Preparation of oligo conjugates
Conjugated molecules are prepared that comprise a predetermined number of oligo conjugation components. The conjugated molecules also may comprise one or more detectable labels. Preparation of these molecules can be implemented according to an asymmetric or a symmetric conjugation strategy.
1. A method of preparing a compound of the formula
comprising
(i) attaching a conjugation component of the formula
wherein R 2 is R 2a or R 2ap ,
to a solid support
to form a compound of the formula
(ii) when R 2 is R 2ap , converting
(iii) contacting
with a conjugation component of the formula
wherein R 3 is R 3a , or R 3ap ;
to form
(iv) when R 3 is R 3ap , converting
to
and
(v) contacting
with a conjugation component of the formula
to provide the compound of the formula
wherein:
is a solid support material;
are independently an oligo, where each oligo is independently a polymer, having from 2 to about 150 covalently linked monomer units, that is characterized by a sequence of 2′-deoxyribosenucleotide residues (DNA), ribonucleotide residues (RNA), and peptide nucleic acids (PNAs), or a combination thereof;
R 1a and R 1b are complementary conjugation functionalities and L 1 is conjugate linker, and R 1a , R 1b , and L 1 are
(a) R 1a is azido, R 1b is —C≡C—R 23 , and L 1 is
or
(b) R 1a is —NHR 23 , R 1b is carboxy, and L 1 is —NR 23 C(═O)—, or
(c) R 1a is carboxy, R 1b is —NHR 23 , and L 1 is —C(═O)NR 23 —, or
(d) R 1a is —NHR 23 , R 1b is halo, and L 1 is —NR 23 —, or
(e) R 1a is —O—P(═O)(OH)(X), R 1b is hydroxy, and L 1 is —O—P(═O)(OH)—O—, or
(f) R 1a is —O—P(═O)(OH)(X), R 1b is —NHR 23 , and L 1 is —O—P(═O)(OH)—NR 23 —, or
(g) R 1a is —O—P(═O)(OH)(X), R 1b is thio, and L 1 is —O—P(═O)(OH)—S—, or
(h) R 1a is halo, R 1b is thio, and L 1 is —S—, or
(i) R 1a is
R 1b is thio, and L 1 is
or
(j) R 1a is —C≡C—R 23 , R 1b is azido, and L 1 is
or
(k) R 1a is halo, R 1b is —NHR 23 , and L 1 is —NR 23 —, or
(l) R 1a is hydroxy, R 1b is —O—P(═O)(OH)(X), and L 1 is —O—P(═O)(OH)—O—, or
(m) R 1a is —NHR 23 , R 1b is —O—P(═O)(OH)(X), and L 1 is —NR 23 —P(═O)(OH)—O—, or
(n) R 1a is thio, R 1b is —O—P(═O)(OH)(X), and L 1 is —S—P(═O)(OH)—O—, or
(o) R 1a is —O—P(═O)(OH)SH, R 1b is —X, and L 1 is —O—P(═O)(OH)—S—, or
(p) R 1a is —X, R 1b is —O—P(═O)(OH)SH, and L 1 is —S—P(═O)(OH)—O—, or
(q) R 1a is —(CR 25 R 25 ) s C(═O)OR 23 , R 1b is —NHR 23 , L 1 is —(CR 25 R 25 ) s C(═O)NR 23 —, or
(r) R 1a is —NHR 23 , R 1b is —(CR 25 R 25 ) s C(═O)OR 23 , L 1 is —NR 23 C(═O)—(CR 25 R 25 ) s —, or
(s) R 1a is thio, R 1b is halo, and L 1 is —S—, or
(t) R 1a is thio, R 1b is
and L 1 is
(u) R 1a is —SH, R 1b is —O—P(═O)(OH)(O—(CH 2 ) n —SH) and L 1 is —S—S—(CH 2 ) n —O—P(OH)(═O)—O—;
R 2a and R 2b are complementary conjugation functionalities and L 2 is conjugate linker, and R 2ap , R 2a , R 2b , and L 2 are
(a′) R 2ap is halo, R 2a is azido, R 2b is —C≡C—R 23 , and L 2 is
or
