Question on hairpin-loop in PDB entry 3uzn

[febos]

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?

[xiangjun]

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

[febos]

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
And this is an example picture:

Oh, and I was using 3DNA ver 1.5.

[xiangjun]

• 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", 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' to make each one focused on a specific topic, and not too lengthy.