A systematic study of selectively modified, 36-mer hammerhead ribozymes has resulted in the identification of a generic, catalytically active and nuclease stable ribozyme motif containing 5 ribose residues, 29 -30 2-O-Me nucleotides, 1-2 other 2-modified nucleotides at positions U4 and U7, and a 3-3-linked nucleotide "cap." Eight 2-modified uridine residues were introduced at positions U4 and/or U7. From the resulting set of ribozymes, several have almost wild-type catalytic activity and significantly improved stability. Specifically, ribozymes containing 2-NH 2 substitutions at U4 and U7, or 2-C-allyl substitutions at U4, retain most of their catalytic activity when compared to the all-RNA parent. Their serum half-lives were 5-8 h in a variety of biological fluids, including human serum, while the all-RNA parent ribozyme exhibits a stability half-life of only ϳ0.1 min. The addition of a 3-3-linked nucleotide "cap" (inverted T) did not affect catalysis but increased the serum half-lives of these two ribozymes to >260 h at nanomolar concentrations. This represents an overall increase in stability/activity of 53,000 -80,000-fold compared to the all-RNA parent ribozyme.Trans-acting ribozymes exert their activity in a highly specific manner and are therefore not expected to be detrimental to non-targeted cell functions. Because of this specificity, the concept of exploiting ribozymes for cleaving a specific target mRNA transcript is now emerging as a therapeutic strategy in human disease and agriculture (Cech, 1992;Bratty et al., 1993). For ribozymes to function as therapeutic agents, they may be introduced exogenously or produced endogenously in the target cells. In the former case, the chemically modified ribozyme must maintain its catalytic activity while also being stable to nucleases. A major advantage of chemically synthesized ribozymes is that site-specific modifications may be introduced at any position in the molecule. This approach provides flexibility in designing ribozymes that are catalytically active and stable to nucleases. In this manuscript we show that using this site-specific, chemical modification strategy, ribozymes can be designed that have wild-type catalytic activity and are not cleaved by nucleases.A variety of selective and uniform structural modifications have been applied to oligonucleotides to enhance nuclease resistance (Uhlmann and Peyman, 1990;Beaucage and Iyer, 1993;Milligan et al., 1993). Improvements in the chemical synthesis of RNA (Scaringe et al., 1990;Wincott et al., 1995) have led to the ability to similarly modify ribozymes containing the hammerhead ribozyme core motif Yang et al., 1992) (Fig. 1). Yang et al. (1992) demonstrated that 2Ј-O-Me modification of a ribozyme at all positions except G5, G8, A9, A15.1, and G15.2 (see numbering scheme in Fig. 1) led to a catalytically active molecule having a greatly decreased k cat value in vitro, but a 1000-fold increase in nuclease resistance over that of an all-RNA ribozyme when tested in a yeast extract. In another study (Paolella...

Kinetic analysis, using substrates that consisted entirely of deoxynucleotides with the exception of the single mandatory ribonucleotide at the cleavage site which contained either a 5‘-oxy- or 5‘-thio-leaving group, demonstrated that the departure of the 5‘-leaving group was not the rate-limiting step of a hammerhead ribozyme-catalyzed reaction [Kuimelis, R. G.; McLaughlin, L. W. J. Am. Chem. Soc. 1995, 117, 11019−11020]. We recently synthesized a natural all-RNA substrate that contains a 5‘-thio-leaving group at the cleavage site and performed detailed kinetic analysis. In contrast to the conclusion of Kuimelis and McLaughlin, we found that (i) the attack by the 2‘-oxygen at C17 on the phosphorus atom is the rate-limiting step only for the substrate that contains a 5‘-thio group (R11S) and (ii) the departure of the 5‘-leaving group is the rate-limiting step for the natural all-RNA substrate (R11O) in both enzymatic and nonenzymatic reactions.

