This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.
Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.
114d
From Proteopedia
(New page: 200px<br /><applet load="114d" size="450" color="white" frame="true" align="right" spinBox="true" caption="114d, resolution 2.500Å" /> '''INOSINE-ADENINE BAS...) |
|||
| Line 1: | Line 1: | ||
| - | [[Image:114d.gif|left|200px]]<br /><applet load="114d" size=" | + | [[Image:114d.gif|left|200px]]<br /><applet load="114d" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="114d, resolution 2.500Å" /> | caption="114d, resolution 2.500Å" /> | ||
'''INOSINE-ADENINE BASE PAIRS IN A B-DNA DUPLEX'''<br /> | '''INOSINE-ADENINE BASE PAIRS IN A B-DNA DUPLEX'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The structure of the synthetic deoxydodecamer d(C-G-C-I-A-A-T-T-A-G-C-G) | + | The structure of the synthetic deoxydodecamer d(C-G-C-I-A-A-T-T-A-G-C-G) has been determined by single crystal X-ray diffraction techniques at 2.5A resolution. The refinement converged with a crystallographic residual, R = 0.19 and the location of 64 solvent molecules. The sequence crystallises as a B-DNA helix with 10 Watson-Crick base-pairs (4 A.T. and 6 G.C) and 2 inosine.adenine (I.A) pairs. The present work shows that in the purine.purine base-pairs the adenine adopts syn orientation with respect to the furanose moiety while the inosine is in the trans (anti) orientation. Two hydrogen bonds link the I.A. base-pair, one between N-1(I) and N-7(A), the other between O-6(I) and N-6(A). This bulky purine.purine base-pair is incorporated in the double helix at two positions with little distortion of either local or global conformation. The pairing observed in this study is presented as a model for I.A base-pairs in RNA codon-anticodon interactions and may help explain the thermodynamic stability of inosine containing base-pairs. Conformational parameters and base stacking interactions are presented and where appropriate compared with those of the native compound, d(C-G-C-G-A-A-T-T-C-G-C-G) and with other studies of oligonucleotides containing purine.purine base-pairs. |
==About this Structure== | ==About this Structure== | ||
| - | 114D is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http:// | + | 114D is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=114D OCA]. |
==Reference== | ==Reference== | ||
| Line 13: | Line 13: | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
[[Category: Brown, T.]] | [[Category: Brown, T.]] | ||
| - | [[Category: Corfield, P | + | [[Category: Corfield, P W.R.]] |
| - | [[Category: Hunter, W | + | [[Category: Hunter, W N.]] |
[[Category: Kennard, O.]] | [[Category: Kennard, O.]] | ||
[[Category: Robinson, P.]] | [[Category: Robinson, P.]] | ||
| Line 22: | Line 22: | ||
[[Category: modified]] | [[Category: modified]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 11:37:36 2008'' |
Revision as of 09:37, 21 February 2008
|
INOSINE-ADENINE BASE PAIRS IN A B-DNA DUPLEX
Overview
The structure of the synthetic deoxydodecamer d(C-G-C-I-A-A-T-T-A-G-C-G) has been determined by single crystal X-ray diffraction techniques at 2.5A resolution. The refinement converged with a crystallographic residual, R = 0.19 and the location of 64 solvent molecules. The sequence crystallises as a B-DNA helix with 10 Watson-Crick base-pairs (4 A.T. and 6 G.C) and 2 inosine.adenine (I.A) pairs. The present work shows that in the purine.purine base-pairs the adenine adopts syn orientation with respect to the furanose moiety while the inosine is in the trans (anti) orientation. Two hydrogen bonds link the I.A. base-pair, one between N-1(I) and N-7(A), the other between O-6(I) and N-6(A). This bulky purine.purine base-pair is incorporated in the double helix at two positions with little distortion of either local or global conformation. The pairing observed in this study is presented as a model for I.A base-pairs in RNA codon-anticodon interactions and may help explain the thermodynamic stability of inosine containing base-pairs. Conformational parameters and base stacking interactions are presented and where appropriate compared with those of the native compound, d(C-G-C-G-A-A-T-T-C-G-C-G) and with other studies of oligonucleotides containing purine.purine base-pairs.
About this Structure
114D is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Inosine.adenine base pairs in a B-DNA duplex., Corfield PW, Hunter WN, Brown T, Robinson P, Kennard O, Nucleic Acids Res. 1987 Oct 12;15(19):7935-49. PMID:3671069
Page seeded by OCA on Thu Feb 21 11:37:36 2008
