You can try 3D-DART webserver (http://haddock.science.uu.nl/services/3DDART/) to model the 3D structure of DNA molecule. Also you can use Discovery studio Visualizer 3.0 for the same.

If there is any problem occurs you can contact.....................

Thank you dear Pavel Komarov for your prompt reply. I have checked your suggested webpage and website. However, this website is the database/depository for crysral structures of macromolecules. Infact, I am looking for some In silico programme that generate/predict Model structure of DNA.

Hi i have developed a webserver for DOuble strand DNA modelling. i can help u with ur ssDNA, but need a little more information. wat secondary structure does the dna adapt?. is its a random loop or a fully stacked like in double stranded DNA. BAsicaly, do u have a idea about the secondary structure. if so i can help u generate the 3d-model.

thanks in advance.

You can use the make-na server based on the NAB (nucleic acid builder) included in the ambertools suite. You need only to define your sequence, to check the single strand box , click on make NA and get your pdb file containing the desired structure.

http://structure.usc.edu/make-na/server.html

Obviously what you get is a B-DNA single strand that you need to optimize before perform any possible docking experiment.

There is QGRS Mapper. It can predict g-quadruplexes in your aptamer.

http://bioinformatics.ramapo.edu/QGRS/analyze.php

You can also use 3DNA package (follow the link http://3dna.rutgers.edu/x3dna/faqs) for building the DNA (A- or B-form). The software is free available.

You can try 3D-DART webserver (http://haddock.science.uu.nl/services/3DDART/) to model the 3D structure of DNA molecule. Also you can use Discovery studio Visualizer 3.0 for the same.

If there is any problem occurs you can contact.....................

Irshad. We did it here: http://www.basepairbio.com/research-and-publications/what-is-an-aptamer-2/

Using the following software.

NAB(part of amber suite) to build molecule from sequence

@Senthilkumar Kailasam. Thank you for your kind suggestion and offering help. I am tried using some prorgammes,however as you mentioned it seems its difficult to perform 3D modelling for ss DNA. Well, yea i have predicted the secondry structure of ss DNA aptamer by M fold programme. I found the aptamers adopt mostly stem/loop structure. I would appreciate,if you can resolve this issue and please give me your email id for further help.

Thanks

Best regards,

Irshad.

@ Federico Iacovelli. Thank you for your kind suggestion. I have tried modeling using your suggested prorgamme and obtained the 3D model,however as you mentioned the aptamer model is in the 'B' form like of typical DNA and the stem/loop feature were lost. I afraid that i may not be able to perform docking with such structure. Also, at the moment, i am not well versed with dynamic simulation/energy minimization to optimize the obtained model. I would appreciate,if you can resolve this issue and reccommend me some programme that may be used to refined this 3D model.

Thanks

Best regards,

Irshad.

@ Florian Mittelberger. Thank you for your kind suggestion. I have used once your QGRS Mapper to find G-quadraplex in my found aptamers.

Best regards,

Irshad.

@ Hiqmet Kamberaj. Thank you for your kind suggestion. I would try using your suggested software to accomplish my goal.

Thanks

Best regards,

Irshad.

I am suprised nobody suggested the UNAFold web server: http://mfold.rna.albany.edu/ It could definitely help you. If not with the entire modelling process, at least with some aspects of it, such as comparing the predicted stability of several alternatives in thermodynamic terms.

@Chhedi Gupta, Thank you for your kind suggestion. I have tried using 3D-DART webserver to model the 3D structure of DNA molecule,however, i never see any results communicated to me. Yea, i contacted them, however, they inform me that this programe is limited to ds DNA modelling, hence may not work to resolve my issue. Also, they reccommend to use RNA modeling programme and convert into DNA. I do not know how far this approach would it be reliable?

Best regards,

Irshad.

@Bill Jackson, Thank you for your kind suggestion. I would try using your suggested software to accomplish my goal.

Thanks

Best regards,

Irshad.

@Matej Lexa, Thank you for your kind suggestion. Yea, infact, i mentioned that i have used the UNAFold web server: http://mfold.rna.albany.edu/l to predict the secondry stucture of ss DNA aptamers. Indeed, it works well and helped me to give secondry strutures of various aptamers, however it does not give any 3D model structure.

Thanks.

Best regards,

Irshad.

So what you have done so far is in the right direction. from secondary structure one has to move to teritiary. serveral tools like ModeRNA, assmble, s2s, RNA3d. exist most of which requires manual intervention and knowledge of wat you are doing. will detail in the email. to have a complete list of programs available start by reading the attached pdf review by Tamar schlick. 2010

Hi Ishad will keep in touch at [email protected].

3D-DART webserver model the ds DNA. It doesn't matter once dsDNA is modeled it can easily make into ssDNA by removing the reverse strand (3' - 5' prime) using freely available softwares. As you said that there is no result communication? Once you would submit the sequence to this server the result will be just available in Zip form on the server. You would download the result and proceed your further studies.

If you would not do this you can simply use Build and Edit Nucleic acid option of Tool menu in Discovery Studio software to model the ssDNA.

We too use UNA-fold. You can buy an academic license for $50 and run it locally on your computer (Mac or Windows). This allows you to control many more parameters and screen thousands of potential structures for those you find potentially interesting.

Dear Dr Campbell. Thank you for your kind suggestion. I have tried UNA-fold web server (Mfold) , however it is confined to secondry structure of DNA oligonucleotide.

As you suggested, I would try for academic license of UNA Fold, if it gives various parameters to build reliable 3D model of DNA oligonucleotide ( in hair/pin loop structure form).

Thank you.

Best regards,

Irshad

hello

are ssdna that generaite in cell selex ir unstaible?

hi

you can use 3d.dart webserver

so far i tried all soft I can find ,but all just designed for dual -DNA or single strand RNA.I  even tried to replace the  U by T using discovery studio 4.1, but  while you have to handle more than 100files which every single file owned 30base  , to change U into  T,that is scary . but this might be the only way till now .And since the conformation of aptamer changed  while the  PH or temperature  or  ionic concentration or  ionic range changed .  

As far as I know, 3D-DART works only with dsDNA. (?)

And what if we don't have a pdb structure? For example I have a ssDNA 80 bases strand (an aptamer basically), so how do I predict its 3D structure? How do I study its interaction with the target ligand?

Hi Richa

since now and based on my researches there is not any software for predicting 3d structure of ssDNA. In most of articles RNA predicting tools are used instead of DNA tools and then for anlaysis of interactions, docking sotwares like haddock and autodock are used.  

U can use of rosetta software for 3D ssDNA Prediction