Human
hepatitis delta (HDV)
ribozyme is one of small
ribozymes, such as hammerhead and hairpin
ribozymes, etc. Its secondary structure shows pseudoknot structure composed of four stems (I to IV) and three single-stranded regions (SSrA, -B and -C). The 3D structure of 3'-cleaved product of genomic HDV
ribozyme provided extensive information about tertiary hydrogen bonding interactions between
nucleotide bases,
phosphate oxygens and 2'OHs including new stem structure P1.1. To analyze the role of these hydrogen bond networks in the catalytic reaction, site-specific atomic-level modifications (such as deoxynucleotides, deoxyribosyl-
2-aminopurine, deoxyribosylpurine, 7-deaza-
ribonucleotide and
inosine) were incorporated in the smallest trans-acting HDV
ribozyme (47-mer). Kinetic analysis of these
ribozyme variants demonstrated the importance of the two W-C base pairs of P1.1 for cleavage; in addition, the results suggest that all hydrogen bond interactions detected in the crystal structure involving 2'-OH and N7 atoms are present in the active
ribozyme structure. In most of the variants, the relative reduction in kobs caused by substitution of the 2'-OH group correlated with the number of hydrogen bonds affected by the substitution. However G74 and C75 may have more than one hydrogen bond involving the 2'-OH in both the trans- and cis-acting HDV
ribozyme. Moreover, in variants in which N7 was deleted, kobs was reduced 5- to 15-fold, it may suggest that N7 assists in coordinating Mg2+
ions or water molecules which bind with weak affinity in the active structure.