WO1995013378A1

WO1995013378A1 - Base-modified enzymatic nucleic acid

Info

Publication number: WO1995013378A1
Application number: PCT/US1994/012806
Authority: WO
Inventors: Nassim Usman; Leonid Beigelman; James A. Mcswiggen
Original assignee: Ribozyme Pharmaceuticals, Inc.
Priority date: 1993-11-08
Filing date: 1994-11-07
Publication date: 1995-05-18
Also published as: JPH09504701A; US20030166896A1; CA2176035A1; AU687479B2; EP0728204A1; US6528639B2; US20010006801A1; AU1090495A

Abstract

Method to produce a more active ribozyme by introducting a modified base into a substrate binding arm of the ribozyme or its catalytic core.

Description

DESCRIPTION

Base-Modified Enzymatic Nucleic Acid

Background of the Invention

This application is a continuation-in-part of McSwiggen, "Optimization of Ribozyme Activity", U.S. Serial No. 07/963,322, filed October 15, 1992, the whole of which is hereby incorporated by reference herein.

This invention relates to enzymatic RNA molecules or ribozymes having a modified nucleotide base sequence.

The following is a brief history of the discovery and activity of enzymatic RNA molecules or ribozymes. This history 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.

Prior to the 1970s it was thought that all genes were direct linear representations of the proteins that they encoded. This simplistic view implied that all genes were like ticker tape messages, with each triplet of DNA "letters" representing one protein "word" in the transla¬ tion. Protein synthesis occurred by first transcribing a gene from DNA into RNA (letter for letter) and then trans¬ lating the RNA into protein (three letters at a time) . In the mid 1970s it was discovered that some genes were not exact, linear representations of the proteins that they encode. These genes were found to contain interruptions in the coding sequence which were removed from, or "spliced out" of, the RNA before it became translated into protein. These interruptions in the coding sequence were given the name of intervening sequences (or introns) and the process of removing them from the RNA was termed splicing. At least three different mechanisms have been discovered for removing introns from RNA. Two of these splicing mechanisms involve the binding of multiple protein factors which then act to correctly cut and join the RNA. A third mechanism involves cutting and joining of the RNA by the intron itself, in what was the first discovery of catalytic RNA molecules.

Cech and colleagues were trying to understand how RNA splicing was accomplished in a single-celled pond organism called Tetrahymena thermophila . Cech proved that the intervening sequence RNA was acting as its own splicing factor to snip itself out of the surrounding RNA. Contin¬ uing studies in the early 1980's served to elucidate the complicated structure of the Tetrahymena intron and to decipher the mechanism by which self-splicing occurs. Many research groups helped to demonstrate that the specific folding of the Tetrahymena intron is critical for bringing together the parts of the RNA that will be cut and spliced. Even after splicing is complete, the re¬ leased intron maintains its catalytic structure. As a consequence, the released intron is capable of carrying out additional cleavage and splicing reactions on itself (to form intron circles) . By 1986, Cech was able to show that a shortened form of the Tetrahymena intron could carry out a variety of cutting and joining reactions on other pieces of RNA. The demonstration proved that the Tetrahymena intron can act as a true enzyme: (i) each intron molecule was able to cut many substrate molecules while the intron molecule remained unchanged, and (ii) reactions were specific for RNA molecules that contained a unique sequence (CUCU) which allowed the intron to recognize and bind the RNA. Zaug and Cech coined the term "ribozyme" to describe any ribonucleic acid molecule that has enzyme-like properties.

Also in 1986, Cech showed that the RNA substrate sequence recognized by the Tetrahymena ribozyme could be changed by altering a sequence within the ribozyme itself. This property has led to the development of a number of site-specific ribozymes that have been individually designed to cleave at other RNA sequences. The Tetrahymena intron is the most well-studied of what is now recognized as a large class of introns, Group I introns. The overall folded structure, including several sequence elements, is conserved among the Group I introns, as is the general mechanism of splicing. Like the Tetrahymena intron, some members of this class are catalytic, i.e., the intron itself is capable of the self-splicing reaction. Other Group I introns require additional (protein) factors, presumably to help the intron fold into and/or maintain its active structure.

Ribonuclease P (RNaseP) is an enzyme comprised of both RNA and protein components which are responsible for con¬ verting precursor tRNA molecules into their final form by trimming extra RNA off one of their ends. RNaseP activity has been found in all organisms tested. Sidney Altman and his colleagues showed that the RNA component of RNaseP is essential for its processing activity; however, they also showed that the protein component also was required for processing under their experimental conditions. After Cech's discovery of self-splicing by the Tetrahymena intron, the requirement for both protein and RNA compo¬ nents in RNaseP was reexamined. In 1983, Altman and Pace showed that the RNA was the enzymatic component of the RNaseP complex. This demonstrated that an RNA molecule was capable of acting as a true enzyme, processing numer¬ ous tRNA molecules without itself undergoing any change.

The folded structure of RNaseP RNA has been deter¬ mined, and while the sequence is not strictly conserved between RNAs from different organisms, this higher order structure is. It is thought that the protein component of the RNaseP complex may serve to stabilize the folded RNA in vivo.

Symons and colleagues identified two examples of a self-cleaving RNA that differed from other forms of catalytic RNA already reported. Symons was studying the propagation of the avocado sunblotch viroid (ASV) , an RNA virus that infects avocado plants. Symons demonstrated that as little as 55 nucleotides of the ASV RNA was capable of folding in such a way as to cut itself into two pieces. It is thought that in vivo self-cleavage of these RNAs is responsible for cutting the RNA into single genome-length pieces during viral propagation. Symons discovered that variations on the minimal catalytic sequence from ASV could be found in a number of other plant pathogenic RNAs as well. Comparison of these sequences revealed a common structural design consisting of three stems and loops connected by a central loop containing many conserved (invariant from one RNA to the next) nucleotides. The predicted secondary structure for this catalytic RNA reminded the researchers of the head of a hammer; thus it was named as such. Uhlenbeck was successful in separating the catalytic region of the ribozyme from that of the substrate. Thus, it became possible to assemble a hammerhead ribozyme from 2 (or 3) small synthetic RNAs. A 19-nucleotide catalytic region and a 24-nucleotide substrate were sufficient to support specific cleavage. The catalytic domain of numer¬ ous hammerhead ribozymes have now been studied by both the Uhlenbeck' s and Symons' groups with regard to defining the nucleotides required for specific assembly and catalytic activity, and determining the rates of cleavage under various conditions.

