Polynucleotides containing a morpholino linker

1. A compound, or a salt thereof, including:

a) a polynucleotide; and

b) at least one of a nucleotide, a second polynucleotide, targeting moiety, small molecule, polypeptide, or polymer,

wherein the polynucleotide of a) is conjugated to the nucleotide, second polynucleotide, targeting moiety, small molecule, polypeptide, or polymer via a linker including the structure of Formula I:

wherein B is a nucleobase, hydrogen, halo, hydroxy, thiol, optionally substituted C 1 -C 6 alkyl, optionally substituted C 2 -C 6 alkenyl, optionally substituted C 2 -C 6 alkynyl, optionally substituted C 1 -C 6 heteroalkyl, optionally substituted C 2 -C 6 heteroalkenyl, optionally substituted C 2 -C 6 heteroalkynyl, optionally substituted amino, azido, optionally substituted C 3 -C 10 cycloalkyl, optionally substituted C 6 -C 10 aryl, or optionally substituted C 2 -C 12 heterocycle;

X 1 is O, S, NR U , or C(R U ) 2 , wherein each R U is, independently, H, halo, or optionally substituted C 1 -C 6 alkyl;

X 2 is —O—, —NR N1 —, —NR N1 NR N1 —, a bond, optionally substituted C 1 -C 10 alkylene, optionally substituted C 2 -C 10 alkenylene, optionally substituted C 2 -C 10 alkynylene, optionally substituted C 2 -C 10 heterocyclylene, optionally substituted C 6 -C 12 arylene, optionally substituted C 2 -C 100 polyethylene glycolene, or optionally substituted C 1 -C 30 heteroalkylene, wherein R N1 is H, optionally substituted C 1 -C 6 alkyl, optionally substituted C 2 -C 6 alkenyl, optionally substituted C 2 -C 6 alkynyl, or optionally substituted C 6 -C 10 aryl;

m is 1, 2, 3, 4, or 5;

each L is, independently, an unbranched or branched linker;

R 1 and R 2 are each, independently, hydrogen, hydroxyl, or C 1 -C 6 alkoxy, and

wherein if B is nucleobase, R 1 and R 2 are hydrogen and the linker conjugates the polynucleotide of a) to the second polynucleotide then X 2 -(L) m is not a furanylmethyl moiety, a pyranylmethyl moiety, —P(O)OH—, or —P(O)N(R N ) 2 —, wherein R N is optionally substituted C 1 -C 6 alkyl.

2. The compound of claim 1 , wherein said compound comprises the structure of Formula II:

wherein A 1 is said first polynucleotide and comprises:

(a) at least one 5′-cap structure;

each C 1 independently comprises said second polynucleotide, a targeting moiety, a small molecule, a polypeptide, or a polymer;

L 1 is an unbranched linker;

L 2 is a branched linker;

n is 0, 1, 2, or 3;

o is 0 or 1;

p is 1, 2, 3, 4, or 5;

X 2 —O—, —NR N1 —, —NR N1 NR N1 —, a bond, optionally substituted C 1 -C 10 alkylene, optionally substituted C 2 -C 10 alkenylene, optionally substituted C 2 -C 10 alkynylene, optionally substituted C 2 -C 10 heterocyclylene, optionally substituted C 6 -C 12 arylene, optionally substituted C 2 -C 100 polyethylene glycolene, or optionally substituted C 1 -C 30 heteroalkylene, wherein R N1 is H, optionally substituted C 1 -C 6 alkyl, optionally substituted C 2 -C 6 alkenyl, optionally substituted C 2 -C 6 alkynyl, or optionally substituted C 6 -C 10 aryl;

Y 1 is O, S, Se, optionally substituted C 1 -C 6 alkylene, or optionally substituted C 1 -C 6 heteroalkylene;

each Y 2 and Y 3 is, independently, O, S, Se, —NR N1 —, optionally substituted C 1 -C 6 alkylene, or optionally substituted C 1 -C 6 heteroalkylene, wherein R N1 is H, optionally substituted C 1 -C 6 alkyl, optionally substituted C 2 -C 6 alkenyl, optionally substituted C 2 -C 6 alkynyl, or optionally substituted C 6 -C 10 aryl; and

each Y 4 is, independently, H, hydroxy, protected hydroxy, halo, thiol, boranyl, optionally substituted C 1 -C 6 alkyl, optionally substituted C 2 -C 6 alkenyl, optionally substituted C 2 -C 6 alkynyl, optionally substituted C 1 -C 6 heteroalkyl, optionally substituted C 2 -C 6 heteroalkenyl, optionally substituted C 2 -C 6 heteroalkynyl, or optionally substituted amino,

wherein when Y 2 , Y 3 , and X 1 are each O, R 1 and R 2 are each hydrogen, Y 1 is CH 2 , Y 4 is hydroxy, n is 1, o is 0, p is 1, and C 1 is a polynucleotide, X 2 -L 1 is not —P(O)OH— or —P(O)N(R N ) 2 —, wherein R N is optionally substituted C 1 -C 6 alkyl.

