Methods for purifying annealed double-stranded oligonucleotides lacking base pair mismatches or nucleotide gaps

A method for purifying double-stranded polynucleotides lacking base pair mismatches, insertion/deletion loops and/or a nucleotide gap or gaps comprising the following steps:

• (a) providing a plurality of polypeptides that specifically bind to a base pair mismatch, an insertion/deletion loop and/or a nucleotide gap or gaps within a double-stranded polynucleotide;
• (b) providing a sample comprising a plurality of double-stranded polynucleotides encoding a fusion protein comprising a polypeptide of interest upstream of an intein, wherein the intein encodes a polypeptide;
• (c) contacting the double-stranded polynucleotides of step (b) with the polypeptides of step (a) under conditions wherein a polypeptide of step (a) can specifically bind to a base pair mismatch, an insertion/deletion loop and/or a nucleotide gap or gaps in a double-stranded polynucleotide of step (b);
• and
• (d) separating the double-stranded polynucleotides lacking a specifically bound polypeptide of step (a) from the double-stranded polynucleotides to which a polypeptide of step (a) has specifically bound, thereby purifying double-stranded polynucleotides lacking base pair mismatches, insertion/deletion loops and/or a nucleotide gap or gaps.

A method for purifying double-stranded polynucleotides lacking base pair mismatches, insertion/deletion loops and/or a nucleotide gap or gaps comprising:

• (a) providing a plurality of polypeptides that specifically bind to a base pair mismatch, an insertion/deletion loop and/or a nucleotide gap or gaps within a double stranded polynucleotide;
• (b) providing a sample comprising a plurality of double-stranded polynucleotides encoding a fusion protein comprising a polypeptide of interest and an intein, wherein the intein encodes a polypeptide;
• (c) contacting the double-stranded polynucleotides of (b) with the polypeptides of (a) under conditions wherein a polypeptide of (a) can specifically bind to a base pair mismatch, an insertion/deletion loop and/or a nucleotide gap or gaps in a double stranded polynucleotide of (b);
• and
• (d) separating the double-stranded polynucleotides lacking a specifically bound polypeptide of (a) from the double-stranded polynucleotides to which a polypeptide of (a) has specifically bound, thereby purifying double-stranded polynucleotides lacking base pair mismatches, insertion/deletion loops and/or a nucleotide gap or gaps.