Messages

1

General discussions (Q&As) / Re: mutations to 3-methyladenine

« 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

2

General discussions (Q&As) / Re: mutations to 3-methyladenine

« 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

3

General discussions (Q&As) / mutations to 3-methyladenine

« 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