3. The compound of claim 2 , wherein A 1 further comprises:

(b) a 5′-UTR;

(c) a coding region; and

(d) a 3′-UTR.

4. The compound of claim 2 , wherein said compound comprises the structure of Formula III:

wherein q is 0, 1, 2, 3, 4, or 5.

5. The compound of claim 2 , wherein said compound comprises the structure of Formula IV:

or wherein said compound comprises the structure of Formula V:

wherein r and s are each, independently, 1, 2, 3, 4, or 5.

6. The compound of claim 2 , wherein the compound includes the structure of Formula XXII:

7. The compound of claim 2 , wherein L 1 comprises the structure of Formula VI:

wherein a, b, c, e, f, and g are each, independently, 0 or 1;

d is 0, 1, 2, or 3;

each of R 3 , R 5 , R 7 , and R 9 , is, independently, selected from optionally substituted C 1 -C 6 alkylene, optionally substituted C 1 -C 6 heteroalkylene, optionally substituted C 2 -C 100 polyethylene glycolene, O, S, Se, and NR 10 ;

R 4 and R 8 are each, independently, carbonyl, thiocarbonyl, sulfonyl, or phosphoryl;

each R 6 is optionally substituted C 1 -C 10 alkylene, optionally substituted C 2 -C 10 alkenylene, optionally substituted C 2 -C 10 alkynylene, optionally substituted C 2 -C 10 heterocyclylene, optionally substituted C 6 -C 12 arylene, optionally substituted C 2 -C 100 polyethylene glycolene, or optionally substituted C 1 -C 10 heteroalkylene, or a bond linking (R 3 ) a —(R 4 ) b —(R 5 ) c to (R 7 ) e —(R 8 ) f —(R 9 )g; and

R 10 is hydrogen, optionally substituted C 1 -C 4 alkyl, optionally substituted C 2 -C 4 alkenyl, optionally substituted C 2 -C 4 alkynyl, optionally substituted C 2 -C 6 heterocyclyl, optionally substituted C 6 -C 12 aryl, or optionally substituted C 1 -C 7 heteroalkyl.

8. The compound of claim 2 , wherein said compound comprises the structure of Formula VII:

9. The compound of claim 2 , wherein said compound has the structure of Formula VIII:

10. The compound of claim 2 , wherein said compound comprises the structure of Formula IX:

11. The compound of claim 2 , wherein said compound comprises the structure of Formula X:

12. The compound of claim 2 , wherein the compound comprises the structure of Formula XI:

or a salt thereof

wherein t is 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10; and

u is 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10.

13. The compound of claim 2 , wherein the compound comprises the structure of Formula XII:

or a salt thereof,

wherein v is 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10.

14. The compound of claim 2 , wherein the compound comprises the structure of Formula XXIII:

15. The compound of claim 2 , wherein said second polynucleotide comprises the structure:

or a salt thereof;

wherein each X is, independently O or S; and

A represents adenine and T represents thymine.

16. A method of modifying a polynucleotide, said method comprising:

contacting a polynucleotide comprising the structure of Formula XIV:

wherein B is a nucleobase; and

X 1 is O, S, NR U , or C(R U ) 2 , wherein each R U is, independently, H, halo, or optionally substituted C 1 -C 6 alkyl;

with a compound having the structure of Formula XV:

H 2 N—R 11   Formula XV

wherein R 11 is optionally substituted C 1 -C 10 alkyl, optionally substituted C 2 -C 10 alkenyl, optionally substituted C 2 -C 10 alkynyl, optionally substituted C 2 -C 10 heterocyclyl, optionally substituted C 6 -C 12 aryl, optionally substituted C 2 -C 100 polyethylene glycol, optionally substituted C 1 -C 10 alkyl conjugated to a polynucleotide, or optionally substituted C 1 -C 10 heteroalkyl;

under suitable conditions to produce a polynucleotide comprising the structure of Formula I:

17. A method of increasing the expression of a recombinant polypeptide of interest in a cell comprising contacting the cell with a polynucleotide encoding said polypeptide, wherein said polynucleotide is a compound of claim 1 , and wherein expression is increased when compared to the unmodified polynucleotide.

18. A method of increasing the half-life of a polynucleotide in a cell comprising contacting the cell with said polynucleotide, wherein the polynucleotide is a compound of claim 1 , and wherein half-life is increased when compared to the unmodified polynucleotide.

19. The compound of claim 2 , wherein A 1 comprises the structure of Formula XXI:

wherein B is a nucleobase; and

R a is hydrogen or methyl.

20. The compound of claim 1 , wherein the compound has the structure of:

wherein mRNA is an mRNA molecule and L-A is L-adenosine;

or

wherein RNA is an mRNA molecule and tail is 10 consecutive L-adenosines;

or

wherein mRNA is an mRNA molecule.