I don't see the red color ...
Anyway ... Since you have A-helical regions at the ends ... you can
apply the protocol I wrote you in the previous mail using A-RNA helices
instead of B-DNA (see my first answer)... You need a software that can
generate A-RNA (NAB should do it)
Chimera or SPBDV can be used to mutate nucleotides.. In Chimera the
command is called "swapna" (see the user guide).
Best,
Vlad
On 01/20/2014 08:17 PM, Asaminew Haile wrote:
> Hi Dear Vlad,
> Here is the solution structure
> GGCU*aaaa*GGCC
> CCGGggggCCGG
>
> final duplex with changed nucleotides with RED color
> G*C*CU*aaaa*GG*G*C
> C*G*GGggggC*C*CG
>
> I thought I can remove the two end GG/CC and append with GC/CG.
> I appreciate your help
>
>
> Thanks again
>
>
> asaminew
>
>
>
>
> On Mon, Jan 20, 2014 at 1:53 PM, Vlad Cojocaru <
> vlad.cojocaru.mpi-muenster.mpg.de> wrote:
>
>> Sory, but this is very scarce additional information ... It is hard to
>> guess how your molecule looks like and what exactly you want to do ...
>> I made some guesses already ... If my previous advices don't help, you'd
>> have to give more detailed info.
>>
>> Best,
>> Vlad
>>
>>
>> On 01/20/2014 07:14 PM, Asaminew Haile wrote:
>>> additional information,
>>> the solution structure contains an internal loop and it is an RNA
>>> molecules.
>>> Thanks again
>>>
>>>
>>> asaminew
>>>
>>>
>>> On Mon, Jan 20, 2014 at 12:25 PM, Vlad Cojocaru <
>>> vlad.cojocaru.mpi-muenster.mpg.de> wrote:
>>>
>>>> To what type of molecule ?
>>>>
>>>> For dsDNA, I usually generate B-DNA helices with the bases I want to add
>>>> + 2 additional bases that are identical to the last 2 bases in the
>>>> starting structure on each side
>>>> .
>>>> Then, I superimpose the generated B helices with the starting structure
>>>> using the 2 bases that are identical on each side ... Finally, I merge
>>>> the starting structure with the 2 helices upon keeping only the bases I
>>>> want to add in the 2 helices ....
>>>>
>>>> For dsRNA a similar procedure can be applied but using A-RNA helices ...
>>>>
>>>> For ss nucleic acids its more tricky since you don't have any info on
>>>> the conformation of the bases you want to add ... Probably I would avoid
>>>> adding anything or if really necessary, make a manual guess and start
>>>> simulations with 2-3 alternative models ....
>>>>
>>>> I hope this helps
>>>> Vlad
>>>>
>>>>
>>>> On 01/20/2014 06:09 PM, Asaminew Haile wrote:
>>>>> Dear amber Scientists,
>>>>> I've a solution structure and for stability purpose, I want to append
>>>> more
>>>>> nucleotides to solution coordinate end.
>>>>> Do you have any idea?
>>>>>
>>>>> Thanks in advance
>>>>>
>>>>> asaminew
>>>>> _______________________________________________
>>>>> AMBER mailing list
>>>>> AMBER.ambermd.org
>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>
>>>>>
>>>> --
>>>> Dr. Vlad Cojocaru
>>>> Max Planck Institute for Molecular Biomedicine
>>>> Department of Cell and Developmental Biology
>>>> Röntgenstrasse 20, 48149 Münster, Germany
>>>> Tel: +49-251-70365-324; Fax: +49-251-70365-399
>>>> Email: vlad.cojocaru[at]mpi-muenster.mpg.de
>>>> http://www.mpi-muenster.mpg.de/research/teams/groups/rgcojocaru
>>>>
>>>>
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>>
>> --
>> Dr. Vlad Cojocaru
>> Max Planck Institute for Molecular Biomedicine
>> Department of Cell and Developmental Biology
>> Röntgenstrasse 20, 48149 Münster, Germany
>> Tel: +49-251-70365-324; Fax: +49-251-70365-399
>> Email: vlad.cojocaru[at]mpi-muenster.mpg.de
>> http://www.mpi-muenster.mpg.de/research/teams/groups/rgcojocaru
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
--
Dr. Vlad Cojocaru
Max Planck Institute for Molecular Biomedicine
Department of Cell and Developmental Biology
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
http://www.mpi-muenster.mpg.de/research/teams/groups/rgcojocaru
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jan 20 2014 - 12:00:02 PST
