Nucleic acid catalysts comprising L-nucleotide analogs

Details Nucleic acid catalysts comprising L-nucleotide analogs Nucleic acid catalysts comprising L-nucleotide analogs

1998-03-25

2001-06-26

Marschel, Ardin H. (Department: 1631)

Chemistry: molecular biology and microbiology

Animal cell, per se ; composition thereof; process of...

C435S091100, C536S023100, C536S024100, C536S025300, C514S04400A

Reexamination Certificate

active

06251666

ABSTRACT:

BACKGROUND OF THE INVENTION
This invention relates to chemically synthesized ribozymes, or enzymatic nucleic acid molecules and derivatives thereof.
The following is a brief description of nucleic acid catalysts. This summary is not meant to be complete but is provided only for understanding of the invention that follows. This summary is not an admission that all of the work described below is prior art to the claimed invention.
Nucleic acid catalysts are nucleic acid molecules capable of catalyzing one or more of a variety of reactions including the ability to repeatedly cleave other separate nucleic acid molecules in a nucleotide base sequence-specific manner. Such enzymatic nucleic acid molecules can used, for example, to target virtually any RNA transcript (Zaug et al., 324,
Nature
429 1986; Cech, 260
JAMA
3030, 1988; and Jefferies et al., 17
Nucleic Acids Research
1371, 1989).
Because of their sequence-specificity, trans-cleaving enzymatic nucleic acid molecules show promise as therapeutic agents for human disease (Usman & McSwiggen, 1995
Ann. Rep. Med. Chem.
30, 285-294; Christoffersen and Marr, 1995
J. Med. Chem.
38, 2023-2037). Enzymatic nucleic acid molecules can be designed to cleave specific RNA targets within the background of cellular RNA. Such a cleavage event renders the mRNA non-functional and abrogates protein expression from that RNA. In this manner, synthesis of a protein associated with a disease state can be selectively inhibited.
There are seven basic varieties of naturally-occurring enzymatic RNAs are known presently. Each can catalyze the hydrolysis of RNA phosphodiester bonds in trans (and thus can cleave other RNA molecules) under physiological conditions. Table I summarizes some of the characteristics of these ribozymes. In general, enzymatic nucleic acids act by first binding to a target RNA. Such binding occurs through the target binding portion of a enzymatic nucleic acid which is held in close proximity to an enzymatic portion of the molecule that acts to cleave the target RNA. Thus, the enzymatic nucleic acid first recognizes and then binds a target RNA through complementary base-pairing, and once bound to the correct site, acts enzymatically to cut the target RNA. Strategic cleavage of such a target RNA will destroy its ability to direct synthesis of an encoded protein. After an enzymatic nucleic acid has bound and cleaved its RNA target, it is released from that RNA to search for another target and can repeatedly bind and cleave new targets.
In addition, several in vitro selection (evolution) strategies (Orgel, 1979,
Proc. R. Soc. London,
B 205, 435) have been used to evolve new nucleic acid catalysts capable of catalyzing a variety of reactions, such as cleavage and ligation of phosphodiester linkages and amide linkages, (Joyce, 1989,
Gene,
82, 83-87; Beaudry et al., 1992,
Science
257, 635-641; Joyce, 1992,
Scientific American
267, 90-97; Breaker et al., 1994,
TIBTECH
12, 268; Bartel et al., 1993,
Science
261:1411-1418; Szostak, 1993,
TIBS
17, 89-93; Kumar et al., 1995,
FASEB J.,
9, 1183; Breaker, 1996,
Curr. Op. Biotech.,
7, 442).
The enzymatic nature of a ribozyme is advantageous over other technologies, since the effective concentration of ribozyme necessary to effect a therapeutic treatment is generally lower than that of an antisense oligonucleotide. This advantage reflects the ability of the ribozyme to act enzymatically. Thus, a single ribozyme molecule is able to cleave many molecules of target RNA. In addition, the ribozyme is a highly specific inhibitor, with the specificity of inhibition depending not only on the base-pairing mechanism of binding, but also on the mechanism by which the molecule inhibits the expression of the RNA to which it binds. That is, the inhibition is caused by cleavage of the RNA target and so specificity is defined as the ratio of the rate of cleavage of the targeted RNA over the rate of cleavage of non-targeted RNA. This cleavage mechanism is dependent upon factors additional to those involved in base-pairing. Thus, it is thought that the specificity of action of a ribozyme is greater than that of antisense oligonucleotide binding the same RNA site.
