1tuq
From Proteopedia
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'''NMR Structure Analysis of the B-DNA Dodecamer CTCtCACGTGGAG with a tricyclic cytosin base analogue''' | '''NMR Structure Analysis of the B-DNA Dodecamer CTCtCACGTGGAG with a tricyclic cytosin base analogue''' | ||
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==About this Structure== | ==About this Structure== | ||
| - | + | Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TUQ OCA]. | |
==Reference== | ==Reference== | ||
DNA adopts normal B-form upon incorporation of highly fluorescent DNA base analogue tC: NMR structure and UV-Vis spectroscopy characterization., Engman KC, Sandin P, Osborne S, Brown T, Billeter M, Lincoln P, Norden B, Albinsson B, Wilhelmsson LM, Nucleic Acids Res. 2004 Sep 27;32(17):5087-95. Print 2004. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15452275 15452275] | DNA adopts normal B-form upon incorporation of highly fluorescent DNA base analogue tC: NMR structure and UV-Vis spectroscopy characterization., Engman KC, Sandin P, Osborne S, Brown T, Billeter M, Lincoln P, Norden B, Albinsson B, Wilhelmsson LM, Nucleic Acids Res. 2004 Sep 27;32(17):5087-95. Print 2004. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15452275 15452275] | ||
| - | [[Category: Protein complex]] | ||
[[Category: Albinsson, B.]] | [[Category: Albinsson, B.]] | ||
[[Category: Billeter, M.]] | [[Category: Billeter, M.]] | ||
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[[Category: Sandin, P.]] | [[Category: Sandin, P.]] | ||
[[Category: Wilhelmsson, L M.]] | [[Category: Wilhelmsson, L M.]] | ||
| - | [[Category: | + | [[Category: B-form dna]] |
| - | [[Category: | + | [[Category: Fluorescent dna base analogue]] |
| - | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 10:23:25 2008'' | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | |
Revision as of 07:23, 3 May 2008
NMR Structure Analysis of the B-DNA Dodecamer CTCtCACGTGGAG with a tricyclic cytosin base analogue
Overview
The influence of the highly fluorescent tricyclic cytosine base analogue (tC) on duplex DNA conformation is investigated. The duplex properties are characterized by absorbance and circular dichroism (CD) for all combinations of neighbouring bases to tC, and an NMR structure is determined for one tC-containing sequence. For the oligonucleotides with one tC incorporated instead of cytosine, the melting temperature is increased on average by 2.7 degrees C above that for the unmodified ones. CD spectra are practically identical for modified and unmodified sequences, indicating an unperturbed B-DNA conformation. The NMR structure determination of the self-complementary sequence 5'-CTC(tC)ACGTGGAG shows a DNA conformation consistent with B-form for the whole duplex. The root-mean-square distance for the nucleotides of the eight central base pairs between the 10 structures with lowest CYANA target functions and a mean structure is 0.45 +/- 0.17 A. The NMR data confirm correct base pairing for tC by the observation of both intrastrand and interstrand imino proton NOEs. Altogether, this suggests that tC works well as a cytosine analogue, i.e. it is situated in the base stack, forming hydrogen bonds with G in the complementary strand, without distorting the DNA backbone conformation. This first example of an artificial, highly fluorescent DNA base that does not perturb the DNA conformation could have valuable applications for the study of the structure and dynamics of nucleic acid systems.
About this Structure
Full crystallographic information is available from OCA.
Reference
DNA adopts normal B-form upon incorporation of highly fluorescent DNA base analogue tC: NMR structure and UV-Vis spectroscopy characterization., Engman KC, Sandin P, Osborne S, Brown T, Billeter M, Lincoln P, Norden B, Albinsson B, Wilhelmsson LM, Nucleic Acids Res. 2004 Sep 27;32(17):5087-95. Print 2004. PMID:15452275 Page seeded by OCA on Sat May 3 10:23:25 2008
