Nucleic acid systems

Callis PR (1983) Electronic states and luminescence of nucleic acid systems. Ann Rev Phys Chem 34 329... 

In the various reviews on self-reproduction in recent years, practically no mention is made of such micelles or vesicle systems. The reason lies most prohahly in the bias of classic hiochemical literature, according to which self-replication is tantamount to nucleic acid systems lacking this are therefore deemed not to he relevant. In this particular regard, it is argued that self-reproduction of micelles and vesicles proceeds without transmission of information. 

Tn orcTer to extend these conformational energy studies to the analysis of multi-stranded nucleic acid systems, it is necessary to devise a procedure to identify the arrangements of the polynucleotide backbone that can acconmodate double, triple, and higher order helix formation. As a first step to this end, a computational scheme is offered here to identify the double helical structures compatible with given base pairing schemes. 

Table 16 summarizes the complexes formed between the vinyl-type analogs of nucleic acid and polynucleotides465,466). Poly(VA)-Poly(U) was assumed to exhibit a planar network structure. In addition, some studies on the interactions occurring in nucleic acid systems and model compounds bearing phosphate ester units on the side chains or the main chains480, and on interactions of poly(A) and quaternized poly(4-vinylpyridine) with bases have been reported48. ... 

In this chapter, we discuss the principles that are applied to automate the individual steps of the analytical process both in individual analyzers and in the integration of automation throughout the dinical labora.tory We provide examples of these principles as implemented in commercially available chemistry, hematology immunoassay, and nucleic acid systems point-of-care (POC) analyzers and automated specimen processing systems. Definitions of terms used in the automation of cfinical chemistry have been published by the International Union of Pure and Applied Chemistry (lUPAC). ... 

More recently, the systematic exploration of alternative nucleic-acid systems from RNA s structural neighborhood has presented us with a further challenging observation. TNA, the threose-analog of RNA (a system containing only four instead of five carbon atoms in its sugar building block), turns out to be a marvelous Watson-Crick base-pairing system. Indeed, not only is TNA very similar to... 

As in the case of the nucleic acids, systems that model various segments of proteins tend to vary in both size and relevance to the full systems. One is beset with the same problems that the CH- X bonds of interest are typically secondary to stronger conventional H-bonds, and consequently distorted. 

Potassium iodide (KI) is commonly used as fluorescent quenching agent because of the heavy atom effect. Therefore, it has wide applications in the study of the interaction mechanism between fluorescence probes and biomacromolecules. But in the study on the interaction mechanism of morin-fish serum nucleic acid system,10 it was found that KI can enhance the fluorescence intensity and lifetime of a system. 

Eschenmoser, A. The TNA-family of nucleic acid systems Properties and prospects. Origins of Life and Evolution of the Biosphere 2004, 34, 277-306. 

The study of membrane and nucleic acid systems presents greater complexities. The study of lipids and insoluble membrane proteins in association with them can be achieved in solution scattering [75,76] by the use of lipid vesicles to solubilize the system of interest. Membrane proteins can alternatively be studied by solubilization using detergent micelles. The exception to this generalization is the group of plasma hpoproteins which are readily soluble in aqueous buffers. Systems with nucleic acids (i.e. protein-nucleic acid complexes, viruses, ribosomes and chromatin) [24-27,77,78] are not affected by these solubihty problems. However, lipid and nucleic acid systems are both further complicated in their analyses by the polyionic character of these macromolecules. Particular care is required concerning the partial specific volumes of the individual components to be used within the system of interest. 

The patterns of autocatalysis with respect to parabolic and exponential reaction courses, which strongly affect the conclusions of Eigen s evolution experiments concerning the decision criteria for mutant selection and coexistence [5 b, 40 h, k], can now be derived from the thermodynamic data of the matrix patterns and their reactivities, and offer quite new views, with autocatalytic cooperation between competitive species [40 k]. Separate from enzyme-catalyzed evolution experiments with RNA and DNA systems, basic questions of prebiotic behavior can for the first time become the subject of detailed experimental research [40 k, 43]. While continuing their studies on more complex autocatalysis patterns, von Kie-drowski et al. diagnosed modulation of molecular recognition as an operational deficit of earlier artificial self-replicational nucleic acid systems with regard to exponential reaction courses, and identified it as an ideal aim for future models [44]. On its way to the nucleoprotein system, evolution must have... 

Carbohydrate-nucleic acid systems - the two sugar mates a) T. Li, Z. Zeng, V. A. Estevez,... 

Figure 6.25 (a) Probing the activity of micrococcal nuclease (MNase) using QDs with a dye (6-carboxy-X-rhodamine, ROX)-modifled nucleic acids (b) Fluorescence spectra corresponding to the QDs/ROX-modifled nucleic acid system upon treatment with different concentrations of MNase. As the... 

Molecular Dynamics Simulations on Nucleic Acid Systems Using the CorneU et al. Force Field and Particle Mesh Ewald Electrostatics... 

In this section we describe a general approach to the development of a mixed quantum/classical simulation protocol suitable for the study of chemical processes in protein and nucleic acid systems. This approach follows closely that recently... 

Such sublethal heat effects arc manifested in a faster yellowing, a lower ability to accumulate and retain substances, and by the lack of competitive capacity, in contrast to non-heated leaves. This complex of manifestations is characteristic for aging leaves and apparently is implicated in a deeper sense, perhaps in the nucleic acid system. 

Over the past few years there has been a significant increase in the number of nucleic acid structures reported. As advances in respective technologies arise, particularly with NMR spectroscopy, so the complexity of systems studied increases. However, more recently there are many new techniques that are being explored to aid structure determination, at least in global terms rather than at the atomic level, of larger and more complex nucleic acid systems. 

Some of the most successful computer simulation studies of nucleic acid systems to date employ models without explicit treatment of counterions, using instead the Manning model for counterion condensation. 4 Manning developed the counterion condensation model from polyelectrolyte theories applied to DNA treated as a charged cylinder. This model, resulting from a series of studies 2,43 is summarized by ... 

Although the results on counterion distributions in nucleic acid systems from X-ray crystallography are fragmentary, there exist several NMR studies about metals in DNA systems. - The data from NMR experiments proved to be difficult to interpret. The quadrupolar relaxation mechanism of this nuclide, originating from the electric field gradients, obfuscates the results, but in general the data are consistent with the counterion condensation theory. 

The gathering together of drug, dye, and nucleic acid systems under the heading of chromonics has been more than just a taxonomic exercise. It has enabled observations from one area of study to throw light on another. The term isodesmic , for example, is not generally used in the dye industry, but it neatly describes a pattern of behavior that... 

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