Compounds, compositions, and methods for isolation of nucleic acids
Provided herein are compounds, compositions, and methods for rapid isolation of nucleic acids from a sample.
1 . A composition comprising:
a solid surface;
a linker covalently attached to the solid surface, wherein the linker has a structure:
—(CH 2 ) n1 —Z—(CH 2 ) n2 —
wherein n1 and n2 are each independently selected from 1, 2, 3, 4, 5, 6, 7, and 8, and Z is selected from —NHC(O)NH—, —C(O)NH—, —OC(O)NH—, —OC(O)O—, —NHC(O)S—, —NHC(S)NH—, and —O—, and —C(O)O—; and
a moiety of formula (I) covalently attached to the linker:
wherein:
X is selected from O, S, S(O), and S(O) 2 ;
R 1 , R 2 , R 3 , R 4 , R 5 , R 6 , R 7 , and R 8 are each independently selected from hydrogen, C 1 -C 6 alkyl, C 2 -C 6 alkenyl, C 2 -C 6 alkynyl, C 1 -C 6 haloalkyl, C 3 -C 6 cycloalkyl, aryl, heteroaryl, heterocyclyl, halo, cyano, nitro, —OR a , —SR b , —C(O)OR c , —C(O)NR d R e , —OC(O)NR f R g , —NR h C(O)NR i R j , and —NR h C(S)NR i R j , wherein each R a , R b , R c , R d , R e , R f , R g , R h , R i , and R j is independently selected from hydrogen, C 1 -C 6 alkyl, C 2 -C 6 alkenyl, C 2 -C 6 alkynyl, C 1 -C 6 haloalkyl, C 3 -C 6 cycloalkyl, and aryl.
2 . The composition of claim 1 , wherein the solid surface comprises a material selected from silica, glass, a polymer, and a metal.
3 . The composition of claim 1 , wherein the solid surface comprises a polymer selected from cellulose, cellulose acetate, nitrocellulose, nylon, a polyester, a polyethylene, a polyethersulfone, a polyolefin, polyvinylidene fluoride, a polyacrylate, a polystyrene, or any combination thereof.
4 . The composition of claim 1 , wherein the solid surface is in the form of a bead, a resin, a magnetic particle, a membrane, a vial, a plate, a film, a tube, a syringe, a cartridge, a cassette, a pipette tip, a microfluidic cartridge, or a cuvette.
5 . The composition of claim 1 , wherein the linker is selected from:
6 . The composition of claim 5 , wherein the linker is:
7 . The composition of claim 1 , wherein X is O.
8 . The composition of claim 1 , wherein R 1 , R 2 , R 3 , R 4 , R 5 , R 6 , R 7 , and R 8 are each hydrogen.
9 . The composition of claim 1 , wherein the solid surface further comprises one or more additional moieties covalently bound to the surface.
10 . The composition of claim 1 , wherein the solid surface further comprises at least one polyethylene glycol (PEG) moiety covalently bound to the surface.
11 . The composition of claim 1 , wherein X is O, and wherein R 1 , R 2 , R 3 , R 4 , R 5 , R 6 , R 7 , and R 8 are each hydrogen.
