triplex building

[temizna]

Hello everyone!

I am trying to build a triplex DNA structure in the form of (PPY) Purine-Purine-Pyrimidine (i.e. GGC and AAT with GC and AT Watson-crick and GG and AA Hoogsten base pairs) repeats.
The fiber option in 3DNA gives YYP triplexes. I am willing  to construct new parameter files. I just need to know how to go about it. What kind of files do i need to create and how to integrate them with 3DNA?

Thanks

Alpay

[xiangjun]

Hi Alpay,

Thanks for posing an interesting question which is, however, beyond 3DNA's current capability. The triplex fiber models with 3DNA are based on experimental data collected from literature, and they require fixed sequences. Are your purine-purine-pyrimidine (RRY) triplex models (AAT and GGC) regular?  If so, do you have the structure data of the corresponding triplet repeats, A.A.T and G.G.C, and how such triplets stack over one another (twist, rise)? I am always interested in extending 3DNA's capabilities to meet users' needs. You may also find NAB (Nucleic Acid Builder) from Dr. David Case's group useful.

Xiang-Jun

[temizna]

Hi Xiang-Jun,

Thanks for the fast reply. Unfortunately, I only have sequence info that is predicted to form a triplex, no structure information at all!. I am assuming that the triplex will form regular W-C bps on the B-DNA double strand and regular Hoogsten bps with the single strand. I am planing to perform simulations to judge the stability and effects of mutations on the stability of the triplex. SO, it is model building from scratch. Unfortunately, NAB is not straightforward and even the examples seems to be not working.

Anyway, thanks again for your help and thanks for a really nice software package.
Alpay

[xiangjun]

I only have sequence info that is predicted to form a triplex, no structure information at all!. I am assuming that the triplex will form regular W-C bps on the B-DNA double strand and regular Hoogsten bps with the single strand.

It is helpful to know this background information. Then the question becomes what the "regular Hoogsten bps with the single strand" look like for the G.G-C and A.A-T triplet building blocks? While the A.U Hoogsteen pair is well-characterized, how about the G.G and A.A Hoogsteen pairs? They are prerequisite to build the triplexes you want. Wherever possible, I'd like to help you get started.

Xiang-Jun

PS. Thanks for your kind words about 3DNA, and for sharing your Python script for the analysis along the md trajectories.

[temizna]

Your welcome. The script is a simple script that reads your nmr_strs script output. I  also have a version of nmr_strs where I use anyhelix instead of analyze just to see if there is any difference in the outputs.

Goin gback to the triplex, by regular G.G and A.A Hoogsten bps, I meant idealized H-bonding with bases lying on the same plane such as the schematic representation supplied on the wiki page of hoogsten base pairs.
My sequence is basically a stretch of GAG repeats (10 of them) where half the repeats loop around and form the anti parallel triplex like this:
3'-CTCCTCCTCCTCCTC
5'-GAGGAGGAGGAGGAG-G
       3'-GAGGAGGAGGAG-GA

where the repeat between the dashes represent a loop.

135D and 136D pdb structures do have the GGC triplex with GG base pair step similar to my repeat. May be that is a good place to start.

A simple way I can think of is: build B-DNA helix of 5 GAG repeats. cp the file, separate the the strands in one file and than dock the single strand on the double helix. I am going to be working this angle as well. ( as soon as I get my hands on a decent docking software )

Thanks again for your help. I appreciate it.
Alpay

[xiangjun]

135D and 136D pdb structures do have the GGC triplex with GG base pair step similar to my repeat. May be that is a good place to start.

I had a quick look of 135D/136D and senses that the GGC triplet could serve a good starting point.

A simple way I can think of is: build B-DNA helix of 5 GAG repeats. cp the file, separate the the strands in one file and than dock the single strand on the double helix. I am going to be working this angle as well. ( as soon as I get my hands on a decent docking software  )

That appears to be a good/practical idea. Remember that [mono:3b4grcve]find_pair[/mono:3b4grcve] and [mono:3b4grcve]rebuild[/mono:3b4grcve] works for single strand as well. As long as you have a duplex, a single strand, and a triplet building block, the utility program [mono:3b4grcve]rotate_mol[/mono:3b4grcve] should be of help in assembling the two parts together, even though it may not qualify as "a decent docking software". Have a try, and see how far you can go. Once you get a prototype for GGC, it should be straightforward to apply it to AAT.

Xiang-Jun

[hr:3b4grcve][/hr:3b4grcve]
PS. Please be a bit patient -- I am quite occupied recently, and could be slow in getting back to you, especially on issues that require more explorations. Hopefully, I will able to devote more time/efforts on 3DNA-related stuffs to respond to the user community more promptly and to the depth/extent I'd like to.

[temizna]

Thanks for the suggestion. I will definitely try that this week.

Alpay

[xiangjun]

Hi Alpay,

You may find it helpful to have a look of the recently published article "Designing Triple Helical Fragments: The Crystal Structure of the Undecamer d(TGGCCTTAAGG) Mimicking T.AT Base Triplets" by Van Hecke et al in Cryst. Growth Des. (DOI: 10.1021/cg1009048).

Xiang-Jun