Nucleic acids overview

In Section II we provide an overview of the current status of nucleic acid simulations, including studies on small oligonucleotides, DNA, RNA, and their complexes with proteins. This is followed a presentation of computational methods that are currently being applied for the study of nucleic acids. The final section of the chapter includes a number of practical considerations that may be useful in preparing, performing, and analyzing MD simulation based studies of nucleic acids. 

The methodological advances just presented have brought the field of nucleic acid force field calculations to a point where results from the calculations can be used with reasonable confidence to aid in the interpretation of experimental data as well as to be used for scientific investigations that are not accessible to experiment. Accordingly, a number of studies based on MD simulations, as well as other methods, have been undertaken to study a wide array of biologically relevant events associated with DNA. A brief overview of some of these efforts follows. 

A good overview of DNA structure and function. E. Pennisi, Science 2003, 300, 282. Reviews of nucleic acid chemistry ... 

Fig. 1. An overview of the DCLD tier/triage flow chart Boxes 1, 2, and 3 are taken from the Office of Device Evaluation decision tree, which is routinely used to determine whether a product can be reviewed as a 510(k) and found substantially equivalent to a predicate (currently marked) device or whether the product must be handled as a fundamentally new product and submitted to a PMA review. Box 4 determines the novelty of the product in terms of analyte, matrix, and/or technology. If new issues of safety and effectiveness are raised, a highly novel product might require review as a PMA. If the issues of safety and effectiveness are not new but require high-level scrutiny, then a tier III review is warranted. Examples of products requiring a tier III review would include 1. Analyte troponin for diagnosis of MI (with creatinine kinase as the predicate) 2. Matrix sweat patches for drugs of abuse (with urine drugs of abuse tests as the predicate) and 3. Technology nucleic acid...

Both approaches are simple and allow efficient encapsulation of nucleic acid-based molecules such as oligonucleotides (9,10) and pDNA (8,10,12) in liposomes that are small in size (about lOOnm diameter) and stable in circulation, protecting the cargo from degradation. In the sections to follow, we will provide a brief overview of these methods. 

A typical DNA array fabrication and application process involves three major steps. First, nucleic acids (the capture sequences or probes) are immobilized at discrete positions on surface activated substrates. Secondly, the resulting array is hybridized with a complex mixture of fluorescently labelled nucleic acids (the target), and thirdly subsequent to hybridization, the fluorescent markers are detected using a high-resolution scanning laser that quantifies the interaction. This chapter focuses on the first of these processes and provides the reader with an overview of substrates, surface activation methods and dehvery systems available for nucleic acid immobilization. 

Optical Spectroscopy General principles and overview, 246, 13 absorption and circular dichroism spectroscopy of nucleic acid duplexes and triplexes, 246, 19 circular dichroism, 246, 34 bioinorganic spectroscopy, 246, 71 magnetic circular dichroism, 246, 110 low-temperature spectroscopy, 246, 131 rapid-scanning ultraviolet/visible spectroscopy applied in stopped-flow studies, 246, 168 transient absorption spectroscopy in the study of processes and dynamics in biology, 246, 201 hole burning spectroscopy and physics of proteins, 246, 226 ultraviolet/visible spectroelectrochemistry of redox proteins, 246, 701 diode array detection in liquid chromatography, 246, 749. 

Figure 9.17. Overview of the manufacture of Ceprotin. As the active ingredient is derived directly from pooled human plasma, particular emphasis is placed upon ensuring that the finished product is pathogen-free. Precautions entail the incorporation of two independent viral inactivation steps and high-resolution chromatographic purification. Additionally, extensive screening of plasma pool source material for blood-borne pathogens is undertaken. Viral screening is undertaken using a combination of immunoassay and PCR analysis for the presence of viral nucleic acid...

An overview of the compartment properties of reverse micelles is illustrated in Figure 9.16, which also gives some of the relevant references. As already mentioned, reverse micelles are dynamic systems that rapidly exchange compartmentalized materials. There is however one limit to this when the enclosed solutes are macromolecules. Thus, if two different populations of reverse micelles are mixed, one, say, with enzymes and the other with nucleic acids, the two macromolecules are not going to interact with each other. 

This chapter provides an overview of the chemical nature of the nucleotides and nucleic acids found in most cells a more detailed examination of the function of nucleic acids is the focus of Part m of this text. 

We will focus our attention in this chapter on an overview of the thermodynamic analysis of metabolism and of the stabilities of two types of biomolecules, proteins and nucleic acids. Rather than provide a comprehensive account of thermodynamic applications to biological systems, we have chosen these two key areas where, historically, thermodynamic measurements have... 

This chapter provides a simplified overview of how researchers use the technique of X-ray crystallography to learn macromolecular structures. Chapters 3-8 are simply expansions of the material in this chapter. In order to keep the language simple, I will speak primarily of proteins, but the concepts I describe apply to all macromolecules and macromolecular assemblies that possess ordered structure, including carbohydrates, nucleic acids, and nucleo-protein complexes like ribosomes and whole viruses. 

An overview on the genosensor technologies for detection of nucleic acids (NA) immobilized onto different transducers by adsorption, cross-linking, complexation and covalent attachment is briefly summarized in Table 19.1. The applications of electrochemical genosensor technology are discussed in the following section. 

Since then much progress has been made in sample preparation techniques that reduce sample complexity. An overview of the sequence of extraction, isolation, and purification of nucleic acids is presented in Figure 8.1. It can be categorized in several unit steps beginning with the extraction of DNA until its sizing and sequencing. The different options within each step are listed in Table 8.1 and are described in this chapter. The technique best suited in a given application depends on ... 

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