Complex formation between dsDNA and oligomer of cyclic heterocycles
First Claim
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1. A cell comprising dsDNA to which is bound in the minor groove at a target site from 1 to 2 oligomers, where the oligomers are selected to provide specific binding to said dsDNA at said target site,each of said oligomers comprising organic cyclic groups of from 5 to 6 annular members, where at least 60% of the groups are heterocycles having from 1 to 3 heteroatoms, where the heteroatoms are nitrogen, oxygen and sulfur, and wherein at least 60% of the heterocycles have at least one nitrogen atom, and said heterocycles are linked by chains of 2 atoms, wherein at least some of the chains have NH,wherein at least one of said oligomers has at least 7 of said nitrogen containing heterocycles, where at least one of said heterocycles is specific for A, G, C or T, and a pair of heterocycles refers to two heterocycles paired to a complementary pair of nucleotides in said dsDNA,each oligomer comprising at least two units of 2 consecutive heterocycles which form, at the target sites, intramolecular pairs of heterocycles with itself or intermolecular pairs of heterocycles with another oligomer,where when an oligomer forms intramolecular pairs, said oligomer comprises an internal molecule which shifts the spacing of the heterocycles or forms a hairpin turn, andwhen two oligomers form intermolecular pairs, each oligomer comprises an internal aliphatic amino acid of from 2 to 6 carbon atoms, where said internal aliphatic amino acid is paired with an A or T;
- andeach of said oligomers comprising at at least one terminus, an aliphatic amino acid of from 2 to 6 carbon atoms or an alkyl chain comprising a polar group 2 to 4 carbon atoms from the bond linking said alkyl chain to the remainder of each oligomer,where each oligomer has one or more hydrogen atoms away from the surface of said minor groove which may be substituted, wherein the total number of carbon atoms of substituents is not more than 100 carbon atoms.
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Abstract
Methods and compositions are provided for forming complexes intracellularly between dsDNA and oligomers of heterocycles, aliphatic amino acids, particularly omega-amino acids, and a polar end group. By appropriate choice of target sequences and composition of the oligomers, complexes are obtained with low dissociation constants. The formation of complexes can be used for modifying the phenotype of cells, either prokaryotic or eukaryotic, for research and therapy.
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Citations
53 Claims
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1. A cell comprising dsDNA to which is bound in the minor groove at a target site from 1 to 2 oligomers, where the oligomers are selected to provide specific binding to said dsDNA at said target site,
each of said oligomers comprising organic cyclic groups of from 5 to 6 annular members, where at least 60% of the groups are heterocycles having from 1 to 3 heteroatoms, where the heteroatoms are nitrogen, oxygen and sulfur, and wherein at least 60% of the heterocycles have at least one nitrogen atom, and said heterocycles are linked by chains of 2 atoms, wherein at least some of the chains have NH, wherein at least one of said oligomers has at least 7 of said nitrogen containing heterocycles, where at least one of said heterocycles is specific for A, G, C or T, and a pair of heterocycles refers to two heterocycles paired to a complementary pair of nucleotides in said dsDNA, each oligomer comprising at least two units of 2 consecutive heterocycles which form, at the target sites, intramolecular pairs of heterocycles with itself or intermolecular pairs of heterocycles with another oligomer, where when an oligomer forms intramolecular pairs, said oligomer comprises an internal molecule which shifts the spacing of the heterocycles or forms a hairpin turn, and when two oligomers form intermolecular pairs, each oligomer comprises an internal aliphatic amino acid of from 2 to 6 carbon atoms, where said internal aliphatic amino acid is paired with an A or T; - and
each of said oligomers comprising at at least one terminus, an aliphatic amino acid of from 2 to 6 carbon atoms or an alkyl chain comprising a polar group 2 to 4 carbon atoms from the bond linking said alkyl chain to the remainder of each oligomer, where each oligomer has one or more hydrogen atoms away from the surface of said minor groove which may be substituted, wherein the total number of carbon atoms of substituents is not more than 100 carbon atoms. - View Dependent Claims (2, 11)
