Novel DNA structures

Hatters DM, Wilson L, Atcliffe BW, Mulhem TD, Guzzo-Pemell N, Howlett GJ (2001) Sedimentation analysis of novel DNA structures formed by homo-oligonucleotides. Biophys J 81 371-381... 

This chapter describes the chemistry of nucleotides and the m or classes of nucleic acids. Chapter 12 presents methods for determination of nucleic acid primary structure (nucleic acid sequencing) and describes the higher orders of nucleic acid structure. Chapter 13 introduces the molecular biology of recombinant DNA the construction and uses of novel DNA molecules assembled by combining segments from other DNA molecules. 

To modify the unique chemical groups on nucleic acids, novel methods have been developed that allow derivatization through discrete sites on the available bases, sugars, or phosphate groups (see Chapter 1, Section 3 for a discussion of RNA and DNA structure). These chemical methods can be used to add a functional group or a label to an individual nucleotide or to one or more sites in oligonucleotide probes or full-sized DNA or RNA polymers. 

The rich variety of DNA structures shown in this review chapter is the result of the combination of knowledge developed in more than one area of research biochemistry, soft matter, statistical physics, and crystallography. We believe that this constant exchange of ideas and methods among different disciplines is a key requisite for maintaining in future years the same rate of scientific discovery and of development of novel technological strategies at the nanoscale. 

Then, close analogs of the first series of hits were assayed, resulting in a total screen of 3000 compounds. This provided 150 hits, clustered into 14 chemical classes. Seven of these classes could be demonstrated as novel DNA gyrase inhibitors competingfor the ATP binding site. Subsequent structure-based optimization resulted in inhibitors with potencies equal to or up to 10 times better than those of known antibiotics. 

Once a note of caution is expressed, novel DNA-based molecular design and architectures have, however, reached levels where the emerging supramolecular structures can perhaps become robust to different electronically working environments. Redox- and fluorophor-labeled molecules offer steps towards device-like function where both structural organization and, as noted, additional sophisticated electronic function can be added to the DNA-based molecules. " " " New electronic conductivity mechanisms based on hopping via a chain of well-defined redox probes bound in the DNA-backbone were noted above." Such... 

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