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Author Topic: 3DNA misses one pair of nucleotides  (Read 4215 times)

Offline pqtak

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3DNA misses one pair of nucleotides
« on: October 28, 2008, 01:16:53 pm »
Hi all,
I have three 20-bp identical DNAs in my pdb. 3DNA finds 59 pairs missing a second pair in one DNA. What can cause such thing?

Offline pqtak

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Re: 3DNA misses one pair of nucleotides
« Reply #1 on: October 31, 2008, 06:26:08 pm »
I figured out what happened. A base of the first nucleotide was making a pair with the base of the  second nucleotide.
I fuxed this problem

Offline ghzheng

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Re: 3DNA misses one pair of nucleotides
« Reply #2 on: November 01, 2008, 09:53:17 pm »
Can you please make clear what was your problem and how you fixed it? I don't get it.
Thanks.

Guohui

Offline pqtak

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Re: 3DNA misses one pair of nucleotides
« Reply #3 on: November 02, 2008, 10:55:01 pm »
The problem was that I have 60 nucleotide pairs (double -stranded DNA), but the program found only 59 pairs. Then I realized that a base from one nucleotide makes a Watson-Crick pair with the wrong nucleotide due to low resolution and poor density. So, I restrained the bases so that they are making right pairs and now the program (3DNA) finds all 60 pairs.

 

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.