6S7D

Self-complementary duplex DNA containing an internucleoside phosphoroselenolate

6S7D の概要

• エントリーDOI: 10.2210/pdb6s7d/pdb
• 分子名称: DNA (5'-D(*GP*(XCI)P*CP*CP*CP*GP*GP*GP*AP*C)-3'), BARIUM ION, SODIUM ION, ... (6 entities in total)
• 機能のキーワード: modified phasing duplex phosphoroselenolate, dna
• 由来する生物種: synthetic construct
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 6744.34

構造登録者

Conlon, P.F.,Steinhogl, J.,Vyle, J.S.,Hall, J.P. (登録日: 2019-07-04, 公開日: 2019-11-06, 最終更新日: 2024-05-15)

主引用文献

Conlon, P.F.,Eguaogie, O.,Wilson, J.J.,Sweet, J.S.T.,Steinhoegl, J.,Englert, K.,Hancox, O.G.A.,Law, C.J.,Allman, S.A.,Tucker, J.H.R.,Hall, J.P.,Vyle, J.S.
Solid-phase synthesis and structural characterisation of phosphoroselenolate-modified DNA: a backbone analogue which does not impose conformational bias and facilitates SAD X-ray crystallography.
Chem Sci, 10:10948-10957, 2019

PubMed Abstract: Oligodeoxynucleotides incorporating internucleotide phosphoroselenolate linkages have been prepared under solid-phase synthesis conditions using dimer phosphoramidites. These dimers were constructed following the high yielding Michaelis-Arbuzov (M-A) reaction of nucleoside -phosphonate derivatives with 5'-deoxythymidine-5'-selenocyanate and subsequent phosphitylation. Efficient coupling of the dimer phosphoramidites to solid-supported substrates was observed under both manual and automated conditions and required only minor modifications to the standard DNA synthesis cycle. In a further demonstration of the utility of M-A chemistry, the support-bound selenonucleoside was reacted with an -phosphonate and then chain extended using phosphoramidite chemistry. Following initial unmasking of methyl-protected phosphoroselenolate diesters, pure oligodeoxynucleotides were isolated using standard deprotection and purification procedures and subsequently characterised by mass spectrometry and circular dichroism. The CD spectra of both modified and native duplexes derived from self-complementary sequences with A-form, B-form or mixed conformational preferences were essentially superimposable. These sequences were also used to study the effect of the modification upon duplex stability which showed context-dependent destabilisation (-0.4 to -3.1 °C per phosphoroselenolate) when introduced at the 5'-termini of A-form or mixed duplexes or at juxtaposed central loci within a B-form duplex (-1.0 °C per modification). As found with other nucleic acids incorporating selenium, expeditious crystallisation of a modified decanucleotide A-form duplex was observed and the structure solved to a resolution of 1.45 Å. The DNA structure adjacent to the modification was not significantly perturbed. The phosphoroselenolate linkage was found to impart resistance to nuclease activity.

PubMed: 32190252
DOI: 10.1039/c9sc04098f

実験手法

X-RAY DIFFRACTION (1.45 Å)