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Author Topic: global bending of a single stranded DNA  (Read 4399 times)

Offline Giulia Palermo

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global bending of a single stranded DNA
« on: July 18, 2016, 04:30:33 pm »
Dear Xiang-Jun Lu,


I have used extensively 3DNA during my work and I am now exploring DSSR.

I am successfully using it for the analysis of a single-strand DNA, for which I can obtain correctly the backbone parameters.

However, I am interested in calculating the global bending of the steel. This , I have not be able to do.

Is it possible with your code? could you please give me some advises?

Thank you very much
Giulia

Offline xiangjun

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Re: global bending of a single stranded DNA
« Reply #1 on: July 18, 2016, 04:54:10 pm »
Hi Giulia,

Thanks for using 3DNA, and now DSSR!

I understand you question in general. However, I am not sure what you mean "in calculating the global bending of the steel". Could you please provide a concrete example to illustrate exactly what (parameters) you are looking for?

Wherever practical, I am interested in expanding DSSR's functionality in ways that make sense to me. I can be more easily convinced by specific examples that I can understand.

Best regards,

Xiang-Jun

Offline Giulia Palermo

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Re: global bending of a single stranded DNA
« Reply #2 on: July 18, 2016, 05:34:17 pm »
Hi Xiang-Jun,

thank you for your reply.
As example, in the case of a double stranded DNA, I was calculating some global parameters like the Total bend , Helical-rise and Helical-Twist.
Of course , since a helix is not present in a double stranded DNA, the Helical-rise and Helical-Twist are not meaningful.
However, for a single stranded DNA, the global bent would be a very useful parameter. Is it possible to have a measure of it using DSSR? If not, can you suggest me some other measures

It is very important for my topic. I need to understand how the motions of my single strand correlate with the other part of the system.
any suggestion is welcomed!

anyway, I am a big fan of 3DNA and now of DSSR too!

many thanks
Giulia



 

Offline xiangjun

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Re: global bending of a single stranded DNA
« Reply #3 on: July 18, 2016, 06:14:45 pm »
Hi Giulia,

Thanks for your clarification.

The 3DNA analyze program can work for single-stranded DNA (or RNA), by successively treating each pair of neighbouring bases. As you noticed, the result may not be that meaningful, but the underlying algorithm is the same as for double helix. For example,

Code: [Select]
# treat as a double help
find_pair 355d.pdb | analyze

# tread as single-stranded (notice the "-s" option)
find_pair -s 355d.pdb | analyze

If I understand you correctly, you are looking for a single ("global") parameter to quantify single-stranded DNA bend (or irregularity). Right? In 3DNA/DSSR output for a double helix, the least-squares fitted global helical axis has a rise value, and the variation associated with it. In the example of 355d, the numbers are 3.30(0.52) as shown below.
Deviation from regular linear helix: 3.30(0.52)    # 3DNA analyze output
helical-rise:   3.30(0.52)   # DSSR output with --more option

The rise variation may serve as a measure of global non-linearity of a DNA duplex since for perfectly regular fiber models, it is zero. While this parameters has been calculated in 3DNA from the very beginning, it has never been put into good use. I sense a similar number for single-stranded structure may be useful for your purpose.

As a side note, DSSR is part of 3DNA. The connection is implicit by the running command 'x3dna-dssr'. DSSR has a complete new code-base, and it is a representative of what would become 3DNA version 3. I am consolidating key features of find_pair/analyze in 3DNA v2.3 into DSSR.

Best regards,

Xiang-Jun


 

Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.