Nucleic acid topology

The general topology of rubredoxins is also observed in the general zinc-ribbon motif in RNA polymerases or in transcription factors (59). The first published zinc-ribbon structure was that of the nucleic-acid binding domain of human transcriptional elongation factor TFIIS (PDB file ITFI) 40). These zinc binding domains and rubredoxins... 

Kuhn H., Demidov V.V., Frank-Kame-NETSKii M.D. Rolling-circle amplification under topological constraints. Nucleic Acids Res. 2002 30 574-580... 

The examples just presented give initial impressions of how DNA can be utilized as a template in the synthesis of nanometric and mesoscopic aggregates. However, the studies emphasize the importance of fundamental research on the interaction between DNA and the various binders, such as metal and organic cations. Of particular importance are the consequences of binding events on the structure and topology of the nucleic acid components involved. 

The refinement of other analytical methods, such as electrophoresis [34,36], the various techniques of optical spectroscopy [103-105], and nuclear magnetic resonance [201], is supplemented by the recent advances in real-time affinity measurements [152,202], contributing to the understanding of biomolecular reactivity. Taken together, the improvement of analytical methods will eventually allow a comprehensive characterization of the structure, topology, and properties of the nucleic acid-based supramolecular components under consideration for distinctive applications in nanobiotechnology. 

Stereochemical probes of the specificity of substrates, products, and effectors in enzyme-catalyzed reactions, receptor-ligand interactions, nucleic acid-ligand interactions, etc. Most chirality probe studies attempt to address the stereospecificity of the substrates or ligands or even allosteric effectors. However, upon use of specific kinetic probes, isotopic labeling of achiral centers, chronfium-or cobalt-nucleotide complexes, etc., other stereospecific characteristics can be identified, aU of which will assist in the delineation of the kinetic mechanism as well as the active-site topology. A few examples of chirality probes include ... 

Burge S, Parkinson GN, Hazel P et al (2006) Quadruplex DNA sequence, topology and structure. Nucleic Acids Res 34 5402-5415... 

Chiral ruthenium complexes, with luminescence characteristics indicative of binding modes, and stereoselectivities that may be tuned to the helix topology, may be useful molecular probes in solution for nucleic acid secondary structure36). 

Pabit, S. A., Qiu, X. Y., Lamb, J. S., Li, L., Meisburger, S. P., and Pollack, L. (2009). Both helix topology and counterion distribution contribute to the more effective charge screening in dsRNA compared with dsDNA. Nucleic Acids Res. 37, 3887—3896. 

---