Heterobimetallic Base Pair Programming in Designer 3D DNA Crystals
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-dimensio...
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Published in | Journal of the American Chemical Society Vol. 145; no. 32; pp. 17945 - 17953 |
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Main Authors | , , , , , , , , , , , , |
Format | Journal Article |
Language | English |
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United States
American Chemical Society
16.08.2023
American Chemical Society (ACS) |
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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. |
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AbstractList | 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. Not provided. 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. |
Author | Canary, James W. Lu, Brandon Rothschild, Lynn J. Sha, Ruojie Vecchioni, Simon Seeman, Nadrian C. Woloszyn, Karol Yang, Chu-fan Mao, Chengde Yoder, Jesse B. Wind, Shalom J. Hendrickson, Wayne A. Ohayon, Yoel P. |
AuthorAffiliation | Department of Chemistry Columbia University Department of Applied Physics and Applied Mathematics Department of Biochemistry and Molecular Biophysics |
AuthorAffiliation_xml | – name: Department of Biochemistry and Molecular Biophysics – name: Department of Chemistry – name: Department of Applied Physics and Applied Mathematics – name: Columbia University |
Author_xml | – sequence: 1 givenname: Brandon orcidid: 0000-0001-6424-2197 surname: Lu fullname: Lu, Brandon organization: Department of Chemistry – sequence: 2 givenname: Yoel P. surname: Ohayon fullname: Ohayon, Yoel P. organization: Department of Chemistry – sequence: 3 givenname: Karol surname: Woloszyn fullname: Woloszyn, Karol organization: Department of Chemistry – sequence: 4 givenname: Chu-fan surname: Yang fullname: Yang, Chu-fan organization: Department of Chemistry – sequence: 5 givenname: Jesse B. surname: Yoder fullname: Yoder, Jesse B. – sequence: 6 givenname: Lynn J. surname: Rothschild fullname: Rothschild, Lynn J. – sequence: 7 givenname: Shalom J. surname: Wind fullname: Wind, Shalom J. organization: Department of Applied Physics and Applied Mathematics – sequence: 8 givenname: Wayne A. surname: Hendrickson fullname: Hendrickson, Wayne A. organization: Columbia University – sequence: 9 givenname: Chengde orcidid: 0000-0001-7516-8666 surname: Mao fullname: Mao, Chengde organization: Department of Chemistry – sequence: 10 givenname: Nadrian C. orcidid: 0000-0002-9680-4649 surname: Seeman fullname: Seeman, Nadrian C. organization: Department of Chemistry – sequence: 11 givenname: James W. orcidid: 0000-0002-0352-8543 surname: Canary fullname: Canary, James W. organization: Department of Chemistry – sequence: 12 givenname: Ruojie orcidid: 0000-0002-0807-734X surname: Sha fullname: Sha, Ruojie organization: Department of Chemistry – sequence: 13 givenname: Simon orcidid: 0000-0001-8243-650X surname: Vecchioni fullname: Vecchioni, Simon email: sv1091@nyu.edu organization: Department of Chemistry |
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Snippet | Metal-mediated DNA (mmDNA) presents a pathway toward engineering bioinorganic and electronic behavior into DNA devices. Many chemical and biophysical forces... Not provided. |
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SubjectTerms | Base Pairing Chemistry DNA - chemistry Mercury - chemistry Silver - chemistry |
Title | Heterobimetallic Base Pair Programming in Designer 3D DNA Crystals |
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