Haseloff and Gerlach showed it was possible to divide the domains of the hammerhead ribozyme in a different manner. By doing so, they placed most of the required sequences in the strand that did not get cut (the ribo- zyme) and only a required UH where H = C, A, or U in the strand that did get cut (the substrate) . This resulted in a catalytic ribozyme that could be designed to cleave any UH RNA sequence embedded within a longer "substrate recognition" sequence. The specific cleavage of a long mRNA, in a predictable manner using several such hammer¬ head ribozymes, was reported in 1988. One plant pathogen RNA (from the negative strand of the tobacco ringspot virus) undergoes self-cleavage but cannot be folded into the consensus hammerhead structure described above. Bruening and colleagues have indepen- dently identified a 50-nucleotide catalytic domain for this RNA. In 1990, Hampel and Tritz succeeded in dividing the catalytic domain into two parts that could act as substrate and ribozyme in a multiple-turnover, cutting reaction. As with the hammerhead ribozyme, the catalytic portion contains most of the sequences required for cata¬ lytic activity, while only a short sequence (GUC in this case) is required in the target. Hampel and Tritz described the folded structure of this RNA as consisting of a single hairpin and coined the term "hairpin" ribozyme (Bruening and colleagues use the term "paper clip" for this ribozyme motif) . Continuing experiments suggest an increasing number of similarities between the hairpin and hammerhead ribozymes in respect to both binding of target RNA and mechanism of cleavage. Hepatitis Delta Virus (HDV) is a virus whose genome consists of single-stranded RNA. A small region (about 80 nucleotides) in both the genomic RNA, and in the comple¬ mentary anti-genomic RNA, is sufficient to support self-cleavage. In 1991, Been and Perrotta proposed a secondary structure for the HDV RNAs that is conserved between the genomic and anti-genomic RNAs and is necessary for catalytic activity. Separation of the HDV RNA into "ribozyme" and "substrate" portions has recently been achieved by Been. Been has also succeeded in reducing the size of the HDV ribozyme to about 60 nucleotides.

The table below lists some of the characteristics of the ribozymes discussed above:

Table 1

Characteristics of Ribozymes Group I Introns

Size: -300 to >1000 nucleotides. Requires a U in the target sequence immediately 5' of the cleavage site.

Binds 4-6 nucleotides at 5' side of cleavage site. Over 100 known members of this class. Found in Tetrahymena thermophila rRNA, fungal mitochondria, chloroplasts, phage T4, blue-green algae, and others.

RNaseP RNA (Ml RNA)

Size: -290 to 400 nucleotides.

RNA portion of a ribonucleoprotein enzyme. Cleaves tRNA precursors to form mature tRNA.

Roughly 10 known members of this group all are bacterial in origin.

Hammerhead Ribozyme

Size: -30 to 40 nucleotides. Requires the target sequence UH immediately 5' of the cleavage site.

Binds a variable number nucleotides on both sides of the cleavage site.

14 known members of this class. Found in a number of plant pathogens (virusoids) that use RNA as the infectious agent.

Hairpin Ribozyme

Size: -50 nucleotides.

Requires the target sequence GUC immediately 3' of the cleavage site.

Binds 4 nucleotides at 5' side of the cleavage site and a variable number to the 3' side of the cleavage site.

Only 1 known member of this class. Found in one plant pathogen (satellite RNA of the tobacco ringspot virus) which uses RNA as the infectious agent.

Hepatitis Delta Virus (HDV) Ribozyme

Size: -60 nucleotides (at present) . Cleavage of target RNAs recently demonstrated. Sequence requirements not fully determined. Binding sites and structural requirements not fully determined, although no sequences 5' of cleavage site are required.

Only 1 known member of this class. Found in human HDV.

As the term is used in this application, ribozymes are generally RNA molecules (which may include modified ribo- or deoxyribonucleotides, or their equivalent) having an enzymatic activity which is able to repeatedly cleave other separate RNA molecules in a nucleotide base sequence specific manner. Such enzymatic RNA molecules can be targeted to virtually any RNA transcript, and efficient cleavage achieved in vi tro . Kim et al . , Proc. Natl . Acad. Sci . (USA) 1987, 84:8788; Haseloff and Gerlach, Nature 1988, 334:585; Cech, JAMA 1988, 260:3030; and Jefferies et al . , Nucleic Acids Research 1989, 27:1371. Thus, the term is distinct from self-splicing RNA molecules, and concerns only those molecules which act on other RNA or single- stranded DNA molecules to cause intermolecular cleavage.

Ribozymes act by first binding to a target RNA. Such binding occurs through the target RNA binding portion of a ribozyme which is held in close proximity to an enzym- atic portion of the RNA which acts to cleave the target RNA. Thus, the ribozyme 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 a ribozyme 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.

The enzymatic nature of a ribozyme is advantageous over other technologies, such as antisense technology (where a nucleic acid molecule simply binds to a nucleic acid target to block its translation) since the effective concentration of ribozyme necessary to effect a thera¬ peutic treatment is lower than that of an antisense oligonucleotide. This advantage reflects the ability of the ribozyme to act enzymatically. Thus, a single ribo¬ zyme 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 cleav¬ age 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, the specificity of action of a ribozyme may be greater than that of antisense oligonucleotide binding the same RNA site. By the phrase "enzymatic RNA molecule" is meant an RNA molecule which has complementarity in a substrate binding region to a specified gene target, and also has an enzym¬ atic activity which is active to specifically cleave RNA in that target. That is, the enzymatic RNA molecule is able to intermolecularly cleave RNA and thereby inactivate a target RNA molecule. This complementarity functions to allow sufficient hybridization of the enzymatic RNA mole¬ cule to the target RNA to allow the cleavage to occur. One hundred percent complementarity is preferred, but complementarity as low as 50-75% may also be useful in this invention.

