Book of Abstracts: Albany 2003
June 17-21 2003
NMR Studies Reveal an A⇐⇒B Structural Intermediate with N Type Sugar Pucker for 2?,5? Linked d(GGGGCCCC): Was the Optimization of Helix Topology a Factor in the Etiology of Nucleic Acid Backbone?
To gain insights into the structural characteristics of 2?, 5? nucleic acids (iso nucleic acids), the constitutional isomer of the naturally occurring 3?,5? nucleic acids, that could have played an important role in the early evolution of RNA, a high resolution NMR structure of a 2?,5? linked 3?deoxyoligonucleotide, iso d(GGGGCCCC), is determined. The oligomer exhibits a helical duplex structure formed out of an extended nucleotide repeat, with N type instead of S type sugar pucker, supporting an earlier observation that change in sugar-phosphate link from 3?,5? to 2?,5? brings forth a concomitant change in sugar pucker preference in nucleic acid duplexes. Base pairs in the two proposed models for iso (G4C4) duplexes exhibit distinct slide and X-displacement just as in the ideal iso BDNA. Magnitude of X-displacement although higher by about an Å, it is still lower than the value found in A DNA. Inclination of base pairs to the helical axis is not prominent while the major and minor grooves display features similar to ideal iso B DNA in the more populated model. The less populated model displays certain other traits of A DNA as manifested in a modest base pair inclination angle concomitant with slightly larger X-displacement and narrowing of the major groove. Thus, duplex models for iso d(G4C4) defy classification either as A DNA or B DNA but are best characterized as A⇐⇒B structural intermediate. The results confirm that iso nucleic acids can support a duplex only with certain traits of A DNA such as base pair slide and X-displacement and cannot form an ideal B DNA topology due to the restriction on the X-displacement range (≥-2.5Å) imposed by 2?,5? linked sugar-phosphate backbone. This is expected to further restrict to some degree the ability of iso DNA duplexes towards bending and kinking since it is known that duplex (B DNA) with zero X-displacement facilitates DNA deformation, which is a critical requirement for DNA compaction and recognition interaction with regulatory proteins. These built-in topological restrictions inherent to iso nucleic acids together with the known low base pair stability of iso DNA/RNA duplexes could have contributed in rejecting 2?,5? links in favour of 3?,5?links. Thus, not only the optimization of the duplex stability but also the helix topology must have been the guiding factors in settling backbone chemistry of nucleic acids. The A⇐⇒B intermediate duplex observed here for iso d(G4C4) might have had some role in the early part of nucleic acid evolution relating to selection of type of linkages and also during transition from RNA world to DNA world. The constrained nature of iso DNA duplexes might prove useful as a tool in structure-based regulation of gene in view of its defiance to provide the biologically predominant canonical B DNA duplex.
Department of Crystallography & Biophysics