Design, synthesis and use of specific polyamide DNA-binding ligands

A method for designing a specific polyamide

• X1X2 . . . Xm-γ-X(m+1) . . . X(2m−1)X2m-R1
• wherein
• X1, X2, Xm, X(m+1), X(2m−1), and X2m are carboxamide residues forming carboxamide binding pairs X1/X2m, X2/X(2m−1), Xm/X(m+1), and wherein one carboxamide binding pair is substituted with a β/β, wherein β is β-alanine;
• γ is γ-aminobutyric acid or 2,4 diaminobutyric acid, and
• R1 is —NH(CH2)0-100NR2R3, —NH(CH2)0-12CONH(CH2)0-100NR2R3, or —NHR2, where R2 and R3 are independently selected from the group consisting of H, Cl, NO, N-acetyl, benzyl, C1-100 alkyl, C1-100 alkylamine, C1-100 alkyldiamine, C1-100 alkylcarboxylate, C1-100 alkenyl, a C1-100 alkynyl, and C1-100 alkyl-L, where L is selected from the group consisting of arylboronic acids, biotins, polyhistidines comprised from about 2 to 8 amino acids, haptens, solid phase supports, oligodeoxynucleotides, N-ethylnitrosourea, fluorescein, bromoacetamide, iodoacetamide, DL-α-lipoic acid, acridine, captothesin, pyrene, mitomycin, texas red, anthracene, anthrinilic acid, avidin, DAPI, and oligodeoxynucleotide, isosulfan blue, malachite green, psoralen, ethyl red, 4-(psoraen-8-yloxy)-butyrate, tartaric acid, and (+)-α-tocopheral, suitable for use as a DNA-binding ligand that is selective for identified target DNA-sequences 5′-WN1N2 . . . NmW-3′ where m is an integer having a value from 3 to 6, the method comprising:
• (a) identifying a target sequence of double stranded DNA having the form 5′WN1N2 . . . NmW-3′, N1N2 . . . Nm being the sequence to be bound by carboxamide residues, wherein each N is independently chosen from the group A, G, C, and T, each W is independently chosen from the group A and T, and m is an integer having a value from 3 to 6;
• (b) representing the identified sequence as 5′-Wab . . . xW-3′, wherein a is a first nucleotide to be bound by the X1 carboxamide residue, b is a second nucleotide to be bound by the X2 carboxamide residue, and x is the corresponding nucleotide to be bound by the Xm carboxamide residue;
• (c) defining a as A, G, C, or T to correspond to the first nucleotide to be bound by a carboxamide residue in the identified sequence;
• (d) selecting Im as the X1 carboxamide residue and Py as the X2m carboxamide residue if a=G;
• (e) selecting Py as the X1 carboxamide residue and Im as the X2m carboxamide residue if a=C;
• (f) selecting Hp as the X1 carboxamide residue and Py as the X2m carboxamide residue if a=T;
• (g) selecting Py as the X1 carboxamide residue and Hp as the X2m carboxamide residue if a=A;
• and
• (h) repeating steps c–g for b through x until all carboxamide residues are selected;
• wherein Im is N-methylimidazole, Hp is 3-hydroxy-N-methylpyrrole, Py is N-methylpyrrole, A is adenine, G is guanine, C is cytosine, and T is thymine;
• and
• synthesizing the polyamide.