Netiquette · Download · News · Gallery · Homepage · DSSR · Web-DSSR · DSSR Manual · G4 Structures · DSSR-Jmol · DSSR-PyMOL · Web-SNAP

Author Topic: epsilon and zeta should be 5'-end or 3'-end of sugar  (Read 1810 times)

Offline lvelve0901

  • regular
  • *
  • Posts: 56
    • View Profile
epsilon and zeta should be 5'-end or 3'-end of sugar
« 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


Offline lvelve0901

  • regular
  • *
  • Posts: 56
    • View Profile
Re: epsilon and zeta should be 5'-end or 3'-end of sugar
« Reply #1 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


Offline xiangjun

  • Administrator
  • regular
  • *****
  • Posts: 1373
    • View Profile
    • 3DNA homepage
Re: epsilon and zeta should be 5'-end or 3'-end of sugar
« Reply #2 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
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

 

Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.