In preferred embodiments of this invention, the enzymatic RNA molecule is formed in a hammerhead motif, but may also be formed in the motif of a hairpin, hepa- titis delta virus, group I intron or RNaseP RNA (in association with an RNA guide sequence) . Examples of such hammerhead motifs are described by Rossi et al . , Aids Research and Human Retroviruses 1992, 8:183; of hairpin motifs by Hampel et al . , "RNA Catalyst for Cleaving Specific RNA Sequences", filed September 20, 1989, which is a continuation-in-part of U.S. Serial No. 07/247,100 filed September 20, 1988, Hampel and Tritz, 28 Biochemistry 1989, 28:4929, 1989 and Hampel et al . , Nucleic Acids Research 1990, 18:299; and an example of the hepatitis delta virus motif is described by Perrotta and Been, 31 Biochemistry 1992, 31:16; of the RNaseP motif by Guerrier-Takada et al . , Cell 1983, 35:849; and of the group I intron by Cech et al . , U.S. Patent 4,987,071. These specific motifs are not limiting in the invention and those skilled in the art will recognize that all that is important in an enzymatic RNA molecule of this inven- tion is that it has a specific substrate binding site which is complementary to one or more of the target gene RNA regions, and that it have nucleotide sequences within or surrounding that substrate binding site which impart an RNA cleaving activity to the molecule. The invention provides a method for designing a class of enzymatic cleaving agents which exhibit a high degree of specificity for the RNA of a desired target. The ribo¬ zyme molecule is preferably targeted to a highly conserved sequence region of a target such that specific treatment of a disease or condition can be provided with a single ribozyme. Such enzymatic RNA molecules can be delivered exogenously to specific cells as required. In the pre¬ ferred hammerhead motif the small size (less than 40 nucleotides, preferably between 32 and 36 nucleotides in length) of the molecule allows the cost of treatment to be reduced compared to other ribozyme motifs.

Synthesis of ribozymes greater than 100 nucleotides in length is very difficult using automated methods, and the therapeutic cost of such molecules is prohibitive. Delivery of ribozymes by expression vectors is primarily feasible using only ex vivo treatments . This limits the utility of this approach. In this invention, small ribo- zyme motifs ( e . g. , of the hammerhead structure) are used for exogenous delivery. The simple structure of these molecules also increases the ability of the ribozyme to invade targeted regions of the mRNA structure. Thus, unlike the situation when the hammerhead structure is included within longer transcripts, there are no non- ribozyme flanking sequences to interfere with correct folding of the ribozyme structure or with complementary region. Eckstein et al . , International Publication No. WO 92/07065; Perrault et al . , Nature 1990, 344:565; Pieken et al . , Science 1991, 253:314; Usman and Cedergren, Trends in Biochem. Sci . 1992, 17:334; Usman et al . , International Publication No. WO 93/15187; and Rossi et al . , WO 91/03162, describe various chemical modifications that can be made to the sugar moieties of enzymatic nucleic acid molecules.

The following discussion of relevant art is dependent on the diagram shown in Figure 5, in which the numbering of various nucleotides in a hammerhead ribozyme is pro¬ vided. This is not to be taken as an indication that the Figure is prior art to the pending claims, or that the art discussed is prior art to those claims.

Odai et al . , FEBS 1990, 267 :150, state that substitu- tion of guanosine at position 5 of a hammerhead ribozyme for inosine greatly reduces catalytic activity, suggesting "the importance of the 2-amino group of this guanosine for catalytic activity."

Fu and McLaughlin, Proc . Natl . Acad . Sci . (USA) 1992, 85:3985, state that deletion of the 2-amino group of the guanosine at position 5 of a hammerhead ribozyme, or dele¬ tion of either of the 2'-hydroxyl groups at position 5 or 8, resulted in ribozymes having a decrease in cleavage efficiency. Fu and McLaughlin, Biochemistry 1992, 31:10941, state that substitution of 7-deazaadenosine for adenosine residues in a hammerhead ribozyme can cause reduction in cleavage efficiency. They state that the "results suggest that the N⁷-nitrogen of the adenosine at position 6 in the hammerhead ribozyme/substrate complex is critical for efficient cleavage activity. " They go on to indicate that there are five critical functional groups located within the tetrameric sequence GAUG in the hammerhead ribozyme.

Summary of the Invention

This invention relates to production of enzymatic RNA molecules or ribozymes having enhanced or reduced binding affinity and enhanced enzymatic activity for their target nucleic acid substrate by inclusion of one or more modi¬ fied nucleotides in the substrate binding portion of a ribozyme such as a hammerhead, hairpin or hepatitis delta virus derived ribozyme. Applicant has recognized that only small changes in the extent of base pairing or hydrogen bonding between the ribozyme and substrate can have significant effect on the enzymatic activity of the ribozyme on that substrate. Thus, applicant has recog¬ nized that a subtle alteration in the extent of hydrogen bonding along a substrate binding arm of a ribozyme can be used to improve the ribozyme activity compared to an unaltered ribozyme containing no such altered nucleotide. Thus, for example, a guanosine base may be replaced with an inosine to produce a weaker interaction between a ribo- zyme and its substrate, or a uracil may be replaced with a bromouracil (BrU) to increase the hydrogen bonding interaction with an adenosine. Other examples of altera¬ tions of the four standard ribonucleotide bases are shown in Figures 4a-d with weaker or stronger hydrogen bonding abilities shown in each figure.

In addition, applicant has determined that base modi¬ fication within some catalytic core nucleotides maintains or enhances enzymatic activity compared to an unmodified molecule. Such nucleotides are noted in Figure 5 by an arrow. Specifically, referring to Figure 5, the preferred sequence of a hammerhead ribozyme in a 5' to 3' direction of the catalytic core is CUG AUG A G*C GAA A. The nature of the base-paired stem II (Figures 1 and 5) and the recognition arms of stems I and III are variable. In this invention, the use of base-modified nucleotides in those regions that maintain or enhance the catalytic activity and/or the nuclease resistance of the hammerhead ribozyme are described.

Examples of base substitutions useful in this inven¬ tion are shown in Figure 6. In preferred embodiments cytidine residues are substituted with 5-alkylcytidines ( e . g. , 5-methylcytidine, Figure 6, R=CH₃, 9), and uridine residues with 5-alkyluridines ( e . g. , ribothymidine (Figure 6, R=CH₃, 4) or 5-halouridine ( e . g. , 5-bromouridine, Figure 6, X=Br, 13) or 6-azapyrimidines (Figure 6, 17) . Guano- sine or adenosine residues may be replaced by diamino- purine residues (Figure 6, 22) in either the core or stems. In those bases where none of the functional groups are important in the complexing of magnesium or other functions of the hammerhead ribozyme, they are optionally replaced with a purine ribonucleoside (Figure 6, 23) , which significantly reduces the complexity of chemical synthesis of the hammerhead ribozyme, as no base- protecting group is required during chemical incorporation of the purine nucleus. Furthermore, as discussed above, base-modified nucleotides may be used to enhance the specificity or strength of binding of the recognition arms in stems I & III with similar modifications. Base- modified nucleotides, in general, may also be used to enhance the nuclease resistance of the catalytic nucleic acids in which they are incorporated.

Substitutions of sugar moieties as described in the art cited above, may also be made to enhance catalytic activity.

