Open AccessThe conformation of single‐stranded nucleic acids
Author(s) -
PAQUETTE Jean,
NICOGHOSIAN Krikor,
QI Guorong,
BEAUCHEMIN Nicole,
CEDERGREN Robert
Publication year - 1990
Publication title -
european journal of biochemistry
Language(s) - English
Resource type - Journals
eISSN - 1432-1033
pISSN - 0014-2956
DOI - 10.1111/j.1432-1033.1990.tb15485.x
Subject(s) - transfer rna , dna , nuclease , transfer dna , rna , cleavage (geology) , nucleic acid , restriction enzyme , biochemistry , rnase p , chemistry , stereochemistry , biology , agrobacterium tumefaciens , paleontology , transgene , fracture (geology) , gene
Conformational analyses using the single‐strand‐specific nuclease from mung bean and restriction endonucleases have been performed on a series of DNA fragments related to the sequence of the yeast initiator tRNA Met . Mung bean nuclease cleaves DNA fragments exclusively in some, but not all, single‐stranded regions as predicted by RNA secondary rules. Comparison of cleavage patterns of yeast initiator tRNA Met , tDNA Met (a DNA oligomer having the sequence of tRNA Met ) and the anti‐tDNA Met (the complement of tDNA Met ) suggests that the conformation of the three molecules is very similar. Furthermore, both tDNA and anti‐tDNA are cleaved by Hha I and Cfo I restriction endonucleases at two GCG/C sites which would be in double‐ stranded regions (the acceptor and dihydrouridine stem), if the two molecules adopt the tRNA cloverleaf structure. On the other hand, minor cleavage products show that the core region, i.e. the extra loop area, is slightly more exposed in tDNA and in anti‐tDNA than in tRNA. Therefore, we submit that the global conformation of nucleic acids is primarily dictated by the interaction of purine and pyrimidine bases with atoms and functional groups common to both RNA and DNA. In this view the 2′‐hydroxyl group, in tRNA at least, is an auxiliary structural feature whose role is limited to fostering local interactions, which increase the stability of a given conformation.