the availability of various powerful tools (such as the polymerase chain reaction, solid-phase synthesizers, sequence analysis, and sensitive assay systems) to both chemists and biologists, and the close interplay between these two disciplines. 

Type III system. DNA synthesis inside fatty acid vesicles. DNA is today the cellular macromolecule where the information about the proteins sequence is stored as ordered nucleobases sequence. DNA is thought to appear later than RNA in the molecular evolution, mainly with the function of storage. Its minor reactivity (due to loss of 2 -OH group) favour its chemical stability. The use of DNA polymerization in vesicle-based cell models aims to demonstrate how nucleic acids can be synthesized inside compartments, again in an origin-of-life perspective. However, due to the recent developments of DNA-based biotechnologies, it is possible that DNA-reactions in micro- or submicro-compartments... 

---