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Questions and answers => General discussions (Q&As) => Topic started by: meixianghao on October 28, 2018, 12:00:42 pm

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Title: mutations to 3-methyladenine
Post by: meixianghao on October 28, 2018, 12:00:42 pm
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
Title: Re: mutations to 3-methyladenine
Post by: xiangjun on October 28, 2018, 12:27:17 pm
Could you please provide a minimal, reproducible example?

Thanks,

Xiang-Jun
Title: Re: mutations to 3-methyladenine
Post by: meixianghao on October 28, 2018, 09:32:39 pm
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
Title: Re: mutations to 3-methyladenine
Post by: xiangjun on October 28, 2018, 09:52:55 pm
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: [Select]
fiber -seq=GACATGATTGCC fiber-BDNA.pdb
# Structure #4; Twist: 36.0 (degrees); Rise: 3.375 (Angstrom)
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

Title: Re: mutations to 3-methyladenine
Post by: xiangjun on November 06, 2018, 11:23:17 am
As a follow-up, I've updated 3DNA to v2.3.4-2018nov06 which includes a 3-methyladenine (3MA (http://www.rcsb.org/ligand/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: [Select]
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
Using the requested case as an example, the following command will mutate A7 to 3MA:

Code: [Select]
mutate_bases "chain=_ s=7 m=3MA" bform.pdb bform-A7to3mA.pdb
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: [Select]
# 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

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
Title: Re: mutations to 3-methyladenine
Post by: meixianghao on January 17, 2019, 02:34:22 am
Dear Mr Lu,

Thanks for your kindly help! It is indeed fast to create a B-form DNA model using the 3DNA fiber program , and the command mutate_bases is easy but strong!

Best wishes!

Ling-Yan

Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids

Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University