ABSTRACT
Although the structure of the hammerhead ribozyme is well characterized, many questions remain about its catalytic mechanism. Extensive evidence suggests the necessity of a conformational change en route to the transition state. We report a steric interference modification approach for investigating this change. By placing large 2' modifications at residues insensitive to structurally conservative 2'-deoxy modifications, we hoped to discover structural effects distal to the site of modification. Of twenty residues tested, six were identified where the addition of 2' bulk inhibits cleavage, even though these bulky modifications could be accommodated in the crystal structure without steric clash. It is proposed that these 2'-modifications inhibit cleavage by preventing formation of the alternate, active conformation. Since these 2' effects are present in both domain I and domain II of the hammerhead, the entire catalytic core must undergo conformational changes during catalysis.
Subject(s)
Nucleic Acid Conformation , RNA, Catalytic/chemistry , Base Sequence , Binding Sites , Catalysis , Crystallization , Kinetics , Models, Chemical , Models, Molecular , Molecular Sequence Data , Purines/chemistry , Pyrimidines/chemistry , Stereoisomerism , Structure-Activity RelationshipABSTRACT
To evaluate potential improvement in tissue specific targeting and cellular uptake of therapeutic ribozymes, we have developed three new phosphoramidite reagents. These reagents can be used in automated solid-phase synthesis to produce oligonucleotide conjugates containing N-acetyl-D-galactosamine (targeting hepatocytes) and folic acid (targeting tumor). N-Acetyl-D-galactosamine was attached through a linker to both 2'-amino-2'-deoxyuridine and D-threoninol scaffolds, and these conjugates were converted to phosphoramidite building blocks. Incorporation of a D-threoninol-based monomer into ribozymes provided multiply labeled ribozyme conjugates. Attachment of the fully protected pteroic acid to the D-threoninol-6-aminocaproyl-L-glutamic acid construct afforded the folic acid conjugate, which was converted into the phosphoramidite and incorporated onto the 5'-end of the ribozyme.
Subject(s)
Drug Delivery Systems/methods , RNA, Catalytic/administration & dosage , Acetylgalactosamine/chemistry , Antineoplastic Agents/chemical synthesis , Cross-Linking Reagents/chemistry , Folic Acid/chemistry , Oligonucleotides/chemical synthesis , Organophosphorus Compounds/chemistry , RNA, Catalytic/chemistryABSTRACT
An in vitro selection was designed to identify RNA-cleaving ribozymes predisposed for function as a drug. The selection scheme required the catalyst to be trans-acting with phosphodiesterase activity targeting a fragment of the Kras mRNA under simulated physiological conditions. To increase stabilization against nucleases and to offer the potential for improved functionality, modified sequence space was sampled by transcribing with the following NTPs: 2'-F-ATP, 2'-F-UTP, or 2'-F-5-[(N-imidazole-4-acetyl) propylamine]-UTP, 2'-NH2-CTP, and GTP. Active motifs were identified and assessed for their modified NMP and divalent metal dependence. The minimization of the ribozyme's size and the ability to substitute 2'-OMe for 2'-F and 2'-NH2 moieties yielded the motif from these selections most suited for both nuclease stability and therapeutic development. This motif requires only two 2'-NH2-Cs and functions as a 36-mer. Its substrate sequence requirements were determined to be 5'-Y-G-H-3'. Its half-life in human serum is >100 h. In physiologically relevant magnesium concentrations [approximately 1 mM] its kcat = 0.07 min(-1), Km = 70 nM. This report presents a novel nuclease stable ribozyme, designated Zinzyme, possessing optimal activity in simulated physiological conditions and ready for testing in a therapeutic setting.