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Good afternoon, mr. Xiang Jun. I have one more question. Yesterday I was looking at different outputs of find_pair and I found this:
A 149 A 162 A-+**-G
A 150 A 161 C-----G
A 151 A 160 C-----G
A 152 A 159 G-----C
A 153 A 158 C-----G
A 154 A 157 G-----C
A 155 A 156 C-----G
This region represent a hairpin loop of length zero (between 155 and 156). But I know that such things don't exist in the real life. This region was found in file 3UZN.pdb. Can you say something about it?
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Could you provide us reproducible details how you got this "hairpin loop of length zero (between 155 and 156)"? Which version of 3DNA are you using? I did not see nucleotides 156-162 (chain A) at all in PDB entry 3uzn downloaded from the current RCSB website.
Xiang-Jun
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I'm sorry this numbers was not from PDB but from the output:
156 155 0 # 39 | A:.171_:[..G]G-----C[..C]:.155_:A 2.13 0.21 41.31 7.67 1.05
157 154 0 # 40 | A:.172_:[..C]C-----G[..G]:.154_:A 1.14 1.05 36.08 8.79 1.74
158 153 0 # 41 | A:.173_:[..G]G-----C[..C]:.153_:A 1.71 0.64 14.01 8.98 1.49
159 152 0 # 42 | A:.174_:[..C]C-----G[..G]:.152_:A 0.91 0.16 13.88 9.06 -0.28
160 151 0 # 43 | A:.175_:[..G]G-----C[..C]:.151_:A 1.08 0.08 18.94 8.86 -0.26
161 150 0 # 44 | A:.176_:[..G]G-----C[..C]:.150_:A 0.47 0.38 12.90 8.88 -0.27
162 149 0 # 45 | A:.177_:[..G]G-**+-A[..A]:.149_:A 7.09 0.33 10.03 9.49 7.75
I also thought you know what hairpin loop is, i don't know why, I'm sorry.
Stem-loop intramolecular base pairing is a pattern that can occur in single-stranded DNA or, more commonly, in RNA. The structure is also known as a hairpin or hairpin loop. It occurs when two regions of the same strand, usually complementary in nucleotide sequence when read in opposite directions, base-pair to form a double helix that ends in an unpaired loop. The resulting structure is a key building block of many RNA secondary structures.
http://en.wikipedia.org/wiki/Stem-loop (http://en.wikipedia.org/wiki/Stem-loop)
And this is an example picture:
(http://upload.wikimedia.org/wikipedia/commons/3/3f/Stem-loop.svg)
Oh, and I was using 3DNA ver 1.5.
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- Well, with the excerpt from find_pair output, I can see what nucleotides (nts) you are referring to. As always, it's the details that count.
I also thought you know what hairpin loop is, i don't know why, I'm sorry.
I know what a hairpin loop is, but I certainly did not see what you were referring to in your previous post. Thanks for your wikipedia quota and link on "step-loop", however, I still miss your point as to how it is related to the helix (see attached figure) formed by nts 149-155 with 171-177 on chain A of PDB entry 3uzn.- So at this point, I have no comment to your initial question: "Can you say something about it?"
Oh, and I was using 3DNA ver 1.5.
I am glad to know that 3DNA v1.5, which was compiled (nearly) a decade ago, is still in use. As noted in "Download instructions (http://forum.x3dna.org/site-announcements/download-instructions/)", that version is obsolete, and "no longer supported". So it's the time to upgrade to v2.1 (beta).
Xiang-Jun
PS. Note that I have once again split the posts on hairpin-loop from the original thread 'Helices and Isolates in output of find_pair (http://forum.x3dna.org/general-discussions/helices-and-isolates-in-output-of-find_pair/)' to make each one focused on a specific topic, and not too lengthy.
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.