Thus, in a first aspect, the invention features a modified ribozyme having one or more substrate binding arms including one or more modified nucleotide bases; and in a related aspect, the invention features a method for production of a more active modified ribozyme (compared to an unmodified ribozyme) by inclusion of one or more of such modified nucleotide bases in a substrate binding arm. The invention provides ribozymes having increased enzymatic activity in vi tro and in vivo as can be measured by standard assays. Thus, the kinetic features of the ribozyme are enhanced by selection of appropriate modified bases in the substrate binding arms. Applicant recognizes that while strong binding to a substrate by a ribozyme enhances specificity, it may also prevent separation of the ribozyme from the cleaved substrate. Thus, applicant provides means by which optimization of the base pairing can be achieved. Specifically, the invention features ribozymes with modified bases with enzymatic activity at least 1.5 fold (preferably 2 or 3 fold) or greater than the unmodified corresponding ribozyme. The invention also features a method for optimizing the kinetic activity of a ribozyme by introduction of modified bases into a ribozyme and screening for those with higher enzymatic activity. Such selection may be in vi tro or in vivo .

By "enzymatic portion" is meant that part of the ribozyme essential for cleavage of an RNA substrate.

By "substrate binding arm" is meant that portion of a ribozyme which is complementary to (i.e., able to base- pair with) a portion of its substrate. Generally, such complementarity is 100%, but can be less if desired. For example, as few as 10 bases out of 14 may be base-paired. Such arms are shown generally in Figures 1-3 as discussed below. That is, these arms contain sequences within a ribozyme which are intended to bring ribozyme and target

RNA together through complementary base-pairing inter¬ actions; e . g. , ribozyme sequences within stems I and III of a standard hammerhead ribozyme make up the substrate- binding domain (see Figure 1) . By "unmodified nucleotide base" is meant one of the bases adenine, cytosine, guanosine, uracil joined to the 1' carbon of β-D-ribo-furanose. The sugar also has a phosphate bound to the 5' carbon. These nucleotides are bound by a phosphodiester between the 3' carbon of one nucleotide and the 5' carbon of the next nucleotide to form RNA. By "modified nucleotide base" is meant any nucleotide base which contains a modification in the chemical struc¬ ture of an unmodified nucleotide base which has an effect on the ability of that base to hydrogen bond with its normal complementary base, either by increasing the strength of the hydrogen bonding or by decreasing it

( e . g. , as exemplified above for inosine and bromouracil) .

Other examples of modified bases include those shown in

Figures 4a-d and other modifications well known in the art, including heterocyclic derivatives and the like. In preferred embodiments the modified ribozyme is a hammerhead, hairpin or hepatitis delta virus derived ribozyme, and the hammerhead ribozyme includes between 32 and 40 nucleotide bases. The selection of modified bases is most preferably chosen to enhance the enzymatic activ- ity (as observed in standard kinetic assays designed to measure the kinetics of cleavage) of the selected ribo¬ zyme, i . e . , to enhance the rate or extent of cleavage of a substrate by the ribozyme, compared to a ribozyme having an identical nucleotide base sequence without any modified base.

By "hammerhead ribozyme" is meant a ribozyme motif as shown in Figure 1 consisting of three duplex stems flank¬ ing a central conserved sequence "core" (indicated by boxes around sequences) . Any or all of the three duplex stems may be extended or closed by attaching additional nucleotides at the end of the stems away from the central core. If only one of the three duplexes is closed the hammerhead ribozyme is divided into a substrate-portion (the segment containing the cleavage site) and ribozyme portion. If two of the three duplexes are closed the hammerhead ribozyme consists of a single molecule that can undergo self-cleavage. The nucleotide sequence of the central core is conserved among the known hammerhead sequences. Single-base substitutions at almost any of the conserved nucleotides results in greater than lOOx reduc¬ tion in ribozyme activity. The A»U base-pair at the bottom of stem III is also required in that orientation; replacement by U*A, G»C, or C*G results in greater than 10Ox reduction in ribozyme activity. The single nucleo¬ tide between stem III and stem I can be C, A, or U (but not G) and still maintain activity. Much of the sequence outside the core region can be substituted by deoxyribo¬ nucleotides or chemically modified nucleotides and still maintain activity. Substitutions within the core region are more limited.

By "hairpin ribozyme" is meant a ribozyme motif as shown in Figure 2 consisting of four duplex stems inter¬ rupted by two pairs of "loop" sequences that are not predicted to form duplex structures (although they may participate in tertiary interactions) . The sequence of the "loop" at the cleavage site is required to be 5'- N-i-GUC-3' for the target sequence, and 3'-AGAA-5' for the ribozyme.

By "hepatitis delta virus (HDV) ribozyme" is meant a ribozyme motif as shown in Figure 3 consisting of four duplex stems interrupted by four sequences that are not predicted to form duplex structures (although they may participate in tertiary interactions) . As defined by Perrotta and Been (Nature 1991, 350:434) the HDV ribozyme contains one "pseudo-knot" sequence (stem II) .

By "kinetic assays" or "kinetics of cleavage" is meant an experiment in which the rate of cleavage of target RNA is determined. Often a series of assays are performed in which the concentrations of either ribozyme or substrate are varied from one assay to the next in order to deter¬ mine the influence of that parameter on the rate of cleavage.

By "rate of cleavage" is meant a measure of the amount of target RNA cleaved as a function of time. In a second aspect, enzymatic nucleic acid having a hammerhead configuration and modified bases which maintain or enhance enzymatic activity is provided. Such nucleic acid is also generally more resistant to nucleases than unmodified nucleic acid. By "modified bases" in this aspect is meant those shown in Figure 6, or their equiva¬ lents; such bases may be used within the catalytic core of the enzyme as well as in the substrate-binding regions. Other features and advantages of the invention will be apparent from the following description of the preferred embodiments thereof, and from the claims.

Description of the Preferred Embodiments

The drawings will first briefly be described.

Drawings Figures 1, 2 and 3 are diagrammatic representations of hammerhead, hairpin and HDV ribozymes, respectively.

Figures 4a-d are diagrammatic representations of standard base modifications for adenine, guanine, cytosine and uracil, respectively; modifications on the upper line of each figure represent structures with stronger base pairing ability compared to those on the lower lines.

Figure 5 is a diagrammatic representation of a position numbered hammerhead ribozyme (according to Hertel et al . , Nucleic Acids Res . 1992, 20:3252) showing specific substitutions in the catalytic core and substrate binding arms.