(b′) R 2ap is —NR 23 Pr, R 2a is —NHR 23 , R 2b is carboxy, and L 2 is —NR 23 C(═O)—, or
(c′) R 2ap is carboxy ester, R 2a is carboxy, R 2b is —NHR 23 , and L 2 is —C(═O)NR 23 —, or
(d′) R 2ap is —NR 23 Pr, R 2a is —NHR 23 , R 2b is halo, and L 2 is —NR 23 —, or
(e′) R 2ap is —OH, phosphate or phosphate ester, R 2a is —O—P(═O)(OH)(X), R 2b is hydroxy, and L 2 is —O—P(═O)(OH)—O—, or
(f) R 2ap is —OH, phosphate or phosphate ester, R 2a is —O—P(═O)(OH)(X), R 2b is —NHR 23 , and L 2 is —O—P(═O)(OH)—NR 23 —, or
(g′) R 2ap is —OH, phosphate or phosphate ester, R 2a is —O—P(═O)(OH)(X), R 2b is thio, and L 2 is —O—P(═O)(OH)—S—, or
(h′) R 2a is —X, R 2b is thio, and L 2 is —S—, or
(i′) R 2a is
R 2b is thio, and L 2 is
or
(j′) R 2a is —C≡C—R 23 , R 2b is azido, and L 2 is
or
(k′) R 2a is halo, R 2b is —NHR 23 , and L 2 is —NR 23 —, or
(l′) R 2a is hydroxy, R 2b is —O—P(═O)(OH)(X), and L 2 is —O—P(═O)(OH)—O—, or
(m′) R 2a is —NHR 23 , R 2b is —O—P(═O)(OH)(X), and L 2 is —NR 23 —P(═O)(OH)—O—, or
(n′) R 2a is thio, R 2b is —O—P(═O)(OH)(X), and L 2 is —S—P(═O)(OH)—O—, or
(o′) R 2ap is —O—P(═O)(OH)SR 24 , R 2a is —O—P(═O)(OH)SH, R 2b is —X, and L 2 is —O—P(═O)(OH)—S—, or
(p′) R 2a is —X, R 2b is —O—P(═O)(OH)SH, and L 2 is —S—P(═O)(OH)—O—, or
(q′) R 2a is —(CR 25 R 25 ) s C(═O)OR 23 , R 2b is —NHR 23 , L 2 is —(CR 25 R 25 ) s C(═O)NR 23 —, or
(r′) R 2a is —NHR 23 , R 2b is —(CR 25 R 25 ) s C(═O)OR 23 , L 2 is —NR 23 C(═O)—(CR 25 R 25 ) s —, or
(s′) R 2a is thio, R 2b is halo, and L 2 is —S—, or
(t′) R 2a is thio, R 2b is
and L 2 is
or
(u′) R 2a is —SH, R 2b is —O—P(═O)(OH)(O—(CH 2 ) n —SH) and L 2 is —S—S—(CH 2 ) n —O—P(OH)(═O)—O—;
R 3a and R 3b are complementary conjugation functionalities and L 3 is conjugate linker, and R 3ap , R 3a , R 3b , and L 3 are
(a″) R 3ap is halo, R 3a is azido, R 3b is —C≡C—R 23 , and L 3 is
or
(b″) R 3a p is —NR 23 Pr, R 3a is —NHR 23 , R 3b is carboxy, and L 3 is —NR 23 C(═O)—, or
(c″) R 3ap is carboxy ester, R 3a is carboxy, R 3b is —NHR 23 , and L 3 is —C(═O)NR 23 —, or
(d″) R 3ap is —NR 23 Pr, R 3a is —NHR 23 , R 3b is halo, and L 3 is —NR 23 —, or
(e″) R 3ap is —OH, phosphate or phosphate ester, R 3a is —O—P(═O)(OH)(X), R 3b is hydroxy, and L 3 is —O—P(═O)(OH)—O—, or
(f″) R 3ap is —OH, phosphate or phosphate ester, R 3a is —O—P(═O)(OH)(X), R 3b is —NHR 23 , and L 3 is —O—P(═O)(OH)—NR 23 —, or
(g″) R 3ap is —OH, phosphate or phosphate ester, R 3a is —O—P(═O)(OH)(X), R 3b is thio, and L 3 is —O—P(═O)(OH)—S—, or
(h″) R 3a is —X, R 3b is thio, and L 3 is —S—, or
(i″) R 3a is
R 3b is thio, and L 3 is
or
(j″) R 3a is —C≡C—R 23 , R 3b is azido, and L 3 is
or
(k″) R 3a is halo, R 3b is —NHR 23 , and L 3 is —NR 23 —, or
(l″) R 3a is hydroxy, R 2b is —O—P(═O)(OH)(X), and L 3 is —O—P(═O)(OH)—O—, or
(m″) R 3a is —NHR 23 , R 3b is —O—P(═O)(OH)(X), and L 3 is —NR 23 —P(═O)(OH)—O—, or
(n″) R 3a is thio, R 3b is —O—P(═O)(OH)(X), and L 3 is —S—P(═O)(OH)—O—, or
