Nucleic acid structures with catalytic and autocatalytic replicating features and methods of use

A composition comprising first and second nucleic acids;

• said first nucleic acid comprising a first section and a second section, each of said sections having a 5' and a 3' end, said first nucleic acid being associated with an inhibitory element;
• said first section comprising a nucleotide sequence substantially identical to MDV-1, said nucleotide sequence being capable of autocatalytic replication under reaction conditions, but incapable of autocatalytic replication while associated with said inhibitory element;
• said second section being positioned at one end of said first section and being capable of assuming a bound position with a target, said second section comprising a cleavage site at which said first section is separated from said inhibitory element upon activation of a ribozyme formed by said first and second nucleic acids and said target;
• said inhibitory element being positioned at the end of said second section opposite to that of said first section;
• said first and said second nucleic acids forming said ribozyme with said target, said ribozyme being of the formula and structure set forth below:
• ##STR6## wherein the letter X generally represents said target, X.sup.1 represents a first target region, X.sup.2 represents a terminal nucleotide of X.sup.1 or a second target region, and X.sup.3 represents a terminal nucleotide of X.sup.1 or a third target region;
• the letter P generally represents said first nucleic acid, P.sup.1 represents said first section, P.sup.2 represents said second section, P.sup.3 represents said inhibitory element, and P.sup.4 represents the terminal nucleotide of P.sup.1 ;
• the letter R generally represents said second nucleic acid, R.sup.1 represents a first area of said second nucleic acid that is capable of forming a ribozyme with P.sup.2 of said first nucleic acid, R.sup.2 represents a terminal nucleotide of R.sup.1 or a second area of said second nucleic acid that is capable of assuming a bound position with said target;
• and at least one of R.sup.1, R.sup.2, P.sup.2, and P.sup.3 is capable of assuming a bound position with said target;
• wherein P.sup.2 comprises the sequence 5'-K'UWJ-3' (SEQ ID NO:49), where W is either C or U, R.sup.1 and X.sup.1 are not the same sequence and are selected from the group of sequences 5'-MGAAAK-3' (SEQ ID NO:2) and 5'-J'CUGANGAM'-3' (SEQ ID NO:3);
• wherein N is one of the nucleotides U, G, A, and C;
• and the letters J, J', K, K', M, and M' each represent a group of four or more nucleotides, wherein J and J' are complementary to each other, K and K' are complementary to each other, and M and M' are complementary to each other.

A composition comprising first and second nucleic acids;

• said first nucleic acid comprising a first section and a second section, each of said sections having a 5' and a 3' end, and said first nucleic acid being associated with an inhibitory element;
• said first section comprising a nucleotide sequence substantially identical to MDV-1, said nucleotide sequence being capable of autocatalytic replication under reaction conditions, but incapable of autocatalytic replication while associated with said inhibitory element;
• said second section being positioned at one end of said first section and being capable of assuming a bound position with a target, said second section comprising a cleavage site at which said first section is separated from said inhibitory element activation of a ribozyme formed by said first and second nucleic acids in the presence of said target;
• said inhibitory element being positioned at the end of said second section opposite to that of said first section;
• said first and second nucleic acids forming said ribozyme with said target, said ribozyme being of the formula and structure set forth below:
• ##STR7## wherein the letter X generally represents said target, X.sup.1 represents a first target region, X.sup.2 represents a terminal nucleotide of X.sup.1 or a second target region, and X.sup.3 represents a terminal nucleotide of X.sup.1 or a third target region;
• the letter P generally represents said first nucleic acid, P.sup.1 represents said first section, P.sup.2 represents said second section, P.sup.3 represents said inhibitory element, and P.sup.4 represents a fourth section of said first nucleic acid capable of contributing nucleotides to the formation of a ribozyme;
• the letter R generally represents said second nucleic acid, R.sup.1 represents a first area of said second nucleic acid that is capable of forming a ribozyme with P.sup.2, and R.sup.2 represents a terminal nucleotide of R.sup.1 or a second area of said second nucleic acid that is capable of assuming a bound position with said target;
• and at least one of R.sup.1, R.sup.2, P.sup.2, and P.sup.3 is capable of assuming a bound position with said target at X.sup.1 , X.sup.2, or X.sup.3 ;
• wherein P.sup.2 comprises the sequence 5'-K'UWJ-3' (SEQ ID NO:49), W is either C or U, R.sup.1 and P.sup.4 are not the same sequence and are selected from the group of sequences 5'-MGAAAK-3' (SEQ ID NO:2) and 5'-J' CUGANGAM'-3' (SEQ ID NO:3);
• N is one of the nucleotides U, G, A, and C;
• and the letters J, J', K, K', M, and M' each represent a group of four or more nucleotides, wherein J and J' are complementary to each other, K and K' are complementary to each other, and M and M' are complementary to each other.

A composition comprising first and second nucleic acids;

• said first nucleic acid comprising a first section and a second section, each of said sections having a 5' and a 3' end, said first nucleic acid being associated with an inhibitory element;
• said first section comprising a nucleotide sequence substantially identical to MDV-1, said nucleotide sequence being capable of autocatalytic replication under reaction conditions, but incapable of autocatalytic replication while associated with said inhibitory element;
• said second section being positioned at one end of said first section and being capable of assuming a bound position with a target, said second section comprising a cleavage site at which said first nucleic acid is separated from said inhibitory element upon activation of a ribozyme formed by said first and second nucleic acids in the presence of said target;
• said inhibitory element being positioned at the end of said second section opposite to that of said first section;
• said first and second nucleic acids forming said ribozyme with said target, said ribozyme being of the formula and structure set forth below:
• ##STR8## wherein the letter X generally represents said target, X.sup.1 represents a first target region, X.sup.2 represents a terminal nucleotide of X.sup.1 or a second target region, and X.sup.3 represents a terminal nucleotide of X.sup.1 or a third target region;
• the letter P generally represents said first nucleic acid, P.sup.1 represents said first section, P.sup.2 represents said second section, P.sup.3 represents said inhibitory element, and P.sup.4 represents a terminal nucleotide of P.sup.1 or a fourth section of said first nucleic acid that is capable of contributing sequences to the formation of said ribozyme;
• the letter R generally represents said second nucleic acid, R.sup.1 represents a first area of said second nucleic acid that is capable of forming a ribozyme with P.sup.2, and R.sup.2 represents a terminal nucleotide of R.sup.1 or a second area of said second nucleic acid that is capable of assuming a bound position with said target;
• and at least one of R.sup.1, R.sup.2, P.sup.2, and P.sup.3 is capable of assuming a bound position with said target at X.sup.1, X.sup.2, and X.sup.3 ;
• wherein P.sup.2 comprises the sequence 5'-FNGUCQ-3' (SEQ ID NO:5), the letter N represents any one of the four nucleotides A, G, U, and C, and R.sup.1 comprises the sequence 5'-Q'AGAAF'ACCAGAGAAACACACGUUG UGGUAUAUUACCUGGUA-3' (SEQ ID NO:6);
• and the letters Q, Q', F, and F' each represent a group of four or more nucleotides, wherein Q and Q' are complementary to each other and F and F' are complementary to each other.