12 . A method of isolating a nucleic acid from a sample, comprising:
(a) providing a sample containing a nucleic acid;
(b) contacting the sample with a composition comprising:
a solid surface;
a linker covalently attached to the solid surface, wherein the linker has a structure:
—(CH 2 ) n1 —Z—(CH 2 ) n2 —
wherein n1 and n2 are each independently selected from 1, 2, 3, 4, 5, 6, 7, and 8, and Z is selected from —NHC(O)NH—, —C(O)NH—, —OC(O)NH—, —OC(O)O—, —NHC(O)S—, —NHC(S)NH—, —O—, and —C(O)O—; and
a moiety of formula (I) covalently attached to the linker:
wherein:
X is selected from O, S, S(O), and S(O) 2 ; and
R 1 , R 2 , R 3 , R 4 , R 5 , R 6 , R 7 , and R 8 are each independently selected from hydrogen, C 1 -C 6 alkyl, C 2 -C 6 alkenyl, C 2 -C 6 alkynyl, C 1 -C 6 haloalkyl, C 3 -C 6 cycloalkyl, aryl, heteroaryl, heterocyclyl, halo, cyano, nitro, —OR a , —SR b , —C(O)OR c , —C(O)NR d R e , —OC(O)NR f R g , —NR h C(O)NR i R j , and —NR h C(S)NR i R j , wherein each R a , R b , R c , R d , R e , R f , R g , R h , R i , and R j is independently selected from hydrogen, C 1 -C 6 alkyl, C 2 -C 6 alkenyl, C 2 -C 6 alkynyl, C 1 -C 6 haloalkyl, C 3 -C 6 cycloalkyl, and aryl;
at a pH of less than about 8.0, wherein the nucleic acid binds to the composition to provide a nucleic acid bound composition; and
(c) separating the nucleic acid bound composition from the sample.
13 . The method of claim 12 , wherein step (b) is conducted at a pH of about 2.0 to less than about 8.0.
14 . The method of claim 12 , wherein step (b) comprises contacting the sample with the composition for about 10 seconds to about 10 minutes.
15 . The method of claim 12 , further comprising one or more steps of washing the nucleic acid bound composition after step (c) by contacting the composition with a wash solution having a pH of less than about 8.0.
16 . The method of claim 12 , further comprising a step of contacting the nucleic acid bound composition with an elution solution at a pH of about 8.5 or higher, to release the nucleic acid from the composition.
17 . The method of claim 12 , wherein the nucleic acid is DNA, and the DNA is selected from total DNA, mtDNA (mitochondrial DNA), gDNA (genomic DNA), cfDNA (cell-free DNA), ccfDNA (circulating cell-free DNA), cffDNA (cell free fetal DNA), bacterial DNA, viral DNA, and ctDNA (circulating tumor DNA).
18 . The method of claim 12 , wherein the nucleic acid is RNA, and the RNA is selected from total RNA, miRNA, mRNA, tRNA, rRNA, siRNA, ctRNA (circulating tumor RNA), and viral RNA.
19 . A compound of formula (IIa):
or a salt thereof, wherein:
X is selected from O, S, S(O), and S(O) 2 ;
L is a linker, wherein the linker has a structure:
—(CH 2 ) n1 —Z—(CH 2 ) n2 —
wherein n1 and n2 are each independently selected from 1, 2, 3, 4, 5, 6, 7, and 8, and Z is selected from —NHC(O)NH—, —C(O)NH—, —OC(O)NH—, —OC(O)O—, —NHC(O)S—, —NHC(S) NH—, —O—, and —C(O)O—;
each R a is independently selected from hydroxy, C 1 -C 6 alkoxy, and halo; and
R 1 , R 2 , R 3 , R 4 , R 5 , R 6 , R 7 , and R 8 are each independently selected from hydrogen, C 1 -C 6 alkyl, C 2 -C 6 alkenyl, C 2 -C 6 alkynyl, C 1 -C 6 haloalkyl, C 3 -C 6 cycloalkyl, aryl, heteroaryl, heterocyclyl, halo, cyano, nitro, —OR a , —SR b , —C(O)OR c , —C(O)NR d R e , —OC(O)NR f R g , NR h C(O)NR i R j , and —NR h C(S)NR i R j , wherein each R a , R b , R c , R d , R e , R f , R g , R h , R i , and R j is independently selected from hydrogen, C 1 -C 6 alkyl, C 2 -C 6 alkenyl, C 2 -C 6 alkynyl, C 1 -C 6 haloalkyl, C 3 -C 6 cycloalkyl, and aryl.
20 . The compound of claim 19 , wherein the compound is:
or a salt thereof.