We identified the previously unknown structures of ribosylated imidazoleacetic acids in rat, bovine, and human tissues to be imidazole-4-acetic acid-ribotide (IAA-RP) and its metabolite, imidazole-4-acetic acid-riboside. We also found that IAA-RP has physicochemical properties similar to those of an unidentified substance(s) extracted from mammalian tissues that interacts with imidazol(in)e receptors (I-Rs). [''Imidazoline,'' by consensus (International Union of Pharmacology), includes imidazole, imidazoline, and related compounds. We demonstrate that the imidazole IAA-RP acts at I-Rs, and because few (if any) imidazolines exist in vivo, we have adopted the term ''imidazol(in)e-Rs.''] The latter regulate multiple functions in the CNS and periphery. We now show that IAA-RP (i) is present in brain and tissue extracts that exhibit I-R activity; (ii) is present in neurons of brainstem areas, including the rostroventrolateral medulla, a region where drugs active at I-Rs are known to modulate blood pressure; (iii) is present within synaptosome-enriched fractions of brain where its release is Ca 2؉ -dependent, consistent with transmitter function; (iv) produces I-R-linked effects in vitro (e.g., arachidonic acid and insulin release) that are blocked by relevant antagonists; and (v) produces hypertension when microinjected into the rostroventrolateral medulla. Our data also suggest that IAA-RP may interact with a novel imidazol(in)e-like receptor at this site. We propose that IAA-RP is a neuroregulator acting via I-Rs.clonidine-displacing substance (CDS) ͉ hypertension ͉ pancreatic beta cells ͉ anti-IAA-RP antibodies ͉ histamine

A site-specific chemical modification strategy has been employed to elucidate structure-function relationships at the only phylogenetically nonconserved position within the core of the hammerhead ribozyme (N7). Four different base substitutions at position 7 resulted in increased catalytic rates. A pyridin-4-one base substitution increased the rate of the chemical step up to 12-fold. These results are the first examples of chemical modifications within a catalytic RNA that enhance the rate of the chemical step. Four base substitutions resulted in decreased catalytic rates. The results do not correlate with proposed hydrogen bond interactions (Pley et al., 1994; Scott et al., 1995). This study demonstrates the utility of using unnatural nucleotide analogs-rather than mutagenesis with the four standard nucleotides alone-to elucidate structure-function relationships of small RNAs.

A synthetic route to nucleoside 5'-deoxy-5'-difluoromethyl phosphonates from ribofuranosyl &deoxy-5-difluoromethyl phosphonate precursors is described. Methyl 5,6-dideoxy-6-(diethoxyphosphinyl)-6,6-difluoro-2,3-0-isopropylidene-fi-~-ribo-hexohranoside (7) was converted, under mild conditions, to the suitable glycosylating agent l-O-acetyl-2,3-di-O-benzoyl-5,6-dideoxyS-(diethoxyphosphinyl)-6,6-difluoro-fi-~-ribo-hexofuranoside (10). 1,2-Di-O-acetyl-3-O-benzyl-5,6-dideoxy-6-(dietho~hos-phinyl)-6,6-difluoro-fi-~-ribo-hexofuranoside (16) was also prepared as a versatile building block for nucleotide synthesis. Condensation of 10 with silylated nucleobases, followed by complete deprotection, afforded 5',6'-dideoxy-6'-(dihydroxyphosphinyl~-6',6'-difluoro nucleoside analogs 22a-c. In the case of the glycosylation of adenine, a considerable quantity of N-7 regioisomer 19 was formed. 5',6'-Dideoxy-6'-(dihydroxyphosphinyl)-6',6'-difluoro adenosine analog 22c was converted into the triphosphate analog 23 using 1,l'-carbonyldiimidazole activation followed by condensation with pyrophosphate. The adenosine 3',5'-cyclic monophosphate analog 24 was obtained through the DCC promoted intramolecular cyclization of 22c. Dinucleoside phosphate analog 27 was prepared by DCC-catalyzed coupling of l-[2,3-di-O-benzoyl-5,6-dideoxy-6-(dihydrox~hosphinyl)-6,6-difluoro-fi-~-ribo-hexofuranosylluraci1(21a) with 2',5'-bis(0-tert-butyldimethylsily1)-N4-acetylcytidine (263, followed by deprotection.