(o″) R 3ap is —O—P(═O)(OH)SR 24 , R 3a is —O—P(═O)(OH)SH, R 3b is —X, and L 3 is —O—P(═O)(OH)—S—, or
(p″) R 3a is —X, R 3b is —O—P(═O)(OH)SH, and L 3 is —S—P(═O)(OH)—O—, or
(q″) R 3a is —(CR 25 R 25 ) s C(═O)OR 23 , R 3b is —NHR 23 , L 3 is —(CR 25 R 25 ) s C(═O)NR 23 —, or
(r″) R 3a is —NHR 23 , R 3b is —(CR 25 R 25 ) s C(═O)OR 23 , L 3 is —NR 23 C(═O)—(CR 25 R 25 ) s —, or
(s″) R 3a is thio, R 3b is —X, and L 3 is —S—, or
(t″) R 3a is thio, R 3b is
and L 3 is
or
(u″) R 3a is —SH, R 3b is —O—P(═O)(OH)(O—(CH 2 ) n —SH) and L 3 is —S—S—(CH 2 ) n —O—P(OH)(═O)—O—;
R 4 is selected from the group consisting of R 3a , R 3ap , halo, —NR 23 Pr, —OH, —O—P(═O)(OH)SR 24 , carboxy ester, phosphate, phosphate ester, azido, —C≡C—R 23 , —NHR 23 , carboxy, hydroxy, —(CR 25 R 25 ) s C(═O)OR 23 , —O—P(═O)(OH)SH, or —O—P(═O)(OH)Br, or an oligo;
X is chlorine, bromine, fluorine, tosylate, mesylate, triflate, or dimethoxy triflate,
n is 1, 2, 3, 4, 5, or 6;
R 23 is selected from the group consisting of hydrogen, alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, aryl, substituted aryl, cycloalkyl, substituted cycloalkyl, cycloalkenyl, substituted cycloalkenyl, cycloalkynyl, substituted cycloalkynyl, heteroaryl, substituted heteroaryl, heterocyclic, and substituted heterocyclic;
Pr is an amino protecting group;
R 24 is trityl or benzyl;
R 25 is hydrogen or C 1-6 alkyl;
n is 1, 2, 3, 4, 5, or 6;
s is an integer of greater than 1;
provided that R 2 does not react with R 1a or R 1b , R 3 does not react with R 2a or R 2b and R 4 does not react with R 3a or R 3b ;
- - - represents the point of connection to the part of the solid support-bound conjugated molecule that is closer to
and represents the point of connection to the part of the solid support-bound conjugated molecule that is further away from
2. The method of claim 1 for preparing a compound of the formula
comprising
(i) attaching a compound of the formula
to a solid support
to form a compound of the formula
and
(iii) reacting
with a compound of the formula
to form
wherein:
is a solid support material;
are independently an oligo;
R 1a and R 1b are complementary conjugation functionalities and L 1 is conjugate linker, R 2a and R 2b are complementary conjugation functionalities and L 2 is conjugate linker, and R 1a , R 1b , L 1 , R 2a , R 2b , L 2 , and R 3a are selected from
R 1a , R 2a , or R 3a
R 1b or R 2b
L 1 or L 2
—C≡C—R 23
azido
azido
—C≡C—R 23
carboxy
—NHR 23
—C(═O)NR 23 —
—NHR 23
carboxy
—NR 23 C(═O)—
halo
—NHR 23
—NR 23 —
—NR 23
halo
—NR 23 —
hydroxy
—O—P(═O)(OH)(X)
—O—P(═O)(OH)—O—
—O—P(═O)(OH)(X)
hydroxy
—O—P(═O)(OH)—O—
—NHR 23
—O—P(═O)(OH)(X)
—NR 23 —P(═O)(OH)—O—
—O—P(═O)(OH)(X)
—NHR 23
—O—P(═O)(OH)—NR 23 —
thio
—O—P(═O)(OH)(X)
—S—P(═O)(OH)—O—
—O—P(═O)(OH)(X)
thio
—O—P(═O)(OH)—S—
thio
—X
—S—
—X
thio
—S—
—O—P(═O)(OH)SH
—X
—O—P(═O)(OH)—S—
—X
—O—P(═O)(OH)SH
—S—P(═O)(OH)—O—
—(CR 25 R 25 ) s C(═O)OR 23
—NHR 23
—(CR 25 R 25 ) s C(═O)NR 23 —
—NHR 23
—(CR 25 R 25 ) s C(═O)OR 23