Figure 6 is a diagrammatic representation of various nucleotides that can be substituted in the catalytic core of a Hammerhead ribozyme. Figure 7 is a diagrammatic representation of the synthesis of a 5-methylcytidine phosphoramidite.

Figure 8 is a diagrammatic representation of the synthesis of 5-bromouridine phosphoramidite.

Figure 9 is a diagrammatic representation of the synthesis of 6-azauridine phosphoramidite. Figure 10 is a diagrammatic representation of the synthesis of ribothymidine phosphoramidite.

Figure 11 is a diagrammatic representation of the synthesis of 2, 6-diaminopurine phosphoramidite.

Modified Ribozymes

There is a narrow range of binding free-energies between a ribozyme and its substrate that will produce maximal ribozyme activity. Such binding energy can be optimized by making ribozymes with G to I and U to BrU substitutions (or equivalent substitutions) in the substrate-binding arms. This allows manipulation of the binding free-energy without actually changing the target recognition sequence, the length of the two substrate- binding arms, or the enzymatic portion of the ribozyme. The shape of the free-energy vs. ribozyme activity curve can be readily determined using data from experiments in which each base (or several bases) is modified or unmodi¬ fied, and without the complication of changing the size of the ribozyme/substrate interaction. Such ' experiments will indicate the most active ribozyme structure. It is likely that only one or two modifications are necessary since a very small change in binding free energy (even one base-pair interaction) can dramatically affect ribozyme activity; the use of modified bases thus permits "fine tuning" of the binding free energy to assure maximal ribozyme activity. In addition, replacement of such bases, e . g. , I for G, may permit a higher level of substrate specificity when cleavage of non-target RNA is a problem.

Method

Modified substrate binding arms can be synthesized using standard methodology. For example, phosphoramidites of inosine and 5-bromouracil can be used. Generally, a target site that has been optimized for stem I and III lengths (in a hammerhead ribozyme -- other ribozymes can be treated in a similar manner) , and that has G and/or U in the ribozyme portion of stem I and III, is selected. Modified ribozymes are made by replacing various G and U residues with I and BrU, respectively, during synthesis of the ribozyme. The modified ribozymes are then tested to determine kinetic parameters using standard procedures (see McSwiggen, "Improved Ribozymes", U.S. Serial No. 07/884,521, filed May 14, 1992, hereby incorporated by reference herein) . The binding affinities for the ribo- zymes can also be determined by standard procedures, e . g. , by T-melt, gel-binding, or by competition kinetics assays. By comparison of binding affinity and ribozyme activity the optimum binding affinity of a ribozyme can then be found. Other combinations of G, I, U BrU, and other bases can then be tested with nearly identical binding free energy, but different base sequence, to determine whether factors other than simple binding free-energy play a role.

It is preferred to perform routine experiments of this type to select a desired ribozyme substrate binding sequence by use of an unmodified ribozyme with a modified substrate (which contains the modified bases) . That is, the reverse experiment to that described above is per¬ formed. Such an experiment is more readily performed since the substrate is generally shorter than the ribo- zyme, and can be readily synthesized without concern about its secondary structure. Thus, a single ribozyme can be tested against a plurality of modified substrates in order to define which of the substrates provides better kinetic results. Once a preferred substrate is identified, the ribozyme can then be modified in a way which mirrors the selected substrate, and then tested against an unmodified substrate.

Such experiments will define useful ribozymes of this invention in which one or more modified bases are provided in the substrate binding arms with greater enzymatic activity in vi tro and in vivo than comparable unmodified ribozymes. Such modifications may also be advantageous if they increase the resistance of a ribozyme to enzymatic degradation in vivo.

Examples

The following are non-limiting examples showing the synthesis of base-modified catalytic nucleic acids.

Example 1: Synthesis of Hammerhead Ribozymes Containing Base-Modified Nucleotides The method of synthesis used follows the procedure for normal RNA synthesis as described in Usman, N. ; Ogilvie, K.K.; Jiang, M.-Y.; Cedergren, R.J. J. Am . Chem . Soc . 1987, 109, 7845-7854 and in Scaringe, S.A.; Franklyn, C; Usman, N. Nucleic Acids Res . 1990, 18, 5433-5441 and makes use of common nucleic acid protecting and coupling groups, such as dimethoxytrityl at the 5' -end, and phosphoramidites at the 3'-end (compounds 4, 9, 13, 17, 22, 23) . The average stepwise coupling yields were >98%. These base-modified nucleotides may be incorporated not only into hammerhead ribozymes, but also into hairpin, hepatitis delta virus, or Group 1 or Group 2 introns. They are, therefore, of general use as replacement motifs in any nucleic acid structure.

In the case of the hammerhead ribozyme the following specific substitutions may be used:

Referring to Figure 5, in the catalytic core (boxed nucleotides) , the pyrimidine C3 may be replaced by the cytosine analogs shown in Figure 4c and compound 9 in Figure 6.

Referring to Figure 5, in the catalytic core (boxed nucleotides) , the pyrimidines U4 and N7 may be replaced by the cytosine analogs shown in Figure 4c, the uridine analogs shown in Figure 4d and compounds 4,9,13 and 17 in

Figure 6.

Referring to Figure 5, in the catalytic core (boxed nucleotides) , the purines G5, G8 and G12 may be replaced by the guanine analogs shown in Figure 4b and compounds 22 and 23 in Figure 6.

Referring to Figure 5, in the catalytic core (boxed nucleotides) , the purines A6, A9, A13 and A14 may be replaced by the adenine analogs shown in Figure 4a and compounds 22 and 23 in Figure 6.

Referring to Figures 1 and 5, in stems I, II and III any of the pyrimidines may be replaced by the pyrimidine analogs shown in Figures 4c and 4d and compounds 4,9,13 and 17 in Figure 6 as long as base-pairing is maintained in the stems.

Referring to Figures 1 and 5, in stems I, II and III any of the purines may be replaced by the purine analogs shown in Figures 4a and 4b and compounds 22 and 23 in Figure 6 as long as base-pairing is maintained in the stems.

Referring to Figures 1 and 5, in loop II (denoted as

J_ l_ in Figure 5) any nucleotide may be replaced by the pyrimidine analogs shown in Figures 4c and 4d, the purine analogs shown in Figures 4a and 4b and compounds 4,9,13, 17, 22 and 23 in Figure 6.

Example 2 : Synthesis of Ribothvmidine Phosphoramidite 4 Referring to Figure 10, Ribothymidine 1 was prepared according to Vorbrϋggen et al . , Chem. Ber. 1981, 114:1234, and tritylated to yield DMT derivative 2. 2 was silylated to yield 2'-0-TBDMS derivative 3. The phosphoramidite 4 was prepared according to Scaringe et al . , Nucleic Acids Res . 1990, 18:5433.

