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Questions and answers > General discussions (Q&As)
mutations to 3-methyladenine
meixianghao:
Hello,
I am a new user for the 3DNA program, and my interests are about the study of the 3-methyladenine.
I have looked through the topic of 'How can I mutate cytosine to 5-methylcytosine' and processed the adenine to 3-methyladenine according the protocol for mutation the cytosine. Unfortunately, it is unavailable and the notification was listed as following:
unrecognized mutation: 1 A: ...7@: [ @@@] ---> *7AM*
0 out of 1 mutation entries are valid.
No valid mutation entries -- check file 'mutations.dat'!
After reading the file 'mutations.dat', I did not find the information about the modified adenine. Hence, I want to ask if you know the method of modification adenine to 3-methyladenine?
Best wishes!
Ling-Yan
xiangjun:
Could you please provide a minimal, reproducible example?
Thanks,
Xiang-Jun
meixianghao:
Dear Mr Lu,
I have created the structure of DNA in B-form using the NAB program. The sequence of the strand I is 5'-GACATGXTTGCC-3', where X represents the adenine in order to distinguish the modified site, and that of the complementary strand is '5-GGCAATCATGTC-3'. Our aim is that base of adenine (X) is mutated to the 3-methyladenine, namely addition of a methyl group to the 3 position of the adenine (X).
The pdb files of created DNA is given in the attachment. Thank you!
Best wishes!
Ling-Yan
xiangjun:
Hi Ling-Yan,
Thanks for your follow-up.
Did you know that you can easily generate a large variety of fiber models using the 3DNA fiber program? For example, to generate a B-form DNA with base sequence GACATGATTGCC, you can:
--- Code: ---fiber -seq=GACATGATTGCC fiber-BDNA.pdb
# Structure #4; Twist: 36.0 (degrees); Rise: 3.375 (Angstrom)
--- End code ---
Do you have a sample structure of 3-methyladenine, in PDB or otherwise? 3DNA needs it as a building block for mutations.
Best regards,
Xiang-Jun
xiangjun:
As a follow-up, I've updated 3DNA to v2.3.4-2018nov06 which includes a 3-methyladenine (3MA) derived from PDB id 3MAG. The building block file is named Atomic_3MA.pdb, stored under the X3DNA/config folder, with the following content:
--- Code: ---REMARK 3DNA v3 (2018), created and maintained by xiangjun@x3dna.org
HETATM 1 N9 3MA A 600 -1.287 4.521 0.006 1.00 49.87 N
HETATM 2 C4 3MA A 600 -1.262 3.133 0.004 1.00 50.46 C
HETATM 3 N3 3MA A 600 -2.337 2.286 -0.009 1.00 50.37 N
HETATM 4 CN3 3MA A 600 -3.743 2.648 -0.047 1.00 50.41 C
HETATM 5 C2 3MA A 600 -1.905 1.013 0.001 1.00 50.11 C
HETATM 6 N1 3MA A 600 -0.662 0.520 0.004 1.00 49.27 N
HETATM 7 C6 3MA A 600 0.366 1.372 -0.003 1.00 48.99 C
HETATM 8 N6 3MA A 600 1.588 0.867 -0.034 1.00 46.12 N
HETATM 9 C5 3MA A 600 0.068 2.768 0.003 1.00 49.89 C
HETATM 10 N7 3MA A 600 0.875 3.914 -0.003 1.00 49.84 N
HETATM 11 C8 3MA A 600 0.026 4.909 -0.003 1.00 49.58 C
END
--- End code ---
Using the requested case as an example, the following command will mutate A7 to 3MA:
--- Code: ---mutate_bases "chain=_ s=7 m=3MA" bform.pdb bform-A7to3mA.pdb
--- End code ---
Note that since the original attached bform.pdb does not include chain id (just a space ' ' character), it is specified as "chain=_" (i.e., using an underscore).
With 3DNA, one can easily generate a B-form (or A-form, or any other of a comprehensive list of 56 fiber-based models) as shown below:
--- Code: ---# generate a B-form DNA with base sequence GACATGATTGCC
fiber -seq=GACATGATTGCC fiber-BDNA.pdb
# mutate A7 to 3MA
mutate_bases "chain=A s=7 m=3MA" fiber-BDNA.pdb fiber-BDNA-A7to3MA.pdb
--- End code ---
Note that 3DNA-generated fiber model has chain id A for the leading strand. For comparison, below is a list of the ATOM records for A7 as directly from the 3DNA fiber program, and those after running mutate_bases to 3MA.
