Water-Mediated Interactions Enhance Alkaline Earth Cation Chelation in Neighboring Cavities of a Cytosine Quartet in the DNA Quadruplex
Abstract
Larger Coulombic repulsion between divalent cations compared to the monovalent counterparts dictates the cation-cation distance in the central ion channel of quadruplexes. In this work, density functional theory and a continuum solvation model were employed to study bond energies of alkaline earth cations in adjacent cavities of the central ion channel. Four crystallized tetramolecular quadruplexes with various geometric constraints and structural motifs available in the Protein Data Bank were examined in order to understand how the cation binding affinities could be increased in aqueous solution. A cytosine quartet sandwiched between guanine quartets has a larger bond energy of the second alkaline earth cation in comparison with guanine and uracil quartets. Four highly conserved hydrogen-bonded water molecules in the center of the cytosine quartet are responsible for a higher electrostatic interaction with the cations in comparison with guanines' carbonyl groups. The reported findings... are valuable for the design of synthetic quadruplexes templated with divalent cations for optoelectronic applications.
Source:
Journal of Physical Chemistry B, 2021, 125, 43, 11996-12005Publisher:
- Amer Chemical Soc, Washington
Funding / projects:
- VRE for regional Interdisciplinary communities in Southeast Europe and the Eastern Mediterranean (EU-675121)
- Ministry of Education, Science and Technological Development, Republic of Serbia, Grant no. 200146 (University of Belgrade, Faculty of Physical Chemistry) (RS-200146)
- Ministry of Education, Science and Technological Development, Republic of Serbia, Grant no. 200053 (University of Belgrade, Institute for Multidisciplinary Research) (RS-200053)
- Qatar National Research Fund (QNRF) [NPRP11S-1126-170033]
DOI: 10.1021/acs.jpcb.1c05598
ISSN: 1520-6106
PubMed: 34694801
WoS: 000716447400020
Scopus: 2-s2.0-85118950672
Collections
Institution/Community
Institut za multidisciplinarna istraživanjaTY - JOUR AU - Milovanović, Branislav AU - Petković, Milena AU - Popov, Igor AU - Etinski, Mihajlo PY - 2021 UR - http://rimsi.imsi.bg.ac.rs/handle/123456789/1499 AB - Larger Coulombic repulsion between divalent cations compared to the monovalent counterparts dictates the cation-cation distance in the central ion channel of quadruplexes. In this work, density functional theory and a continuum solvation model were employed to study bond energies of alkaline earth cations in adjacent cavities of the central ion channel. Four crystallized tetramolecular quadruplexes with various geometric constraints and structural motifs available in the Protein Data Bank were examined in order to understand how the cation binding affinities could be increased in aqueous solution. A cytosine quartet sandwiched between guanine quartets has a larger bond energy of the second alkaline earth cation in comparison with guanine and uracil quartets. Four highly conserved hydrogen-bonded water molecules in the center of the cytosine quartet are responsible for a higher electrostatic interaction with the cations in comparison with guanines' carbonyl groups. The reported findings are valuable for the design of synthetic quadruplexes templated with divalent cations for optoelectronic applications. PB - Amer Chemical Soc, Washington T2 - Journal of Physical Chemistry B T1 - Water-Mediated Interactions Enhance Alkaline Earth Cation Chelation in Neighboring Cavities of a Cytosine Quartet in the DNA Quadruplex EP - 12005 IS - 43 SP - 11996 VL - 125 DO - 10.1021/acs.jpcb.1c05598 ER -
@article{ author = "Milovanović, Branislav and Petković, Milena and Popov, Igor and Etinski, Mihajlo", year = "2021", abstract = "Larger Coulombic repulsion between divalent cations compared to the monovalent counterparts dictates the cation-cation distance in the central ion channel of quadruplexes. In this work, density functional theory and a continuum solvation model were employed to study bond energies of alkaline earth cations in adjacent cavities of the central ion channel. Four crystallized tetramolecular quadruplexes with various geometric constraints and structural motifs available in the Protein Data Bank were examined in order to understand how the cation binding affinities could be increased in aqueous solution. A cytosine quartet sandwiched between guanine quartets has a larger bond energy of the second alkaline earth cation in comparison with guanine and uracil quartets. Four highly conserved hydrogen-bonded water molecules in the center of the cytosine quartet are responsible for a higher electrostatic interaction with the cations in comparison with guanines' carbonyl groups. The reported findings are valuable for the design of synthetic quadruplexes templated with divalent cations for optoelectronic applications.", publisher = "Amer Chemical Soc, Washington", journal = "Journal of Physical Chemistry B", title = "Water-Mediated Interactions Enhance Alkaline Earth Cation Chelation in Neighboring Cavities of a Cytosine Quartet in the DNA Quadruplex", pages = "12005-11996", number = "43", volume = "125", doi = "10.1021/acs.jpcb.1c05598" }
Milovanović, B., Petković, M., Popov, I.,& Etinski, M.. (2021). Water-Mediated Interactions Enhance Alkaline Earth Cation Chelation in Neighboring Cavities of a Cytosine Quartet in the DNA Quadruplex. in Journal of Physical Chemistry B Amer Chemical Soc, Washington., 125(43), 11996-12005. https://doi.org/10.1021/acs.jpcb.1c05598
Milovanović B, Petković M, Popov I, Etinski M. Water-Mediated Interactions Enhance Alkaline Earth Cation Chelation in Neighboring Cavities of a Cytosine Quartet in the DNA Quadruplex. in Journal of Physical Chemistry B. 2021;125(43):11996-12005. doi:10.1021/acs.jpcb.1c05598 .
Milovanović, Branislav, Petković, Milena, Popov, Igor, Etinski, Mihajlo, "Water-Mediated Interactions Enhance Alkaline Earth Cation Chelation in Neighboring Cavities of a Cytosine Quartet in the DNA Quadruplex" in Journal of Physical Chemistry B, 125, no. 43 (2021):11996-12005, https://doi.org/10.1021/acs.jpcb.1c05598 . .