Example 3 : S y n t h e s i s o f 5 - M e t h v 1 c v t i d i n e Phosphoramidite 9

Referring to Figure 7, Ribothymidine 1 (4 g, 15.5 mmol) was coevaporated with dry pyridine (2 x 100 ml) and redissolved in dry pyridine (100 ml) . To the resulting solution 4,4'-DMT-Cl (6.3 g, 18.6 mmol) was added and the reaction mixture was left at room temperature (about 20-25°C for 16 hours. The reaction mixture was quenched with methanol (25 ml) and evaporated to dryness. The residue was partitioned between chloroform and 5% sodium bicarbonate. The organic layer was washed with 5% sodium bicarbonate and brine, then dried over sodium sulfate and evaporated. The residue was additionally dried by coevap- oration with dry pyridine (2 x 50 ml) then redissolved in dry pyridine (100 ml) and acetic anhydride (4.4 ml, 46.5 mmol) was added to the resulting solution. The reaction mixture was left at room temperature overnight, then quenched with methanol (25 ml) , evaporated and worked-up as outlined above. The crude 5' -O-dimethoxytrityl-2' ,3' , - di-O-acetyl-ribo-thymidine 5 was purified by flash chroma- tography on silica gel, (hexanes:ethylacetate:triethyl- amine/45 :45 :10 to give 6.86 g (68.7%) of 5 as a yellowish foam.

Triethylamine (14.72 ml, 105.6 mmol) was added drop- wise to a stirred ice-cooled mixture of triazole (6.56 g, 95.04 mmol) and phosphorous oxychloride (2 ml, 21.2 mmol) in 100 ml of dry acetonitrile. A solution of nucleoside 5 (6.89, 10.56 mmol) in 50 ml of dry acetonitrile was added dropwise to the resulting suspension and the reac¬ tion mixture was stirred at room temperature for 4 hours. The reaction was concentrated, dissolved in chloroform and washed with a saturated aqueous solution of sodium bicar¬ bonate, water, dried over sodium sulfate and evaporated to dryness. To a solution of the residue (7.24 g) in dioxane (120 ml) was added 40 ml of 29% aqueous NH₄OH and the resulting solution was left overnight, then evaporated to dryness to yield 6.86 g of crude cytidine derivative 6 which was used without purification.

To a solution of 6 (3.5 g, 6.25 mmol) in dry pyridine (100 ml) was added 3.97 ml of trimethylchlorosilane to transiently protect free sugar hydroxyls. The reaction mixture was then treated with isobutyryl chloride (0.98 ml, 9.375 mmol) for 5 hours. The resulting mixture was quenched with 10 ml of methanol, then 10 ml of water was added and after 10 minutes 10 ml of 29% aq. ammonia was added and the reaction mixture was stirred for 2 hours and evaporated to dryness. The resulting residue was worked- up as outlined above for the compound 5 and purified by flash chromatography on silica gel (ethylacetate:hexanes/ 1:3) to yield 2.37 g (60%) of the nucleoside 7.

To a solution of compound 7 (1.3 g, 2.06 mmol) in dry pyridine 0.97 g (5.72 mmol) of silver nitrate was added followed by 2.86 ml of a 1 M solution of tert- butyldimethyl chloride in THF. The reaction mixture was left for 8 hours, evaporated, and dissolved in chloroform. The silver salt precipitate was filtered off and the reac¬ tion solution was washed with 5% aq. sodium bicarbonate and brine, dried over sodium sulfate and evaporated. The mixture of 2'- and 3'-isomers was separated by flash chromatography on silica gel (hexanes:ethylacetate/4 :1) to yield 0.62 g (40%) of 2'-isomer 8, which was converted to the phosphoramidite 9 by the general method described in Scaringe et al . , Nucleic Acids Res . 1990, 18:5433.

Example 4 : Synthesis of 5-Bromouridine Phosphoramidite

13 (See, Talbat et al. , Nucl. Acids Res.

18:3521-21, 1990)

Referring to Figure 8, 5-Bromouridine 10 (1.615 g, 5 mmol) was coevaporated with dry pyridine and redissolved in dry pyridine. To the resulting solution 2.03 g (6 mmol) of DMT-C1 was added and the reaction mixture was left overnight. After work-up and purification by flash chromatography on silica gel (chloroform:methanol/95 :5)

2.5 g (80%) of the dimethoxytritylated compound 11 was obtained.

To a solution of 11 (2 g) in dry pyridine was added 1.5 eq. of TBDMS-Cl for 2 days. The reaction mixture was evaporated, dissolved in chloroform, washed with 5% aq. sodium bicarbonate and brine. The organic layer was dried over sodium sulfate, evaporated and purified by flash chromatography on silica gel (ethylacetate:hexanes/l:2) to yield 1.4 g (60%) of 2'-isomer 12, which was converted to the phosphoramidite 13 by the general method described in Scaringe et al . , Nucleic Acids Res . 1990, 18:5433.

Example 5: Synthesis of 6-azauridine Phosphoramidite 17 Referring to Figure 9, 6-Azauridine (4.9 g, 20 mmol) was evaporated with dry pyridine (2 x 100 ml) and dis¬ solved in dry pyridine (100 ml) and, after addition of 4,4'-DMT-Cl (7.45 g, 22 mmol) left for 16 hours at room temperature. The reaction mixture was diluted with dry MeOH (50 ml) , evaporated to dryness, coevaporated with toluene (2x 100 ml) , the residue dissolved in CHC1₃ (500 ml) and washed with 5% NaHC0₃ (100 ml) , brine (100 ml) , dried, and purified by flash chromatography (a gradient CHC1₃ to 5% EtOH/CHCl₃ to yield lg (92.2%) of intermediate) 15.

To a ^' solution of 15 (3.23 g, 5.9 mmol) in 100 ml of dry THF, AgN0₃ (7.08 mmol) and dry pyridine (2.1 ml, 4.4 mmol) were added. The reaction mixture was stirred at room temperature until full dissolution of AgN0₃ (about 1 hour) occurred. Then 7 ml of a 1 M solution of TBDMS-Cl in THF was added and the reaction mixture stirred for 16 hours at room temperature. The reaction mixture was filtered and the filtrate evaporated to dryness. The resulting residue was dissolved in CHC1₃ (300 ml) and washed with 5% NaHC0₃ (100 ml) , brine (100 ml) , dried, and purified by flash chromatography (gradient of hexanes to hexanes:ethyl acetate/ 1:1) to yield 3.71g (62%) of 2' -TBDMS-isomer 16 which was converted to the phosphor¬ amidite 17 by the general method described in Scaringe et al., Nucleic Acids Res . 1990, 18:5433.

