3DNA Forum

Questions and answers => General discussions (Q&As) => Topic started by: mikeshelk on October 30, 2010, 04:17:28 pm

Title: Rebuild from sugar-phosphate backbone
Post by: mikeshelk on October 30, 2010, 04:17:28 pm: Hello, dear Xiang-Jun!

As far as I understood, "rebuild" builds structure from base parameters. So you wrote in your blog "The structural parameters can be used to rebuild the structure, which is virtually identical in base geometry (i.e., without taking consideration of the sugar-phosphate backbone) to the original structure"
Tell me please, is it possible somehow to rebuild structure using only sequence and sugar-phosphate backbone parameters? I.e. without time-consuming minimization to define approximately Calladine parameters for each nucleotide pair of a given sequence, having only backbone?

Thanks,
Mikhail Schelkunov
Title: Re: Rebuild from sugar-phosphate backbone
Post by: xiangjun on October 30, 2010, 08:56:41 pm: Quote
As far as I understood, "rebuild" builds structure from base parameters. So you wrote in your blog "The structural parameters can be used to rebuild the structure, which is virtually identical in base geometry (i.e., without taking consideration of the sugar-phosphate backbone) to the original structure"
Yes, as shown in Table 3 of the 2003 3DNA NAR papers (http://http://nar.oxfordjournals.org/content/31/17/5108/T3.expansion.html), and the corresponding examples in the directory [mono:3i9kwmym]$X3DNA/examples/analyze_rebuild/[/mono:3i9kwmym].

Quote
Tell me please, is it possible somehow to rebuild structure using only sequence and sugar-phosphate backbone parameters? I.e. without time-consuming minimization to define approximately Calladine parameters for each nucleotide pair of a given sequence, having only backbone?
No, as far as 3DNA is concerned. Also, what do you mean exactly by "sugar-phosphate backbone parameters"?
[hr:3i9kwmym][/hr:3i9kwmym]
Please note that the 3DNA [mono:3i9kwmym]analyze/rebuild[/mono:3i9kwmym] pair is purely geometry-based, without any "time-consuming minimization" involved. Building a DNA structure with or without the sugar-phosphate backbone should be (virtually) equally efficient.

HTH,

Xiang-Jun