Nucleic acid-protein interaction

P2j Z = 2 DX = 1.43 R = 0.067 for 1269 intensities. The uracil residue is in the anti (63.4°) disposition. The conformation of the D-ribosyl group is 2T3 (176.8°, 37.5°). The orientation about the exocyclic, C-4 -C-5 bond is t (—174.2°). The phenyl and uracil ringsofthe same molecule lie in almost parallel planes, 120 pm apart. The phenyl group is disordered. The uracil ring is sandwiched by the phenyl rings, and vice versa. The 0-1 and N-a atoms of the peptide backbone are hydrogen-bonded to 0-4 and N-3 of atranslationally related uracil to form cyclic dimers. Such interactions serve as models for nucleic acid-protein interactions. [Coordinate errors H(02 ) x should be —1574, instead of —1474 H(Na)2 z should be —145 instead of— 645.]... 

Metal ions are usually required to promote and stabilize functionally active or native conformations of nucleic acids, as well as to mediate nucleic acid-protein interactions. However, metal ions can also cause structural transformation of nncleic acids, or denature their native structures. In addition to structural roles, some metal compounds can indnce cleavage (i.e. scission, fragmentation, or depolymerization) and modification (withont cleavage) of nucleic acids. Metal-nucleic acid interactions can be either nonspecific or dependent on the chemical nature of nucleotide residues, nucleic acid sequence, or secondary and/or tertiary structure of nucleic acids. The specificity of these interactions is dependent... 

Molecular structure of nucleic acids and nucleic acid-protein interaction mechanism 89YZ439. 

The potential utility of N-labelcd oligonucleotides to probe unique nucleic acid structure, drug binding, and nucleic acid- protein interactions has led to considerable interest in the development of routes to the requisite N-labeled monomers. In the purine series, chemically synthesized N 1-labeled hypoxanthine was incorporated into a yeast tRNA by fermentation and... 

In the analysis of nucleic acid protein interactions, it is generally advantageous to distinguish between interactions which define affinity and specificity. Affinity and specificity are sometimes erroneously equated but the affinity can be increased by fairly unspecific... 

The last example is based on the interaction between a new receptor (ap-tamer) able to interact with a specific protein and represents an example of nucleic acid-protein interaction. The aptamers can represent an alternative to an antibody-based sensor and are an interesting challenge in biosensing research. 

The last step to liberating all the inherent potential of these early nucleoproteinic systems of RNA and protein was found in the dual conformational abilities of the small 2 -deoxy-D-ribose cycle to account for a conformationally amplifying switch between A- and B-type nucleic acid versions [7 a, 8 c, 33]. The discovery of the information store of DNA enabled the systems to separate the replication of a more densely packed DNA message from the informational and functional instruments needed in the hitherto existing nucleic-acid-protein interaction schemes and promoted by this... 

The various forms of electron microscopy (EM) have been used to examine structural features of nucleic acid-protein interactions. EM structures include protein interactions with the ribosome, an activator-dependent transcription initiation complex, the core editing complex in trypanosomatid mitochondria, human Dicer from the RISC complex showing that it has an L-shaped structure, the RNA editing complex from trypanosomes and loading of minichromosome maintenance proteins (Mcm2-7) onto DNA during DNA replication. Scanning electrochemical microscopy (SECM) with DNA attached to an electrode has been used to detect an A-C mismatch site, and to visualise the activity of an enzyme to detect hybridisation. " Cryo-EM (CEM) has also been... 

The morphogenesis of phage particles is a model not only for the assembly of organelles but also for regulation of protein specificity and nucleic acid-protein interactions. The advantage of this over other models is that the study of virus assembly is amenable to a wider variety of chemical, physical and genetic techniques. 

The best way to vary at will the information content of a macromolecule is to use some sort of backbone and to peg on it various arrays of side chains. Each side chain may carry well-defined information regarding interactions between themselves or with a specific substrate in order to perform specific bond-making or -breaking functions. Nucleic acid-protein interactions should also be mentioned because of their fundamental importance in the evolution of the genetic code. 

Well before life arrived on Earth, however, a self-replicating process was necessary. How It seems reasonable to suppose that specific nucleic acid-nucleic acid and nucleic acid-protein interactions were of fundamental importance for the replication of nucleic acids and the evolution of the genetic code (48). Such recognition processes are dependent on base sequence and amino acid sequence. According to R. D. MacElroy from NASA, these would probably play a key role in the formation of protein nucleic acid complexes. 

At present, DNA research is increasingly directed toward the study of nucleic acid-protein interactions (see Chapter 9) (33), as a means of probing the nature of the intermediates in the whole process of genetic expression. 

The field of nucleic acid-protein interactions has become increasingly active in the last few years, and it is thus difficult to be up-to-date here. This discussion will focus on the structural factors that determine the interactions between nucleic acids and proteins. [An excellent account of DNA-protein interactions has been written by von Hippel and McGhee (1).]... 

The subject of nucleic acid-protein interactions is one of the most fascinating areas of molecular biology today, and it is a good topic on which to close this book on nucleic acid structure. 

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