Example 6 : Synthesis of 2 , 6-diaminopurine

Phosphoramidite 22 Referring to Figure 11, phosphoramidite 22 was pre¬ pared by the general method described in Scaringe et al . , Nucleic Acids Res . 1990, 28:5433. Specifically, guanosine (11.32 g, 40 mmol) was dried by coevaporation with dry pyridine and redissolved in dry pyridine. Chlorotri- methylsilane (26.4 ml, 208 mmol) was added under stirring to the above solution and the reaction mixture was stirred overnight. To the resulting persilylated guanosine derivative phenylacetylchloride (12.7 ml, 96 mmol) was added dropwise and the reaction mixture was stirred for 12 hours. The reaction was quenched with 50 ml of methanol and 50 ml of water and stirred for 15 minutes, then 50 ml of 29% ammonia was added and the reaction mixture left for an additional 2 hours. Solvents were removed in vacuo, and the resulting oil was partitioned between ethyl acetate and water. The separated water layer was washed with ethyl acetate and was precipitated at 4 °C. The resulting solid was filtered off to give 8 g of N- henyl - acetylguanosine 18. The mother liquor was concentrated to give additional crop (4 g) . Overall yield -12 g (75%) .

N-Phenylacetylguanosine 18 (2.3 g, 5.73 mmol) was dried by coevaporation (3 times) with dry pyridine and dissolved in 50 ml of dry pyridine. To the resulting solution dimethoxytritylchloride (2.33 g, 6.88 mmol) was added and the reaction mixture was left at room temperature for 5 hours. The reaction was quenched with 25 ml of methanol and evaporated to dryness. The residue was dissolved in dichloromethane, washed with 5% aq. sodium bicarbonate and brine, dried over sodium sulfate and evaporated. The resulting oil was further dried by coevaporation with dry pyridine, dissolved in pyridine and treated with acetic anhydride (1.4 ml) for 4 hours at room temperature. The reaction mixture was quenched and worked-up as described above. The crude final compound was purified by flash chromatography on silica gel using dichloromethane: methanol/98 :2 mixture as eluent. The desired fractions were collected and evaporated to give 3.5 g (77%) of 5'-0- dimethoxytrityl-2' ,3' -di- 0-acetyl-N^!-phenylacetylguanosin e 19 as a yellowish foam. To a solution of compound 19 (3.5 g, 4.45 mmol) in 50 ml of dry dichloromethane, containing 3.11 ml of diiso- propylethylamine, was added mesitylenesulfonyl chloride (1.9 g, 8.9 mmol) and dimethylaminopyridine (0.28 g) . The reaction mixture was stirred for 30 minutes, evaporated and purified by flash chromatography on silica gel using dichloromethane (11) followed by 2% Methanol in dichloro¬ methane (0.71) to give 2.8 g (64%) of 0⁶-mesitylene inter¬ mediate 20. To a solution of 20 in 40 ml of dry tetra- hydrofuran lithium disulfide (0.3 g, 6.8 mmol) was added and the reaction mixture was stirred for 20 hours. The resulting clear solution was evaporated and worked-up as described above. The residue was purified by flash chromatography on silica gel in 1% Methanol in dichloro- methane to give 1.1 g (31%) of 5' -O-dimethoxytrityl-2' ,3' - di- 0-acetyl-N^!phenylacetyl-6-thiogua nosine 21.

To an ice-cooled (0 °C) solution of 5' -O-dimethoxy¬ trityl-2' ,3' -di-0-acetyl-N²phenylacetyl-6-thiogua nosine 21 (1 g) in pyridine:methanol/20 ml:2.6 ml, 2.4 ml of IM aq. sodium hydroxide were added and the reaction mixture was allowed to stay at 0 °C for 20 minutes. The solution was neutralized with Dowex 2x8 (Pyr⁺) to pH 7. The resin was filtered off and washed with aq. pyridine. The combined filtrate and washings were evaporated and dried in vacuo togive quantitatively5' - O-dimethoxytrityl-N-phenylacetyl- 6-thioguanosine.

To a stirred suspension of 5' -O-dimethoxytrityl- i\?phenylacetyl-6-thioguanosine (1.13 g, 1.57 mmol) in dry acetonitrile (35 ml) and triethylamine (1 ml) was added dinitrofluorobenzene (0.34 g, 1.88 mmol) and the reaction mixture was stirred under anhydrous conditions for 2 hours. The reaction was evaporated and worked-up as described for compound 20 and purified by flash chromato¬ graphy on silica gel in 1% methanol in chloroform (con- taining 1% triethylamine) as an eluent to give 0.93 g (67%) of 5' - 0-dimethoxytrityl -N²phenylacetyl - 6 -S- dinitrophenyl guanosine. To a solution of 5' -O-dimethoxytrityl-N-phenylacetyl-6 - S-dinitrophenyl guanosine (0.^*9 g ,1 mmol) in dry pyridine t-butyldimethylsilylchloride (0.46 g, 3 mmol) and tetra- butylammonium nitrate (3 mmol) were added and the reaction mixture was left for 50 hours. TLC (hexane:ethyl acetate/ 3:1) showed disappearance of the starting material and formation of two new compounds with a predominance of a lower R_f (3'-0-silyl isomer according to ^XH-NMR) . The desired 2' -isomer (70 mg) was obtained after evaporation and work-up and separation by flash chromatography on silica gel using hexane:ethyl acetate/4 :1 as eluent. The remaining mixture was rearranged in methanol with 2 drops of triethylamine and separated as above. This rearrange¬ ment procedure was repeated twice to finally give 250 mg of the desired 2' -isomer. 5' -O-dimethoxytrityl-2' -O-t- butyldimethylsilyl -N²phenylacetyl - 6 - S- dinitrophenyl guanosine.