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3. A cell comprising dsDNA to which is bound in the minor groove at a target site from 1 to 2 oligomers of N-heterocycles consisting of N-methyl pyrrole (Py) and N-methyl imidazole (Im), where the oligomers are selected to provide specific binding to said dsDNA at said target site,
wherein at least one of said oligomers comprises at least 7 said heterocycles, where the pairing of heterocycles in relation to said target dsDNA is defined as Im/Py to G/C, Py/Im to C/G, and Py/Py to A/T and T/A and a pair of heterocycles refers to two heterocycles that are paired to a complementary pair of nucleotides in said dsDNA, and said heterocycles are linked by chains of 2 atoms, wherein at least some of the chains have NH, each oligomer comprising at least two units of consecutive heterocycles which form, at target sites, intramolecular pairs of heterocycles with itself or intermolecular pairs of heterocycles with another oligomer, where when an oligomer forms intramolecular pairs, said oligomer comprises an internal molecule γ - -aminobutyric acid, and
when two oligomers form intermolecular pairs, each oligomer comprises an internal β
-alanine, said internal β
-alanine is paired with an A or T;where each oligomer terminates, at one or both termini, in a glycine or β
-alanine amino acid joined to an alkyl chain of from 2 to 4 carbon atoms comprising a polar group, with the proviso that a γ
-aminobutyric acid may join the termini to circularize an oligomer,where each oligomer has one or more hydrogen atoms away from the surface of said minor groove which may be substituted, wherein the total number of carbon atoms of substituents is not more than 30 carbon atoms. - View Dependent Claims (4, 5, 6, 7, 8, 9, 10, 12)
- -aminobutyric acid, and
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13. A cell comprising dsDNA to which is bound in the minor groove at a target site from 1 to 2 oligomers of N-heterocycles consisting of N-methyl pyrrole (Py) and N-methyl imidazole (Im), where the oligomers are selected to provide specific binding to said dsDNA at said target site,
wherein each of said oligomers is of not more than 5 kD and at least one oligomer comprises at least 7 said heterocycles, where the pairing of heterocycles in relation to said target dsDNA is defined as Im/Py to G/C, Py/Im to C/G, and Py/Py to A/T and T/A and a pair of heterocycles refers to two heterocycles that are paired to a complementary pair of nucleotides in said dsDNA, and said heterocycles are linked by chains of 2 atoms, wherein at least some of the chains have NH, each oligomer comprising at least two units of consecutive heterocycles which form, at target sites, intramolecular pairs with itself or intermolecular pairs with another oligomer, where when an oligomer forms intramolecular pairs, said oligomer comprises an internal molecule γ - -aminobutyric acid, and
when two oligomers form intermolecular pairs, each oligomer comprises an internal β
-alanine, said internal β
-alanine is paired with an A or T;where each oligomer terminates, at one or both termini, in a glycine or β
-alanine amino acid joined to an alkyl chain of from 2 to 4 carbon atoms comprising a polar group, with the proviso that a γ
-aminobutyric acid may join the termini to circularize an oligomer andwhere each oligomer has one or more hydrogen atoms away from the surface of said minor groove which may be substituted, wherein the total number of carbon atoms of substituents is not more than 30 carbon atoms. - View Dependent Claims (14, 15, 16, 42, 43, 44, 45, 46)
- -aminobutyric acid, and
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17. A cell comprising dsDNA to which is bound in the minor groove at a target site an oligomer of N-heterocycles consisting of N-methyl pyrrole (Py) and N-methyl imidazole (Im), where said oligomer is selected to provide specific binding to said dsDNA at said target site, at a Ka of not less than about 109 M-1, wherein said oligomer is of not greater than about 5 kD and comprises at least 7 said heterocycles, where the pairing of heterocycles in relation to said target dsDNA is defined as Im/Py to G/C, Py/Im to C/G, and Py/Py to A/T and T/A and a pair of heterocycles refers to two heterocycles that are paired to a complementary pair of nucleotides in said dsDNA, and said heterocycles are linked by chains of 2 atoms, wherein at least some of the chains have NH,
said oligomer comprising at least two units of consecutive heterocycles which form intramolecular pairs, said oligomer comprising an internal molecule γ - -aminobutyric acid between said two units, and a unit of 6 N-heterocycles comprises an internal β
-alanine, said internal β
