Methods for predicting stability and melting temperatures of nucleic acid duplexes
View Patent ↗The present invention provides methods that more accurately predict melting temperatures for duplex oligomers. The invented methods predict the T m of chimeric duplexes containing various amounts of locked nucleic acid modifications in oligonucleotide strands.
1. A method of predicting the melting temperature of an oligonucleotide comprising:
(a) a computer system receiving a data input from a user, the computer comprising a processor, and instructions executable by the processor;
(b) responsive to the data input from a user, the computer system calculating a T m value using the equation:
T
m
=
Δ
H
o
Δ
S
o
+
R
ln
(
C
1
-
C
2
/
2
)
,
wherein
Δ H°=ΔH° DNA +ΔΔH° LNA
and
Δ S°=ΔS° DNA +ΔΔS° LNA ; and
(c) providing an output to a display;
wherein the oligonucleotide comprises at least two Locked Nucleic Acid (LNA) modifications.
2. The method of claim 1 , wherein
Δ
Δ
H
LNA
o
=
∑
i
,
j
=
A
,
C
,
G
,
T
N
ij
n
-
n
ΔΔ
H
ij
n
-
n
.
3. The method of claim 1 , wherein
ΔΔ
S
LNA
o
=
∑
i
,
j
=
A
,
C
,
G
,
T
N
ij
n
-
n
ΔΔ
S
ij
n
-
n
.
4. The method of claim 2 or 3 , wherein the values are determined using nearest neighbor parameters.
5. A method of predicting the melting temperature of an oligonucleotide comprising:
(a) a networked server receiving data input from a communication device associated with a user, the server comprising the communication interface, a processor, and instructions executable by the processor;
(b) responsive to receiving the data input, the networked server sending via the communication interface to the communication device, calculation of a T m value using the equation:
T
m
=
Δ
H
o
Δ
S
o
+
R
ln
(
C
1
-
C
2
/
2
)
,
wherein
Δ H°=ΔH° DNA +ΔΔH° LNA
and
Δ S°=ΔS° DNA +ΔΔS° LNA ; and
(c) sending the T m value via the communication interface to the user communication device;
wherein the oligonucleotide comprises at least two Locked Nucleic Acid (LNA) modifications.
6. The method of claim 5 , wherein the user interacts with the networked server via a web-browsing application running on the communication device.
7. The method of claim 5 , wherein the communication device comprises at least one of a computer, a desktop computer, or a laptop computer.
8. The method of claim 5 , wherein
Δ
Δ
H
LNA
o
=
∑
i
,
j
=
A
,
C
,
G
,
T
N
ij
n
-
n
ΔΔ
H
ij
n
-
n
.
9. The method of claim 5 , wherein
ΔΔ
S
LNA
o
=
∑
i
,
j
=
A
,
C
,
G
,
T
N
ij
n
-
n
ΔΔ
S
ij
n
-
n
.
10. The method of claim 8 or 9 , wherein the values are determined using nearest neighbor parameters.