1TUQ

NMR Structure Analysis of the B-DNA Dodecamer CTCtCACGTGGAG with a tricyclic cytosin base analogue

1TUQ の概要

• エントリーDOI: 10.2210/pdb1tuq/pdb
• 分子名称: 5'-D(P*CP*TP*CP*(TC1)P*AP*CP*GP*TP*GP*GP*AP*G)-3' (1 entity in total)
• 機能のキーワード: fluorescent dna base analogue, b-form dna, dna
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 7539.07

構造登録者

Engman, K.C.,Sandin, P.,Osborne, S.,Brown, T.,Billeter, M.,Lincoln, P.,Norden, B.,Albinsson, B.,Wilhelmsson, L.M. (登録日: 2004-06-25, 公開日: 2004-10-05, 最終更新日: 2024-05-22)

主引用文献

Engman, K.C.,Sandin, P.,Osborne, S.,Brown, T.,Billeter, M.,Lincoln, P.,Norden, B.,Albinsson, B.,Wilhelmsson, L.M.
DNA adopts normal B-form upon incorporation of highly fluorescent DNA base analogue tC: NMR structure and UV-Vis spectroscopy characterization.
Nucleic Acids Res., 32:5087-5095, 2004

PubMed Abstract: 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.

PubMed: 15452275
DOI: 10.1093/nar/gkh844

実験手法

SOLUTION NMR