2gun
From Proteopedia
| Line 1: | Line 1: | ||
[[Image:2gun.gif|left|200px]] | [[Image:2gun.gif|left|200px]] | ||
| - | + | <!-- | |
| - | + | The line below this paragraph, containing "STRUCTURE_2gun", creates the "Structure Box" on the page. | |
| - | + | You may change the PDB parameter (which sets the PDB file loaded into the applet) | |
| - | + | or the SCENE parameter (which sets the initial scene displayed when the page is loaded), | |
| - | | | + | or leave the SCENE parameter empty for the default display. |
| - | | | + | --> |
| - | + | {{STRUCTURE_2gun| PDB=2gun | SCENE= }} | |
| - | + | ||
| - | + | ||
| - | }} | + | |
'''RNA-Binding Affinities and Crystal Structure of Oligonucleotides containing Five-Atom Amide-Based Backbone Structures''' | '''RNA-Binding Affinities and Crystal Structure of Oligonucleotides containing Five-Atom Amide-Based Backbone Structures''' | ||
| Line 19: | Line 16: | ||
==About this Structure== | ==About this Structure== | ||
| - | + | Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GUN OCA]. | |
==Reference== | ==Reference== | ||
RNA-Binding affinities and crystal structure of oligonucleotides containing five-atom amide-based backbone structures., Pallan PS, von Matt P, Wilds CJ, Altmann KH, Egli M, Biochemistry. 2006 Jul 4;45(26):8048-57. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16800629 16800629] | RNA-Binding affinities and crystal structure of oligonucleotides containing five-atom amide-based backbone structures., Pallan PS, von Matt P, Wilds CJ, Altmann KH, Egli M, Biochemistry. 2006 Jul 4;45(26):8048-57. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16800629 16800629] | ||
| - | [[Category: Protein complex]] | ||
[[Category: Egli, M.]] | [[Category: Egli, M.]] | ||
[[Category: Pallan, P S.]] | [[Category: Pallan, P S.]] | ||
| - | [[Category: | + | [[Category: Amide bearing dna]] |
| - | [[Category: | + | [[Category: Dna]] |
| - | [[Category: | + | [[Category: Dna:rna hybrid]] |
| - | [[Category: | + | [[Category: Internucleosidic amide linkage]] |
| - | [[Category: | + | [[Category: Rna]] |
| - | [[Category: | + | [[Category: Thymidine dimer]] |
| - | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 05:33:25 2008'' | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | |
Revision as of 02:33, 4 May 2008
RNA-Binding Affinities and Crystal Structure of Oligonucleotides containing Five-Atom Amide-Based Backbone Structures
Overview
Among the hundreds of nucleic acid analogues that have been studied over the last two decades only very few exhibit backbones with linkers between residues that are either shorter or longer than the four-atom linker O3'-P-O5'-C5' connecting sugar ring moieties in DNA and RNA. 2'-Deoxyribonucleoside dimers connected by a five-atom linker O3'-CH(CH(3))-CO-NH-CH(2) (*designates a chiral center) were reported to lead to only a slight destabilization of RNA-DNA hybrids in which the DNA strand contained one or several of these amide-linked dimers (De Napoli, L., Iadonisi, A., Montesarchio, D., Varra, M., and Piccialli, G. (1995) Synthesis of thymidine dimers containing a new internucleosidic amide linkage and their incorporation into oligodeoxyribonucleotides, Bioorg. Med. Chem. Lett. 5, 1647-1652). To analyze the influence of various chemistries of such five-atom amide linkers on the RNA-binding affinity of modified DNA strands, we have synthesized five different amide-linked dimers, including structures with homochiral linkers of the type X3'-C*H(CH(3))-CO-NH-CH(2) (X = O, CH(2)) as well as the corresponding analogues carrying methoxy groups at the 2'-position of the 3'-nucleosides. We have conducted a detailed thermodynamic analysis of duplex formation between the modified DNA and RNA, with the DNA strands containing between one and seven consecutive modified dimers. Some of the five-atom-linked dimers lead to significantly higher RNA-binding affinities compared with that of native DNA. Interestingly, the linkers with opposite stereochemistry at the chiral center stabilize duplexes between the modified DNA and RNA to different degrees. CD spectroscopy in solution and a crystal structure of an RNA-DNA duplex with a single amide-linked dimer demonstrate that the longer amide backbones do not disrupt the duplex geometry. These observations provide further evidence that stable cross-pairing between two different types of nucleic acids does not require the numbers of atoms linking their individual residues to match.
About this Structure
Full crystallographic information is available from OCA.
Reference
RNA-Binding affinities and crystal structure of oligonucleotides containing five-atom amide-based backbone structures., Pallan PS, von Matt P, Wilds CJ, Altmann KH, Egli M, Biochemistry. 2006 Jul 4;45(26):8048-57. PMID:16800629 Page seeded by OCA on Sun May 4 05:33:25 2008