-alanine is paired with A and T,said oligomer terminating, at one or both termini, in a glycine or β
-alanine amino acid joined to an alkyl chain of from 2 to 4 carbon atoms comprising a polar group, andwhere said oligomer has one or more hydrogen atoms away from the surface of said minor groove which may be substituted, wherein the total number of carbon atoms of substituents is not more than 30 carbon atoms. - View Dependent Claims (18, 19, 21)
- -aminobutyric acid between said two units, and a unit of 6 N-heterocycles comprises an internal β
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20. A cell comprising dsDNA to which is bound in the minor groove at a target site a pair of oligomers of N-heterocycles consisting of N-methyl pyrrole (Py) and N-methyl imidazole (Im), where the oligomers are selected to provide specific binding to said dsDNA at said target site of a Ka of not less than about 109 M-1,
wherein each of said oligomers is of not greater than about 5 kD and comprises at least 6 said heterocycles, where the pairing of heterocycles in relation to said target dsDNA is defined as Im/Py to G/C, Py/Im to C/G, and Py/Py to A/T and T/A and a pair of heterocycles refers to two heterocycles that are paired to a complementary pair of nucleotides in said dsDNA, and said heterocycles are linked by chains of 2 atoms, wherein at least some of the chains have NH, each of said oligomers comprising at least one unit of 3 consecutive heterocycles which form intermolecular pairs with the other oligomer of the pair of oligomers, each of said oligomers comprises an internal β - -alanine, said internal β
-alanine is paired with an A or T;each oligomer terminating, at one or both termini, in a glycine or β
-alanine amino acid joined to an alkyl chain of from 2 to 4 carbon atoms comprising a polar group, andwhere each oligomer has one or more hydrogen atoms away from the surface of said minor groove which may be substituted, wherein the total number of carbon atoms of substituents is not more than 30 carbon atoms. - View Dependent Claims (41)
- -alanine, said internal β
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22. A method for reducing transcription of a gene in a cell, said method comprising:
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bringing together a cell and oligomers selected to provide specific binding either singly or in pairs to dsDNA at a target site in the minor groove at said target site, each of said oligomers comprising organic cyclic groups of from 5 to 6 annular members, where at least 60% of the groups are heterocycles having from 1 to 3 heteroatoms, where the heteroatoms are nitrogen, oxygen and sulfur, and wherein at least 60% of the heterocycles have at least one nitrogen atom, and said heterocycles are linked by chains of 2 atoms, wherein at least some of the chains have NH, wherein at least one of said oligomers has at least 7 of said nitrogen containing heterocycles, where at least one of said heterocycles is specific for A, G, C or T, and a pair of heterocycles refers to two heterocycles paired to a complementary pair of nucleotides in said dsDNA, each oligomer comprising at least two units of 2 consecutive heterocycles which form, at the target sites, intramolecular pairs of heterocycles with itself or intermolecular pairs of heterocycles with another oligomer, where when an oligomer forms intramolecular pairs, said oligomer comprises an internal molecule which shifts the spacing of the heterocycles or forms a hairpin turn, and when two oligomers form intermolecular pairs, each oligomer comprises an internal aliphatic amino acid of from 2 to 6 carbon atoms, where said internal aliphatic amino acid is paired with an A or T; and each of said oligomers comprising at at least one terminus, an aliphatic amino acid of from 2 to 6 carbon atoms or an alkyl chain comprising a polar group 2 to 4 carbon atoms from the bond linking said alkyl chain to the remainder of each oligomer, where each oligomer has one or more hydrogen atoms away from the surface of said minor groove which may be substituted, wherein the total number of carbon atoms of substituents is not more than 100 carbon atoms; whereby said oligomers bind to said target dsDNA and reduce the level of transcription. - View Dependent Claims (23, 24, 25, 26, 27, 47)
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28. A method for reducing transcription of a gene in a cell, said method comprising:
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bringing together said cell and oligomers of N-heterocycles consisting of N-methyl pyrrole (Py) and N-methyl imidazole (Im), where the oligomers are selected to provide specific binding either singly or in pairs to dsDNA in said cell in the minor groove of said dsDNA at a target site, wherein each of said oligomers comprises at least 6 said heterocycles, where the pairing of heterocycles in relation to said target dsDNA is defined as Im/Py to G/C, Py/Im to C/G, and Py/Py to A/T and T/A and a pair of heterocycles refers to two heterocycles that are paired to a complementary pair of nucleotides in said dsDNA, and said heterocycles are linked by chains of 2 atoms, wherein at least some of the chains have NH, each oligomer comprising at least two units of consecutive heterocycles which form, at target sites, intramolecular pairs of heterocycles with itself or intermolecular pairs of heterocycles with another oligomer, where when an oligomer forms intramolecular pairs, said oligomer comprises an internal molecule γ
-aminobutyric acid, andwhen two oligomers form intermolecular pairs, each oligomer comprises an internal β
-alanine, said internal β
-alanine is paired with an A or T;where each oligomer terminates, at one or both termini, in a glycine or β
-alanine amino acid joined to an alkyl chain of from 2 to 4 carbon atoms comprising a polar group, with the proviso that a γ
-aminobutyric acid may join the termini to circularize an oligomer,where each oligomer has one or more hydrogen atoms away from the surface of said minor groove which may be substituted, wherein the total number of carbon atoms of substituents is not more than 30 carbon atoms; whereby said oligomers bind to said target dsDNA and reduce the level of transcription. - View Dependent Claims (29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 48, 49, 50, 51)
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40. A method for inhibiting proliferation of cells in a mammalian host, said method comprising:
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administering a proliferation inhibiting amount of oligomers of N-heterocycles consisting of N-methyl pyrrole (Py) and N-methyl imidazole (Im), where the oligomers are selected to provide specific binding either singly or in pairs to dsDNA in the minor groove of said dsDNA at a target site, wherein each of said oligomers comprises at least 6 said heterocycles, where the pairing of heterocycles in relation to said target dsDNA is defined as Im/Py to G/C, Py/Im to C/G, and Py/Py to A/T and T/A and a pair of heterocycles refers to two heterocycles that are paired to a complementary pair of nucleotides in said dsDNA, and said heterocycles are linked by chains of 2 atoms, wherein at least some of the chains have NH, each oligomer comprising at least two units of consecutive heterocycles which form, at target sites, intramolecular pairs of heterocycles with itself or intermolecular pairs of heterocycles with another oligomer, where when an oligomer forms intramolecular pairs, said oligomer comprises an internal molecule γ
-aminobutyric acid, andwhen two oligomers form intermolecular pairs, each oligomer comprises an internal β
-alanine, said internal β
-alanine is paired with an A or T;where each oligomer terminates, at one or both termini, in a glycine or β
-alanine amino acid joined to an alkyl chain of from 2 to 4 carbon atoms comprising a polar group, with the proviso that a γ
-aminobutyric acid may join the termini to circularize an oligomer,where each oligomer has one or more hydrogen atoms away from the surface of said minor groove which may be substituted, wherein the total number of carbon atoms of substituents is not more than 30 carbon atoms, wherein said target dsDNA is a gene essential for proliferation of said cells; and said 1 to 2 oligomers bind to said target site, inhibiting transcription of said gene and reducing the proliferation of said cells. - View Dependent Claims (52, 53)
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Current AssigneeCalifornia Institute of Technology, The Scripps Research Institute
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Original AssigneeCalifornia Institute of Technology, The Scripps Research Institute
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InventorsDervan, Peter B., Gottesfeld, Joel M.
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Primary Examiner(s)Houtteman, Scott W.
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Application NumberUS08/853,525Time in Patent Office943 DaysField of Search435/6, 536/24.3, 536/24.5US Class Current435/6.12CPC Class CodesA61K 38/00 Medicinal preparations cont...A61K 47/645 Polycationic or polyanionic...A61P 35/00 Antineoplastic agentsC07D 207/34 with hetero atoms or with c...C07D 233/90 Carbon atoms having three b...C07D 403/14 containing three or more he...C07K 7/02 Linear peptides containing ...C12N 15/63 Introduction of foreign gen...
