Structural basis for the unusual properties of 2′,5′ nucleic acids and their complexes with RNA and DNA

Abstract

To provide insights into the unusual properties of 2′,5′ nucleic acids ( iso nucleic acids), that includes their rejection by Nature as information molecules, modeling studies have been carried out to examine if they indeed possess the stereochemical ability to form helical duplexes and triplexes, just as their 3′,5′ linked constitutional isomers. The results show that the formation of helical duplexes with 2′,5′ linkages demands a mandatory displacement of the Watson and Crick base pairs from the helical axis, as a direct consequence of the lateral shift of the sugar–phosphate backbone from the periphery towards the interior of the helix. Thus, both duplexes and triplexes formed with a 2′,5′-sugar–phosphate backbone possess this intrinsic trait, manifested normally only in A type duplexes of DNA and RNA. It was found that only a 10-fold symmetric parallel triplex with isomorphous T·AT triplets is stereochemically favorable for isoDNA with ‘ extended’ nucleotide repeats, unlike the 12-fold symmetric triplex favored by DNA. The wider nature of a 12-fold triplex, concomitant with mandatory slide requirement for helix formation in isoDNA, demands even larger displacement, especially with ‘ extended’ nucleotide structural repeats, thereby violating symmetry. However, a symmetric triplex possessing higher twist, can be naturally formed for isoDNA with a ‘ compact’ nucleotide repeat. Two nanosecond molecular dynamics simulation of a 2′,5′-B DNA duplex, formed with an intrinsic base pair displacement of −3.3 Å, does not seem to favor a total transition to a typical A type duplex, although enhanced slide, X-displacement, decrease in helical rise and narrowing of the major groove during simulation seem to indicate a trend. Modeling of the interaction between the chimeric isoDNA·RNA duplex and E. coli RNase H has provided a structural basis for the inhibitory action of the enzyme. Interaction of residues Gln 80, Trp 81, Asn 16 and Lys 99, of E. coli RNase H with DNA of the DNA·RNA hybrid, are lost when the DNA backbone is replaced by isoDNA. Based on modeling and experimental observations, it is argued that 2′,5′ nucleic acids possess restricted conformational flexibility for helical polymorphism. The inability of isoDNA to favor the biologically relevant B form duplex and the associated topological inadequacies related to nucleic acid compaction and interactions with regulatory proteins may be some of the factors that might have led to the rejection of 2′,5′ links.