7SM9

[U:Hg2+/Ag+:U--pH 10] Metal-mediated DNA base pair in tensegrity triangle in Ag+ and Hg2+ solution

7SM9 の概要

• エントリーDOI: 10.2210/pdb7sm9/pdb
• 関連するPDBエントリー: 7SD8 7SM6
• 分子名称: DNA (5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*UP*TP*GP*GP*AP*CP*AP*TP*CP*A)-3'), DNA (5'-D(P*CP*CP*AP*UP*AP*CP*A)-3'), DNA (5'-D(P*GP*GP*CP*TP*GP*CP*T)-3'), ... (6 entities in total)
• 機能のキーワード: tensegrity triangle, self-assembling crystal, metal-mediated mismatch, dna
• 由来する生物種: synthetic construct; 詳細
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 13067.82

構造登録者

Lu, B.,Vecchioni, S.,Seeman, N.C.,Sha, R.,Ohayon, Y.P. (登録日: 2021-10-25, 公開日: 2022-11-23, 最終更新日: 2023-08-30)

主引用文献

Lu, B.,Ohayon, Y.P.,Woloszyn, K.,Yang, C.F.,Yoder, J.B.,Rothschild, L.J.,Wind, S.J.,Hendrickson, W.A.,Mao, C.,Seeman, N.C.,Canary, J.W.,Sha, R.,Vecchioni, S.
Heterobimetallic Base Pair Programming in Designer 3D DNA Crystals.
J.Am.Chem.Soc., 145:17945-17953, 2023

PubMed Abstract: Metal-mediated DNA (mmDNA) presents a pathway toward engineering bioinorganic and electronic behavior into DNA devices. Many chemical and biophysical forces drive the programmable chelation of metals between pyrimidine base pairs. Here, we developed a crystallographic method using the three-dimensional (3D) DNA tensegrity triangle motif to capture single- and multi-metal binding modes across granular changes to environmental pH using anomalous scattering. Leveraging this programmable crystal, we determined 28 biomolecular structures to capture mmDNA reactions. We found that silver(I) binds with increasing occupancy in T-T and U-U pairs at elevated pH levels, and we exploited this to capture silver(I) and mercury(II) within the same base pair and to isolate the titration points for homo- and heterometal base pair modes. We additionally determined the structure of a C-C pair with both silver(I) and mercury(II). Finally, we extend our paradigm to capture cadmium(II) in T-T pairs together with mercury(II) at high pH. The precision self-assembly of heterobimetallic DNA chemistry at the sub-nanometer scale will enable atomistic design frameworks for more elaborate mmDNA-based nanodevices and nanotechnologies.

PubMed: 37530628
DOI: 10.1021/jacs.3c05478

実験手法

X-RAY DIFFRACTION (3.24 Å)