Nucleic acids secondary structure

Metz, D.H., and Brown, G.L. (1969) The investigation of nucleic acid secondary structure by means of chemical modification with a carbodiimide reagent. I. The reaction between N-cyclohexyl-N -b-(4-methylmorpholinium)ethyl carbodiimide and model nucleotides. Biochemistry 8, 2312-2328. 

Ladame, S. Whimey, A. Balasubramanian, S. Targeting nucleic acid secondary structures with polyamides using an optimized dynamic combinatorial approach. Angew. Chem. Int. Ed. 2005,44, 5736-5739. 

Our objective is to understand how the noncovalent interactions responsible for nucleic acid secondary structure (i.e. base stacking and base pairing) affect the photophysics of these multichromophoric systems. Here we describe initial experimental results that demonstrate dramatic differences in excited-state dynamics of nucleic acid polymers compared to their constituent monomers. Although ultrafast internal conversion is the dominant relaxation pathway for single bases, electronic energy relaxation in single-stranded polynucleotides... 

M. Zuker. Calculating nucleic acid secondary structure. Curt Opin. Struct. Biol., 10 303-310, 2000. 

Zuker, M. (2000) Calculating nucleic acid secondary structure. Current Opinion in Structural Biology 10, 303-310. 

Mishra, R.K., Le Tinevez, R. and Toulme, J.J. (1996) Targeting nucleic acid secondary structures by antisense oligonucleotides designed through in vitro selection. Proc. Natl. Acad. Sci. USA, 93, 10679-10684. 

Finally, the recent discovery of the unusual left-handed polydinucleotide helices for the alternating purine-pyrimidine polymers opens up a whole new field of nucleic acid secondary structures. The relevance and importance of these new structures in the visualization of overwound, as well as underwound, and supercoiled DNA molecules in biological.systems need hardly be emphasized. 

The stability of multistrand nucleic acid secondary structures depends both on internal and external factors. Since the G-C base pair contains three H-bonds compared with two for the A-T (or A U) base pair (Figure 2a), and because stacking interactions decrease in the order G>A>C>U, a duplex with greater GC content is expected to be more stable. 

Armitage BA. The impact of nucleic acid secondary structure on PNA hybridization. Drug Disc. Today 2003 8 222-228. 

Bruccoleri, R. and Heinrich, G. (1988) An improved algorithm for nucleic acid secondary structure display. Comput. Appl. Biosci. 4, 167-173. 

A Raman spectroscopic method to obtain information about dynamic aspects of nucleic acid secondary structure monitors the deuterium exchange of the C-8 purine hydrogen. The exchange... 

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