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Questions and answers => General discussions (Q&As) => Topic started by: lvelve0901 on December 23, 2016, 07:41:03 pm

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Title: epsilon and zeta should be 5'-end or 3'-end of sugar
Post by: lvelve0901 on December 23, 2016, 07:41:03 pm

Hi, xiangjun,

I am confused about the phosphorous label in DNA.

Normally, phosphorous of a given NTP is the one connected to the 5'-end of sugar right?
So when we say phosphorous of a DA or DT etc., we mean 5'-phosphorous of DA and DT, is it correct?

However, epsilon and zeta by definition is at the 3'-end of a sugar (related to BI/BII). So when we say BI/BII of a residue, it is related to the 3'-end of the phosphorous which is the next residue's phosphorous, am I right?

The reason why I ask this question is I find that some papers label the 31P to be 3'-end of the sugar and other label the 31P to be 5'-end of the sugar which are not consistent.

Is there any standard opinion about which phosphorous belongs to which residue?

Thanks.

Best,
Honglue

Title: Re: epsilon and zeta should be 5'-end or 3'-end of sugar
Post by: lvelve0901 on December 23, 2016, 07:44:40 pm

For example,

A DNA single strand: 5'-DA-P-DT-P-DC-P-DG-OH-3'

what is the phosphorus of DT, the first P or the second P?

Best,
Honglue

Title: Re: epsilon and zeta should be 5'-end or 3'-end of sugar
Post by: xiangjun on December 23, 2016, 08:13:48 pm

The first P in your sequence.

To see the convention of atom labeling in nucleic acid structures, have a look of DNA structures, e.g., 355d. For your case, O5'(i)--[P/OP1/OP2...base...O3'](i+1).

Xiang-Jun

Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids

Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University