—NR 23 C(═O)—(CR 25 R 25 ) s —
thio
thio
—SH
—O—P(═O)(OH)(O—(CH 2 ) n —SH)
—S—S—(CH 2 ) n —O—P(OH)(═O)—O—
wherein the selection of R 1a , R 2a , or R 3a is independent of each other provided that L 1 and L 2 are different, R 2a does not react with R 1a or R 1b , and R 3a does not react with R 2a or R 2b ;
X is chlorine, bromine, fluorine, tosylate, mesylate, triflate, or dimethoxy triflate;
R 23 is selected from the group consisting of hydrogen, alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, aryl, substituted aryl, cycloalkyl, substituted cycloalkyl, cycloalkenyl, substituted cycloalkenyl, cycloalkynyl, substituted cycloalkynyl, heteroaryl, substituted heteroaryl, heterocyclic, and substituted heterocyclic;
R 25 is hydrogen or C 1-6 alkyl;
s is an integer of greater than 1;
- - - represents the point of connection to the part of the solid support-bound conjugated molecule that is closer to
and represents the point of connection to the part of the solid support-bound conjugated molecule that is further away from
3. A method of preparing a compound of the formula
comprising
cleaving the bond between
and L 1 of the compound of the formula
thereby obtaining
wherein:
the compound of
is prepared according to the method of claim 1 ;
L 1 , L 2 , R 3 , R 4 ,
are as defined in claim 1 ; and
Z is —OH, OH—(C 1 -C 10 )alkylene-, —COOH, NH 2 C(O)—, NH 2 NH—C(O)—, COOH—(C 1 -C 10 )alkylene-, NH 2 C(O)—(C 1 -C 10 )alkylene-, NH 2 NH—C(O)—(C 1 -C 10 )alkylene-, CH 2 ═CH—(C 1 -C 10 )alkylene-, C≡C—(C 1 -C 10 )alkylene- or HS—(C 1 -C 10 )alkylene- and any alkylene is optionally substituted by one or more groups selected from —OH, halogen, —NHR″, —NHC(O)—(C 1 -C 10 )alkylene-C≡CH, and —NHC(O)—(C 1 -C 10 )alkylene-CH═CH 2 ;
R″ is selected from (C 1 -C 10 )alkyl, (C 3 -C 10 )cycloalkyl, or (C 3 -C 10 )aryl.
4. The method of claim 1 , wherein the method further comprises preparing a compound of the formula
comprising
(i) converting the compound of formula
to
and
(ii) contacting
with a conjugation component of the formula
wherein steps (i) and (ii) are performed a sufficient number of times to provide the compound of the formula
wherein:
n is an integer between 2 and 25, and
L 1 , L 2 , R 3a , R 4 ,
are as defined in claim 1 .
5. A method for preparing a compound of the formula
comprising cleaving a compound of formula
from the solid support, wherein
Z is —OH, OH—(C 1 -C 10 )alkylene-, —COOH, NH 2 C(O)—, NH 2 NH—C(O)—, COOH—(C 1 -C 10 )alkylene-, NH 2 C(O)—(C 1 -C 10 )alkylene-, NH 2 NH—C(O)—(C 1 -C 10 )alkylene-, CH 2 ═CH—(C 1 -C 10 )alkylene-, C≡C—(C 1 -C 10 )alkylene- or HS—(C 1 -C 10 )alkylene- and the alkylene can be optionally substituted by one or more groups selected from —OH, halogen, —NHR″, —NHC(O)—(C 1 -C 10 )alkylene-C≡CH, or —NHC(O)—(C 1 -C 10 )alkylene-CH═CH 2 ;
R″ is (C 1 -C 10 )alkyl, (C 3 -C 10 )cycloalkyl, or (C 3 -C 10 )aryl; and
L 1 , L 2 , L 3 , R 4 ,
are as defined in claim 1 .