The development of ribozymes that are optimal for catalytic activity would contribute significantly to any strategy that employs RNA-cleaving ribozymes for the purpose of regulating gene expression. The hammerhead ribozyme functions with a catalytic rate (k
cat
) of ~1 min
−1
in the presence of saturating (10 mM) concentrations of Mg
2+
cofactor. However, the rate for this ribozyme in Mg
2+
concentrations that are closer to those found inside cells (0.5-2 mM) can be 10- to 100-fold slower. In contrast, the RNase P holoenzyme can catalyze pre-tRNA cleavage with a k
cat
of ~30 min
−1
under optimal assay conditions. An artificial ‘RNA ligase’ ribozyme has been shown to catalyze the corresponding self-modification reaction with a rate of ~100 min
−1
. In addition, it is known that certain modified hammerhead ribozymes that have substrate binding arms made of DNA catalyze RNA cleavage with multiple turn-over rates that approach 100 min
−1
. Finally, replacement of a specific residue within the catalytic core of the hammerhead with certain nucleotide analogs gives modified ribozymes that show as much as a 10-fold improvement in catalytic rate. These findings demonstrate that ribozymes can promote chemical transformations with catalytic rates that are significantly greater than those displayed in vitro by most natural self-cleaving ribozymes. It is then possible that the structures of certain self-cleaving ribozymes may not be optimized to give maximal catalytic activity, or that entirely new RNA motifs could be made that display significantly faster rates for RNA phosphoester cleavage.
Chemically-modified ribozymes can be synthesized which are stable in human serum for up to 260 hours (Beigelman et al., 1995,
J. Biol. Chem.,
270, 25702) and maintain near wild type (chemically unmodified equivalent of modified ribozyme) activity in vitro. A number of laboratories have reported that the enhanced cellular efficacy of phosphorothioate-substituted antisense molecules. The enhanced efficacy appears to result from either i) increased resistance to 5′-exonuclease digestion (De Clercq et al., 1970
Virology
42, 421-428; Shaw et al., 1991
Nucleic Acids Res.
19, 747-750), ii) intracellular localization to the nucleus (Marti et al., 1992
Antisense Res. Dev.
2, 27-39), or iii) sequence-dependent non-specific effects (Gao et al., 1992
Molec. Pharmac.
41, 223-229; Bock et al., 1992
Nature
355, 564-566; and Azad, et al., 1993
Antimicrob. Agents Chemother.
37, 1945-1954) which are not manifested in non-thioated molecules. Many effects of thioated compounds are probably due to their inherent tendency to associate non-specifically with cellular proteins such as the Sp1 transcription factor (Perez et al., 1994
Proc. Natl Acad Sci. U.S.A.
91, 5957-5961). Chemical modification of enzymatic nucleic acids that provide resistance to cellular nuclease digestion without reducing the catalytic activity or cellular efficacy will be important for in vitro and in vivo applications of ribozymes.
The references cited above are distinct from the presently claimed invention since they do not disclose and/or contemplate the enzymatic nucleic acid molecules of the instant invention.
SUMMARY OF THE INVENTION
This invention relates to nucleic acid catalysts with one or more L-nucleotide-substitutions. These substitutions alone or in combination with other D- and L-chemical substitutions protect the nucleic acids from nuclease degradation without entirely inhibiting their catalytic activity. Resistance to nuclease degradation can increase the half-life of these nucleic acids inside a cell and improve the overall effectiveness of nucleic acid catalysts. These modifications may also be used to facilitate efficient uptake of nucleic acid catalysts by cells, transport and localization of these nucleic acids within a cell,

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