5' -O-Dimethoxytrityl-2' -O- -butyldimethylsilyl- i^phenylacetyl -6-S-dinitrophenyl guanosine (0.18 g, 0.18 mmol) was dissolved in dry tetrahydrofuran under dry argon. N-Methylimidazole (0.01 ml, 0.09 mmol) and sym- collidine (0.178 ml, 1.35 mmol) were added and the solution was ice-cooled. 2-Cyanoethyl N, N' - diisopropylchlorophosphoramidite (0.083 ml, 0.36 mmol) was added dropwise and stirring was continued for 3 hours at room temperature. The reaction mixture was again ice- cooled and quenched with 6 ml of dry degassed ethyl acetate. After 5 min stirring the mixture was concentrated in vacuo (40 °C) , dissolved in chloroform, washed with 5% aq sodium bicarbonate, then with brine and evaporated. The residue was purified by flash chromatography on silica gel using ethyl acetate:hexane/:3 containing 2% triethylamine as an eluent to yield 0.14 g (64%) 5'-O-dimethoxytrityl-2' -O- -butyldimethylsilyl- N²phenylacetyl - 6 - S -dinitrophenyl guanosine-3 ' - (2- cyanoethyl N, N-diisopropylphosphoramidite) 22 as a yellow foam. Other embodiments are within the following claims.

"Sequence Listing" (1) GENERAL INFORMATION:

(i) APPLICANT: USMAN, Nassim

BEIGELMAN, Leonid McSWIGGEN, James A.

(ii) TITLE OF INVENTION: BASE-MODIFIED ENZYMATIC NUCLEIC ACID

(iii) NUMBER OF SEQUENCES:

(iv) CORRESPONDENCE ADDRESS:

(A) ADDRESSEE: Lyon & Lyon

(B) STREET: 611 West Sixth Street

(C) CITY: Los Angeles

(D) STATE: California

(E) COUNTRY: USA

(F) ZIP: 90017

(v) COMPUTER READABLE FORM:

(A) MEDIUM TYPE: 3.5" Diskette, 1.44 Mb storage

(B) COMPUTER: IBM Compatible

(C) OPERATING SYSTEM: IBM P.C. DOS (Version

5.0)

(D) SOFTWARE: WordPerfect (Version

5.1)

(vi) CURRENT APPLICATION DATA:

(A) APPLICATION NUMBER:

(B) FILING DATE:

(C) CLASSIFICATION:

(vii) PRIOR APPLICATION DATA: Prior applications total, including application described below: one

(A) APPLICATION NUMBER: 07/963,322

(B) FILING DATE: 15-OCT-1992

(viii) ATTORNEY/AGENT INFORMATION:

(A) NAME: Warburg, Richard J.

(B) REGISTRATION NUMBER: 32,327

(C) REFERENCE/DOCKET NUMBER: 201/206

(ix) TELECOMMUNICATION INFORMATION:

(A) TELEPHONE: (213) 489-1600

(B) TELEFAX: (213) 955-0440

(C) TELEX: 67-3510

(2) INFORMATION FOR SEQ ID NO:

(i) SEQUENCE CHARACTERISTICS:

(A) LENGTH: 11

(B) TYPE: nucleic acid

(C) STRANDEDNESS single

(D) TOPOLOGY: linear

(ix) FEATURE:

(D) OTHER INFORMATION: The letter "N" stands for any base. "H" represents nucleotide C, A, or U.

(ii) SEQUENCE DESCRIPTION: SEQ ID NO: 1: NNNNUHNNNN N 11

(2) INFORMATION FOR SEQ ID NO:

(i) SEQUENCE CHARACTERISTICS:

(A) LENGTH: 32

(B) TYPE: nucleic acid

(C) STRANDEDNESS: single

(D) TOPOLOGY: linear

(ix) FEATURE:

(D) OTHER INFORMATION: The letter "N" stands for any base.

(ii) SEQUENCE DESCRIPTION: SEQ ID NO: 2

NNNNNCUGAN GAGGCCGAAA GGCCGAAANN NN 32

(2) INFORMATION FOR SEQ ID NO: 3

(i) SEQUENCE CHARACTERISTICS

(A) LENGTH: 14

(B) TYPE: nucleic acid

(C) STRANDEDNESS single

(D) TOPOLOGY: linear

(ix) FEATURE:

(D) OTHER INFORMATION: The letter "N" stands for any base.

(ii) SEQUENCE DESCRIPTION: SEQ ID NO: 3

NNNNNGUCNN NNNN 14 (2) INFORMATION FOR SEQ ID NO: 4

(i) SEQUENCE CHARACTERISTICS

(A) LENGTH: 50

(B) TYPE: nucleic acid

(C) STRANDEDNESS single

(D) TOPOLOGY: linear

(ix) FEATURE:

(D) OTHER INFORMATION: The letter ^»N" stands for any base.

(ii) SEQUENCE DESCRIPTION: SEQ ID NO: 4

NNNNNNAGAA NNNNACCAGA GAAACACACG UUGUGGUAUA UUACCUGGUA50

(2) INFORMATION FOR SEQ ID NO:

(i) SEQUENCE CHARACTERISTICS:

(A) LENGTH: 85

(B) TYPE: nucleic acid

(C) STRANDEDNESS: single

(D) TOPOLOGY: linear

(ii) SEQUENCE DESCRIPTION: SEQ ID NO:

UGGCCGGCAU GGUCCCAGCC UCCUCGCUGG CGCCGGCUGG GCAACAUUCC50

GAGGGGACCG UCCCCUCGGU AAUGGCGAAU GGGAC 85

Claims

1. Method for production of a modified ribozyme having a higher biological activity compared to an unmodi¬ fied ribozyme recognizing the same substrate as said modified ribozyme, said modified and unmodified ribozyme having identical enzymatic portions, comprising the step of forming said modified ribozyme with one or more modified bases in a substrate binding arm of said modified ribozyme.

2. The method of claim 1, wherein said modified base has a modification in the chemical structure of a nucleo¬ tide base selected from adenosine, guanosine, cytosine or uracil which has an effect on the ability of that base to hydrogen bond with its normal complementary base, either by increasing or decreasing the strength of the hydrogen bonding.

3. The method of claim 1, wherein said modified ribozyme has the structure of a hammerhead, hairpin or hepatitis delta virus derived ribozyme.

4. The method of claim 3, wherein said hammerhead ribozyme consists of 32 to 40 nucleotide bases.

5. The method of claim 1, wherein said modified ribozyme and unmodified ribozyme have different binding free-energies with a target RNA.

6. The method of claim 1, wherein said modified base is selected from one shown in Figures 4a-d or Figure 6.

7. Enzymatic nucleic acid having a non-natural base which enhances the enzymatic activity of said nucleic acid compared to an identical nucleic acid having a naturally- occurring base in place of said non-natural base.

8. The enzymatic nucleic acid of claim 7, wherein said non-natural base is selected from one shown in Figures 4a-d or Figure 6.

9. The enzymatic nucleic acid of claim 7, wherein said nucleic acid has a hammerhead motif.