6. A method for preparing a compound of the formula
comprising cleaving a compound of formula
from
wherein
Z is —OH, OH—(C 1 -C 10 )alkylene-, —COOH, NH 2 C(O)—, NH 2 NH—C(O)—, COOH—(C 1 -C 10 )alkylene-, NH 2 C(O)—(C 1 -C 10 )alkylene-, NH 2 NH—C(O)—(C 1 -C 10 )alkylene-, CH 2 ═CH—(C 1 -C 10 )alkylene-, C≡C—(C 1 -C 10 )alkylene- or HS—(C 1 -C 10 )alkylene- and the alkylene can be optionally substituted by one or more groups selected from —OH, halogen, —NHR″, —NHC(O)—(C 1 -C 10 )alkylene-C≡CH, or —NHC(O)—(C 1 -C 10 )alkylene-CH═CH 2 ;
R″ is (C 1 -C 10 )alkyl, (C 3 -C 10 )cycloalkyl, or (C 3 -C 10 )aryl; and
n,
L 1 , L 2 , L 3 , L 4 ,
are as defined in claim 4 .
7. A method of preparing a compound of the formula
comprising
(i) attaching a conjugation component of the formula
wherein R 2 is R 2a or R 2ap ,
to a solid support
to form a compound of the formula
(ii) when R 2 is R 2ap , converting
to
(iii) contacting
with a conjugation component of the formula
wherein R 3 is R 3a , or R 3ap ;
to form
(iv) when R 3 is R 3ap , converting
to
and
(v) contacting
with a conjugation component of the formula
to provide the compound of the formula
wherein:
is a solid support material;
are independently an oligo, where each oligo is independently a polymer, having from 2 to about 150 covalently linked monomer units, that is characterized by a sequence of 2′-deoxyribosenucleotide residues (DNA), ribonucleotide residues (RNA), and peptide nucleic acids (PNAs), or a combination thereof;
wherein
(a) R 1a is azido, R 1b is —C≡C—R 23 , and L 1 is
(a′) R 2ap is halo, R 2a is azido, R 2b is —C═C—R 23 , and L 2 is
(a″) R 3ap is halo, R 3a is azido, R 3b is —C≡C—R 23 , and L 3 is
or
R 4 is selected from the group consisting of R 3a , R 3ap , halo, —NR 23 Pr, —OH, —O—P(═O)(OH)SR 24 , carboxy ester, phosphate, phosphate ester, azido, —C≡C—R 23 , —NHR 23 , carboxy, hydroxy, —(CR 25 R 25 ) s C(═O)OR 23 , —O—P(═O)(OH)SH, or —O—P(═O)(OH)Br, or an oligo;
n is 1, 2, 3, 4, 5, or 6;
R 23 is selected from the group consisting of hydrogen, alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, aryl, substituted aryl, cycloalkyl, substituted cycloalkyl, cycloalkenyl, substituted cycloalkenyl, cycloalkynyl, substituted cycloalkynyl, heteroaryl, substituted heteroaryl, heterocyclic, and substituted heterocyclic;
Pr is an amino protecting group;
R 24 is trityl or benzyl;
R 25 is hydrogen or C 1-6 alkyl;
s is an integer of greater than 1;
provided that R 2 does not react with R 1a or R 1b , R 3 does not react with R 2a or R 2b and R 4 does not react with R 3a or R 3b ;
- - - represents the point of connection to the part of the solid support-bound conjugated molecule that is closer to
and represents the point of connection to the part of the solid support-bound conjugated molecule that is further away from
8. The method of claim 7 , wherein the method further comprises preparing a compound of the formula
comprising
(i) converting the compound of formula
to
(ii) when R 3 is R 3ap , converting
to
and
(iii) contacting
with a conjugation component of the formula
wherein steps (i), (ii) and (iii) are performed a sufficient number of times to provide the compound of the formula
wherein:
n is an integer between 2 and 25, and
L 1 , L 2 , L 3a , R 3b , R 4 ,
are as defined in claim 7 .