Method for stabilizing DNA aptamers
An object of the present invention is to provide a convenient and low-cost method for enhancing the stability of a DNA aptamer and/or its capacity to bind to a target molecule, and a DNA aptamer obtained by the method. The object is solved by substituting an internal hairpin structure (stem-loop structure) of the DNA aptamer with a structure called mini-hairpin structure and optionally increasing GC pairs in a stem portion of the DNA aptamer.
1. A method for producing a DNA aptamer being stabilized and/or having enhanced capacity to bind to a target molecule, comprising the steps of:
designing a base sequence of a DNA aptamer in accordance with a method for designing a base sequence that enhances the capacity of an existing DNA aptamer to bind to a target molecule and/or stabilizes the aptamer; and
producing a DNA aptamer on the basis of the designed base sequence,
wherein the method for designing a base sequence comprises
substituting a hairpin structure consisting of one pair of stem structure and loop structure of the DNA aptamer comprising at least one stem structure and at least one loop structure with a mini-hairpin structure, wherein the stem structure is formed by base pairing of 2 or more consecutive bases constituting one strand with bases constituting another strand,
wherein the mini-hairpin structure comprises:
nucleic acid regions (A) to (C) below sequentially ligated from the 5′ end toward the 3′ end:
(A) a first nucleic acid region comprising 2 to 5 arbitrary nucleotides;
(B) a second nucleic acid region comprising a “gna” or “gnna” base sequence wherein each “n” independently represents either “g”, “t”, “a”, or “c”, a base analogue, or a modified base; and
(C) a third nucleic acid region comprising a base sequence complementary to the first nucleic acid region,
wherein the first nucleic acid region and the third nucleic acid region form a stem portion by base pairing with each other and the second nucleic acid region forms a loop portion.
2. The method according to claim 1 , wherein the DNA aptamer comprises at least one base analogue and/or modified base.
3. The method according to claim 2 , wherein the base analogue is 7-(2-thienyl)-3H-imidazo[4,5-b]pyridin-3-yl.
4. The method according to claim 1 , comprising increasing one or more GC pairs in a stem structure other than that constituting the mini-hairpin.
5. The method according to claim 1 , wherein the DNA aptamer comprises one of the at least one stem structure at the 5′ and/or 3′ ends thereof, wherein the method comprises increasing one to five GC pairs in the 5′ and/or 3′ ends of the DNA aptamer.
6. The method according to claim 1 , comprising adding a further mini-hairpin structure as defined in claim 1 to one end of the DNA aptamer.
7. The method according to claim 1 , wherein the difference in nucleotide length between the hairpin structure to be substituted and the mini-hairpin structure after the substitution is 3, 2, 1, or 0.