REMARK 3DNA fiber-derived atomic coordinates for A7
ATOM 126 P DA A 7 -5.130 -7.667 -18.402 1.00 1.00 P
ATOM 127 OP1 DA A 7 -5.914 -8.669 -17.645 1.00 1.00 O
ATOM 128 OP2 DA A 7 -4.303 -8.192 -19.510 1.00 1.00 O
ATOM 129 O5' DA A 7 -6.107 -6.526 -18.955 1.00 1.00 O
ATOM 130 C5' DA A 7 -6.430 -5.410 -18.104 1.00 1.00 C
ATOM 131 C4' DA A 7 -6.362 -4.119 -18.895 1.00 1.00 C
ATOM 132 O4' DA A 7 -5.026 -3.539 -18.898 1.00 1.00 O
ATOM 133 C3' DA A 7 -6.720 -4.227 -20.377 1.00 1.00 C
ATOM 134 O3' DA A 7 -7.422 -3.053 -20.768 1.00 1.00 O
ATOM 135 C2' DA A 7 -5.374 -4.251 -21.100 1.00 1.00 C
ATOM 136 C1' DA A 7 -4.689 -3.199 -20.234 1.00 1.00 C
ATOM 137 N9 DA A 7 -3.204 -3.200 -20.351 1.00 1.00 N
ATOM 138 C8 DA A 7 -2.369 -4.263 -20.542 1.00 1.00 C
ATOM 139 N7 DA A 7 -1.114 -3.940 -20.604 1.00 1.00 N
ATOM 140 C5 DA A 7 -1.115 -2.562 -20.442 1.00 1.00 C
ATOM 141 C6 DA A 7 -0.082 -1.611 -20.412 1.00 1.00 C
ATOM 142 N6 DA A 7 1.215 -1.922 -20.551 1.00 1.00 N
ATOM 143 N1 DA A 7 -0.430 -0.323 -20.234 1.00 1.00 N
ATOM 144 C2 DA A 7 -1.720 -0.020 -20.096 1.00 1.00 C
ATOM 145 N3 DA A 7 -2.766 -0.816 -20.107 1.00 1.00 N
ATOM 146 C4 DA A 7 -2.390 -2.099 -20.287 1.00 1.00 C
----------------------------------------------------------------------------------------
REMARK Mutation#1 A:...7@:[@@@] to [3MA]
ATOM 126 P 3MA A 7 -5.130 -7.667 -18.402 1.00 1.00 P
ATOM 127 OP1 3MA A 7 -5.914 -8.669 -17.645 1.00 1.00 O
ATOM 128 OP2 3MA A 7 -4.303 -8.192 -19.510 1.00 1.00 O
ATOM 129 O5' 3MA A 7 -6.107 -6.526 -18.955 1.00 1.00 O
ATOM 130 C5' 3MA A 7 -6.430 -5.410 -18.104 1.00 1.00 C
ATOM 131 C4' 3MA A 7 -6.362 -4.119 -18.895 1.00 1.00 C
ATOM 132 O4' 3MA A 7 -5.026 -3.539 -18.898 1.00 1.00 O
ATOM 133 C3' 3MA A 7 -6.720 -4.227 -20.377 1.00 1.00 C
ATOM 134 O3' 3MA A 7 -7.422 -3.053 -20.768 1.00 1.00 O
ATOM 135 C2' 3MA A 7 -5.374 -4.251 -21.100 1.00 1.00 C
ATOM 136 C1' 3MA A 7 -4.689 -3.199 -20.234 1.00 1.00 C
ATOM 137 N9 3MA A 7 -3.223 -3.222 -20.359 1.00 1.00 N
ATOM 138 C4 3MA A 7 -2.403 -2.103 -20.290 1.00 1.00 C
ATOM 139 N3 3MA A 7 -2.789 -0.805 -20.095 1.00 1.00 N
ATOM 140 CN3 3MA A 7 -4.138 -0.309 -19.891 1.00 1.00 C
ATOM 141 C2 3MA A 7 -1.705 -0.010 -20.097 1.00 1.00 C
ATOM 142 N1 3MA A 7 -0.410 -0.311 -20.238 1.00 1.00 N
ATOM 143 C6 3MA A 7 -0.063 -1.589 -20.408 1.00 1.00 C
ATOM 144 N6 3MA A 7 1.224 -1.873 -20.512 1.00 1.00 N
ATOM 145 C5 3MA A 7 -1.110 -2.559 -20.445 1.00 1.00 C
ATOM 146 N7 3MA A 7 -1.113 -3.952 -20.602 1.00 1.00 N
ATOM 147 C8 3MA A 7 -2.377 -4.283 -20.541 1.00 1.00 C
The new 3-methyl carbon in 3MA is named CN3. Note also the order of atom names in 3MA is as in PDB id 3MAG, and it does not follow the convention for adenine.
For completeness, attached are four PDB files mentioned in this post.
Xiang-Jun
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Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.