Nucleic acids, complexes with

Nucleic acids, complexes with metals of platinum group and their role in antitumor activity of Pt(n) complexes 83RTC121. 

The influence of added Zn on structure and stability of DNA has long been a topic of interest.In spite of the importance of Zn in biochemistry, and the common use of the analogue Cd, few of structures of nucleic acid complexes with these ions are available. Many Zn - or Cd -nucleotide models have been characterized. 

Macromolecular models should have a level of resolution commensurate with the quality and quantity of available data. We have developed a package of programs for building and refining models of nucleic acids and protein-nucleic acid complexes, with different levels of detail in different parts of the molecule. The method incorporates data from a variety of experiments. Our RNA models have atomic detail in some regions and lower resolution (typically one pseudoatom per nucleotide) in others. We are using this approach to refine models for the 308 subunit of the E. coli ribosome, with emphasis on the decoding site, where the 168 rRNA holds the mRNA and two tRNAs. 

It iaterferes with the synthesis of the hyphal walls, the biosynthesis of nucleic acids, and the synthesis of chitin. The iateraction with microtubules has also been described. The sensitivity of a cell seems to depend particularly on the abiUty to form griseofulvin—nucleic acid complexes. Further information concerning griseofulvin is available (21). 

To date, a number of simulation studies have been performed on nucleic acids and proteins using both AMBER and CHARMM. A direct comparison of crystal simulations of bovine pancreatic trypsin inliibitor show that the two force fields behave similarly, although differences in solvent-protein interactions are evident [24]. Side-by-side tests have also been performed on a DNA duplex, showing both force fields to be in reasonable agreement with experiment although significant, and different, problems were evident in both cases [25]. It should be noted that as of the writing of this chapter revised versions of both the AMBER and CHARMM nucleic acid force fields had become available. Several simulations of membranes have been performed with the CHARMM force field for both saturated [26] and unsaturated [27] lipids. The availability of both protein and nucleic acid parameters in AMBER and CHARMM allows for protein-nucleic acid complexes to be studied with both force fields (see Chapter 20), whereas protein-lipid (see Chapter 21) and DNA-lipid simulations can also be performed with CHARMM. 

The formation of the CLS/nucleic acid complex was performed by mixing an aqueous suspension of CLS with a solution containing the nucleic acids [19,50,56],... 

There have been two basic approaches. First one involves isolation of the chromatin and nucleosome from the healthy and diseased cell line. The second approach is the reconstitution of the model target such as nucleosome followed by the association with the drug(s). The second approach has been extensively employed to identify the binding site in the protein-nucleic acid complex. A pre-knowledge about the components and their arrangements in the reconstituted system sometime makes it the preferred approach. Different biophysical, biochemical and genetic techniques have been employed to understand the mode of association and the effect of the drugs upon chromatin/nucleosome structure and function. 

An imderstanding of the mechanism by which the highly specific and selective recognition of a nucleotide sequence is achieved is only possible with knowledge of the structural details of specific protein-nucleic acid complexes. For the regulation of gene activity the binding of proteins to double-stranded DNA is of central importance. We... 

In order to avoid misleading spots on the 2-DE profile and to remove salts, lipids, polysaccharides, or nucleic acids interfering with separation, samples should be solubilized. Solubilization procedure involves disruption of all noncovalently bond protein complexes into a solution of polypeptides. It is the most critical step of 2-DE. 

All types of nucleic acids interact with proteins. Chromosomal DNA forms stable nonspecific complexes with structural proteins that stabilize their tertiary structure it also forms transient complexes with enzymes and regulatory proteins that modulate DNA and RNA metabolism. The gross tertiary structure of DNA in E. coli and a typical eukaryotic chromosome is described in the next section. 

M24. Munns, T. W., Liszewski, M. K., and Hahn, B. H., Antibody-nucleic acid complexes. Conformational and base associated with spontaneously occurring poly- and monoclonal anti-DNA antibodies from autoimmune mice. Biochemistry 23, 2964-2970 (1984). 

It is also possible to incubate radioactive or fluorescent nucleic acid probes with sections of tissues or even chromosomes, wash away excess probe and then detect where the probe has hybridized. This technique (in situ hybridization) has proved to be very powerful in determining which cells in a complex tissue such as the mammalian brain express a particular gene and for locating specific genes on individual chromosomes. 

This contribution complements an earlier review (11) which summarized our NMR research on synthetic DNA s and RNA s with alternating inosine-cytidine and guanosine-cytidine polynucleotides and the structure and dynamics of ethidium-nucleic acid complexes. 

Overlap Geometry at the Intercalation Site We shall attempt to utilize the nucleic acid base and anthracycline ring proton com-plexation shifts to deduce which anthracycline aromatic ring(s) overlap with nearest neighbor base pairs in the daunomycin poly-(dA-dT) intercalation complex. It should be noted that the nonplanarity of ring A in the antibiotic requires that the aromatic portion of the anthracycline chromophore cannot intercalate with its long axis colinear to the direction of the Watson-Crick hydrogen bonds at the intercalation site as was demonstrated for proflavine-nucleic acid complexes. 

Nitrobenzofurazans have been observed as powerful inhibitors of nucleic acid biosynthesis, with an especially toxic effect on leukocyte metabolism in vitro. These compounds exhibit an extremely high electrophilic reactivity as reflected judging by their ability to form Meisenheimer c-complexes, investigated in detail in [761-773],... 

Our concern in this section, however, is not the application to biopolymers of methods that are equally applicable to smaller molecules. Rather, we discuss here a totally different approach to the determination of precise three-dimensional structures of these molecules, in which NMR data play a key role. We illustrate the concept with proteins, which have yielded particularly useful information, but the general approach can also be used with nucleic acids and with complexes of a protein and a nucleic acid. 

Interactions of the same water molecules with RNA nucleotides (via H-bonding) and metal ions (via inner-sphere coordination) could stabilize specific metal ion-nucleic acid complexes (e.g. in Mg + -tRNA chelates) and also create the possibility for direct proton transfer through a water chain that could play a role in ribozyme-metal ion catalysis and in the mechanism of metal-dependent nucleases and polymerases. Similar types of H-bonds between different nucleotide residues have been found in tRNA tertiary structures, where they provide additional stabilization of tertiary interactions. 

The relative rates of reaction of the nucleic acid bases with heavy transition metal ions at neutral pH are in the same order as the relative nucleophilicites of the bases, that is G > A > C > U or T. This order parallels the relative rates of reactions for cA-[(NH3)2Pt(OH2)2] (see Figure 9), while the equilibrium constants for the same reactions are very close in magnitude. In contrast, HsCHgOH, which is more labile to substitution, nndergoes more favorable binding with deprotonation at N-3 of thymine residues in nucleic acids. Thus the relative facilities of individual reactions can lead to differences in initial product formation (kinetic control). Subsequent changes in the metal-nucleic acid complexes can be nnder kinetic or thermodynamic control. 

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