System and method for propagating information using modified nucleic acids

1. A nucleic acid-based molecular computing system, comprising:

(i) an input nucleic acid strand comprising a first fragment (A) and a second fragment (B);

(ii) a first target, incompletely base-paired nucleic acid duplex comprising a first strand and a second strand,

wherein the first strand comprises a first fragment (B′) and a second fragment (A′), the second strand comprises a first fragment (B) and a second fragment (C) and the first target duplex comprises a duplex region formed by base-pairing between B and B′ and two single-stranded regions, A′ and C, and

wherein A and B of the input strand can bind with A′ and B′ of the first strand of the first target duplex, respectively, under hybridizing conditions to invoke a strand displacement reaction to produce a first output duplex;

(iii) a second target, incompletely base-paired nucleic acid duplex comprising a first strand and a second strand,

wherein the first strand comprises a first fragment (C′) and a second fragment (B′), the second strand comprises a first fragment (C) and a second fragment (D) and the second target duplex comprises a duplex region formed by base-pairing between C and C′ and two single-stranded regions B′ and D,

wherein B and C of the second strand of the first target duplex can bind with B′ and C′ of the first strand of the second target duplex, respectively, under hybridizing conditions to invoke a strand displacement reaction to produce a second output duplex, and

wherein the second fragment (B) of the input strand can bind with the single-stranded region B′ of the second target duplex under hybridizing conditions; and

(iii) a third target, incompletely base-paired nucleic acid duplex comprising a first strand and a second strand,

wherein the first strand comprises a first fragment (D′) and a second fragment (C′), the second strand comprises a first fragment (D) and a second fragment (E) and the third target duplex comprises a duplex region formed by base-pairing between D and D′ and two single-stranded regions C′ and E,

wherein C and D of the second strand of the second target duplex can bind with C′ and D′ of the first strand of the third target duplex, respectively, under hybridizing conditions to invoke a strand displacement reaction to produce a third output duplex, and

wherein the second fragment (C) of the second strand of the first target duplex can bind with the single-stranded region C′ of the third target duplex under hybridizing conditions,

wherein

the first fragment (B) of the second strand of the first target duplex comprises a first chemical modification, relative to a natural nucleic acid, that causes binding with the second fragment (B′) of the first strand of the second target duplex to have a decreased hybridization free energy and/or

the second fragment (B) of the input strand comprises a second chemical modification, relative to a natural nucleic acid, that causes binding with the second fragment (B′) of the first strand of the second target duplex to have an increased hybridization free energy,

such that the first fragment (B) of the second strand of the first target duplex, as compared to the second fragment (B) of the input strand, binds to the second fragment (B′) of the first strand of the second target duplex to form a more stable duplex region; and

wherein

the first fragment (C) of the second strand of the second target duplex comprises a third chemical modification, relative to a natural nucleic acid, that causes binding with the second fragment (C′) of the first strand of the third target duplex to have a decreased hybridization free energy and/or

the second fragment (C) of the second strand of the first target duplex comprises a fourth chemical modification, relative to a natural nucleic acid, that causes binding with the second fragment (C′) of the first strand of the third target duplex to have an increased hybridization free energy,

such that the first fragment (C) of the second strand of the second target duplex, as compared to the second fragment (C) of the second strand of the first target duplex, binds to the second fragment (C′) of the first strand of the third target duplex to form a more stable duplex region.

2. The system of claim 1 , wherein the input strand, the first target duplex, and the second target duplex form part of an enzyme-free, nucleic acid logic gate selected from the group consisting of an AND gate, a NOT gate, an OR gate, a NAND gate, a NOR gate, an XOR gate, and an XNOR gate.

3. The system of claim 1 , wherein the first, the second, the third, or the fourth chemical modification is selected from the group consisting of (i) replacing the sugar-phosphodiester backbone of said nucleosides with a pseudo-peptide backbone, (ii) modifying the sugar moiety of said nucleosides, and (iii) substituting an analogue for the nitrogenous base of at least one of said nucleosides.

4. The system of claim 3 , wherein the first, the second, the third, or the fourth chemical modification comprises replacing the sugar-phosphodiester backbone of said nucleosides with a pseudo-peptide backbone into which a guanidinium functional group is incorporated.

5. The system of claim 4 , wherein the first, the second, the third, or the fourth chemical modification comprises introducing a heteroatom at the 2′-position of said sugar moiety.

6. The system of claim 4 , wherein the first, the second, the third, or the fourth chemical modification comprises substituting a tricyclic cytosine analogue for the nitrogenous base of at least one of said nucleosides.

7. The system of claim 1 , wherein the strand displacement reaction comprises a toe-hold-mediated strand displacement.

8. The system of claim 1 , wherein the first chemical modification is the same as the third chemical modification.

9. The system of claim 1 , wherein the second chemical modification is the same as the fourth chemical modification.