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Several 2'-modified ribonucleoside phosphoramidites have been prepared for structure-activity studies of the hammerhead ribozyme. The aim of these studies was to design and synthesize catalytically active and nuclease-resistant ribozymes. Synthetic schemes for stereoselective synthesis of the R isomer of 2'-deoxy-2'-C-allyl uridine and cytidine phosphoramidites, based on the Keck allylation procedure, were developed. Protection of the 2'-amino group in 2'-deoxy-2'-aminouridine was optimized and a method for the convenient preparation of 5'-O-dimethoxytrityl-2'-deoxy-2'-phthalimidouridine 3'-O-(2-cyanoethyl-N,N-diisopropylphosphoramidite) was developed. During the attempted preparation of the 2'-O-t-butyldimethylsilyl-3'-O-phosphoramidite of arabinouridine a reversed regioselectivity in the silylation reaction, compared with the published procedure, was observed, as well as the unexpected formation of the 2,2'-anhydronucleoside. A possible mechanism for this cyclization is proposed. The synthesis of 2'-deoxy-2'-methylene and 2'-deoxy-2'-difluoromethylene uridine phosphoramidites is described. Based on a '5-ribose' model for essential 2'-hydroxyls in the hammerhead ribozyme these 2'-modified monomers were incorporated at positions U4 and/or U7 of the catalytic core. A number of these ribozymes had almost wild-type catalytic activity and improved stability in human serum, compared with an all-RNA molecule.

VP55, the vaccinia poly(A) polymerase catalytic subunit, interacts with oligonucleotide primers via two uridylate recognition sites (Deng, L., and Gershon, P. D. (1997) EMBO J. 16, 1103-1113). Here, we show that the cognate RNA sequence comprises a 5-rU 2 -N 15 -rU-3 motif (where N ‫؍‬ any deoxyribo or ribonucleotide), embedded within oligonucleotide primers 29 -30 nucleotides (nt), or greater, in length. Nine residues separate the 3-most ribouridylate of the optimally positioned motif from the primer 3-OH. A ribose sugar at the extreme 3-terminal nucleotide of the primer is absolutely required for VP55's adenylyltransferase activity, but not for stable VP55-RNA interaction. A ribose at position ؊3 markedly stimulates both adenylyltransferase activity and stable binding. The use of uridine analogs indicated (i) those functional groups of the uracil base which contribute to stable VP55-primer interaction, and (ii) that VP55's ability to discriminate uracil from cytosine stems largely from the requirement for a protonated N3 nitrogen within the pyrimidine ring. The rU 2 -N 15 -rU motif was identified within the uridylate-rich 3 end of a naturally occurring vaccinia mRNA. However, oligonucleotides whose only internal uridylates comprised the motif supported only a 3-5-nt processive burst of oligo(A) tail addition, as opposed to the ϳ30 -35-nt burst observed with the naturally occurring 3 end.One unusual feature of the poly(A) polymerase (PAP) 1 encoded by vaccinia virus is its heterodimeric structure (2-4). However, roles for the individual subunits within the heterodimer have been established by examination of the in vitro properties of the individual subunits. Thus, the isolated larger (VP55) subunit possesses PAP catalytic activity, and is able to add ϳ30 -35-nt oligo(A) tails to RNA 3Ј ends in a rapid and processive burst of polyadenylylation, before switching, abruptly, to a very slow and non-processive mode of adenylate addition (2, 5). The isolated smaller (VP39) subunit has no PAP catalytic activity, but its addition to VP55 permits tails that are greater than ϳ35 nt in length to be processively elongated to an overall length of several hundred nucleotides, in vitro (6). In addition to its activity as a PAP processivity factor, VP39 has an entirely unrelated function, at the mRNA 5Ј end. Thus, as an mRNA cap-specific 2Ј-O-methyltransferase, VP39 modifies the ribose sugar of the penultimate nucleotide of the mRNA type 0 cap structure to a 2Ј-O-methylated nucleotide (7).Since VP55 extends oligo(A) primers greater than 30 -35 nt in length in only a slow, non-processive mode of adenylate addition, the ability of this subunit to catalyze the processive polyadenylylation burst is apparently triggered by some signal other than oligo(A) or poly(A) (5). This signal was shown to comprise, in some manner, a high content of uridylate residues within the 3Ј-terminal 30 -40 nt of the initial RNA primer, in no obvious arrangement or pattern (8). Consistent with this, VP55 interacts stably with uridylate-rich RNA segments ...