Role of the backbone of nucleic acids in the stability of Hg2+-mediated canonical base pairs and thymine–thymine mispair: a DFT study

Abstract Metallo-nucleic acids have been investigated for their applications in the field of nanodevices and genetic expansion. The cytosine-Ag+-cytosine mismatch base pair interactions and their stability in nucleic acids have attracted the attention of chemists. We report a systematic study of canonical, mismatch, Ag+ mediated system with CC, AT, and GC base pairs computationally. The stability of such mismatch base pairs is dependent on the pH range ~5 to 9 and the duplexes beyond this range are unstable. The DFT calculations performed with the model DNA duplexes comprising of such mismatch pairs reveal the stability trend while varying the pH conditions. The stability of canonical Watson-Crick ATGC base pairs was compared with the CCAT and CCGC mismatch base pairs and the calculated results at B3LYP-D3/6-31G* level of theory in the aqueous phase suggest that the base stacking and hydrogen bonding are well maintained in the former case, however, the larger perturbations in the geometry are observed with the mispair and relatively unstable. The calculated binding energy at B3LYP/6-31G* level of theory of ATGC is energetically more stable (~15 kcal/mol) than the mismatch base pairs. The Ag+ mediated mismatch base pairs i.e., C_CAT and C_CGC examined at the same level of theory suggest that the CC mismatch base pairs complexed with proper alignment to the Ag+ ion and the AT and GC bases maintained the hydrogen bonding interactions. The mismatched base pair duplex systems i.e., C_CAT and C_CGC are structurally similar to the canonical Watson-Crick base pairs and energetically stable by ~40 and ~50 kcal/mol compared to the canonical ATGC base pairs. The experimental report on the thermal transition profile in 5’-(A)10C(A)10-3’ and 5’ (T)10C(T)10-3’ duplexes showed remarkable stability and corroborate the calculated results.[1] The stability of Ag+ mediated mismatch bases at the higher pH 9 was also examined and the nucleobases such as guanine and thymine would be deprotonated under this condition. The calculated results suggest that the CCA_T and CCG_C duplexes are largely distorted with the complexation of Ag+ with the AT and GC base pairs and would in turn denature the duplex. The AIM analysis performed at B3LYP-D3/6-31G* level of theory for all the studied Ag+ mediated complexes reveals that the Ag+ interaction with the corresponding nucleobases was electrostatic in nature. The role of pH in governing the stability of C-Ag+-C complex formation in mismatch base nucleic acids is crucial for their application of genetic expansion and nucleic acid-based nanodevices.

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Role of sulfonation in the stability, reactivity, and selectivity of poly(ether imide) used to develop ion exchange membranes: DFT study with application to fuel cells

Journal of Molecular Modeling ◽

10.1007/s00894-014-2325-2 ◽

2014 ◽

Vol 20 (7) ◽

Cited By ~ 6

Author(s):

Ernesto López-Chávez ◽

Yésica A. Peña-Castañeda ◽

L. César de la Portilla-Maldonado ◽

Javier Guzmán-Pantoja ◽

José Manuel Martínez-Magadán ◽

...

Keyword(s):

Fuel Cells ◽

Ion Exchange ◽

Dft Study ◽

Ion Exchange Membranes ◽

The Stability

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Periodic DFT study of water adsorption on m-WO3(001), m-WO3(100), h-WO3(001) and h-WO3(100). Role of hydroxyl groups on the stability of polar hexagonal surfaces

Surface Science ◽

10.1016/j.susc.2019.121558 ◽

2020 ◽

Vol 694 ◽

pp. 121558 ◽

Cited By ~ 2

Author(s):

Oscar Hurtado-Aular ◽

Alba B. Vidal ◽

Aníbal Sierraalta ◽

Rafael Añez

Keyword(s):

Water Adsorption ◽

Dft Study ◽

Hydroxyl Groups ◽

The Stability ◽

Periodic Dft

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On the role of mercury in the non-covalent stabilisation of consecutive U–HgII–U metal-mediated nucleic acid base pairs: metallophilic attraction enters the world of nucleic acids

Physical Chemistry Chemical Physics ◽

10.1039/c0cp01534b ◽

2011 ◽

Vol 13 (1) ◽

pp. 100-103 ◽

Cited By ~ 25

Author(s):

Ladislav Benda ◽

Michal Straka ◽

Yoshiyuki Tanaka ◽

Vladimír Sychrovský

Keyword(s):

Nucleic Acid ◽

Nucleic Acids ◽

Acid Base ◽

Base Pairs ◽

The World ◽

Nucleic Acid Base

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Probing the role of hydrogen bonds in the stability of base pairs in double-helical DNA

Biopolymers ◽

10.1002/bip.20811 ◽

2007 ◽

Vol 87 (2-3) ◽

pp. 165-173 ◽

Cited By ~ 13

Author(s):

Alicia E. Every ◽

Irina M. Russu

Keyword(s):

Hydrogen Bonds ◽

Base Pairs ◽

The Stability

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2′-O-Methyl- and 2′-O-propargyl-5-methylisocytidine: synthesis, properties and impact on the isoCd–dG and the isoCd–isoGd base pairing in nucleic acids with parallel and antiparallel strand orientation

Organic & Biomolecular Chemistry ◽

10.1039/c6ob00622a ◽

2016 ◽

Vol 14 (21) ◽

pp. 4927-4942 ◽

Cited By ~ 3

Author(s):

Sunit K. Jana ◽

Peter Leonard ◽

Sachin A. Ingale ◽

Frank Seela

Keyword(s):

Nucleic Acids ◽

Base Pairing ◽

Base Pairs ◽

Chain Orientation ◽

Strand Orientation ◽

Synthesis Properties ◽

The Stability ◽

The Impact

The impact of 2′-O-alkyl residues on the stability of iCd–dG and iCd–iGd base pairs was studied in DNA with parallel and antiparallel chain orientation.

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Synthesis and structure of fluoroindole nucleosides

Canadian Journal of Chemistry ◽

10.1139/v07-020 ◽

2007 ◽

Vol 85 (4) ◽

pp. 283-292 ◽

Cited By ~ 8

Author(s):

Jelena Božilović ◽

Jan W Bats ◽

Joachim W Engels

Keyword(s):

Nucleic Acid ◽

Nucleic Acids ◽

Driving Forces ◽

Rna Stability ◽

Building Blocks ◽

Biologically Active ◽

Dna And Rna ◽

The Stability ◽

Indole Synthesis

Chemically modified bases are frequently used to stabilize nucleic acids, to study the driving forces for nucleic acid structure formation, and to tune DNA and RNA hybridization conditions. Nucleoside analogues are chemical means to investigate hydrogen bonds, base stacking, and solvation as the three predominant forces that are responsible for the stability of nucleic acids. To obtain deeper insight into the contributions of these interactions to RNA stability, we decided to synthesize some novel nucleic acid analogues where the nucleobases are replaced by fluoroindoles. Fluorinated indoles can be compared with fluorinated benzimidazoles to determine the role of nitrogen in five-membered ring systems. The synthesis of fluoroindole ribonucleosides as well as the X-ray crystal structures of all synthesized fluoroindole ribonucleosides are reported here. These compounds could also be building blocks for a variety of biologically active RNA analogues.Key words: indoles, nucleosides, crystal structure, glycosilation, indole-synthesis.

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