Syntheses and characterizations of DNA duplexes having metal ion mediated base pairs

2014 ◽  
Author(s):  
Akira Ono ◽  
Itaru Okamoto ◽  
Hideo Urata ◽  
Hidetake Torigoe ◽  
Hisao Saneyoshia ◽  
...  
Keyword(s):  
Metal Ion ◽  
Dna Duplexes ◽  
Base Pairs

Metal ion-binding properties of DNA duplexes containing thiopyrimidine base pairs

2012 ◽  
Vol 48 (36) ◽  
pp. 4347 ◽  
Author(s):  
Itaru Okamoto ◽  
Takashi Ono ◽  
Rimi Sameshima ◽  
Akira Ono
Keyword(s):  
Metal Ion ◽  
Ion Binding ◽  
Dna Duplexes ◽  
Metal Ion Binding ◽  
Base Pairs ◽  
Binding Properties

scholarly journals Dynamic Structure and Stability of DNA Duplexes Bearing a Dinuclear Hg(II)-Mediated Base Pair

Molecules ◽  
2020 ◽  
Vol 25 (21) ◽  
pp. 4942
Author(s):  
Jim Bachmann ◽  
Isabell Schönrath ◽  
Jens Müller ◽  
Nikos L. Doltsinis
Keyword(s):  
Base Pair ◽  
Metal Ion ◽  
Model Building ◽  
Dynamic Structure ◽  
Quantum Mechanical ◽  
Distance Constraint ◽  
Dna Duplexes ◽  
Base Pairs ◽  
Intramolecular Bonding ◽  
Dynamics Simulations

Quantum mechanical (QM) and hybrid quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulations of a recently reported dinuclear mercury(II)-mediated base pair were performed aiming to analyse its intramolecular bonding pattern, its stability, and to obtain clues on the mechanism of the incorporation of mercury(II) into the DNA. The dynamic distance constraint was employed to find initial structures, control the dissociation process in an unbiased fashion and to determine the free energy required. A strong influence of the exocyclic carbonyl or amino groups of neighbouring base pairs on both the bonding pattern and the mechanism of incorporation was observed. During the dissociation simulation, an amino group of an adenine moiety of the adjacent base pair acts as a turnstile to rotate the mercury(II) ion out of the DNA core region. The calculations provide an important insight into the mechanism of formation of this dinuclear metal-mediated base pair and indicate that the exact location of a transition metal ion in a metal-mediated base pair may be more ambiguous than derived from simple model building.

Metal ion binding of modified pyrimidine-base pairs in DNA duplexes

2009 ◽  
Vol 53 (1) ◽  
pp. 17-18
Author(s):  
A. Ono ◽  
K. Iwamoto ◽  
K. Sugiyama ◽  
I. Okamoto
Keyword(s):  
Metal Ion ◽  
Ion Binding ◽  
Dna Duplexes ◽  
Metal Ion Binding ◽  
Base Pairs ◽  
Pyrimidine Base

Studies on the thymine–mercury–thymine base pairing in parallel and anti-parallel DNA duplexes

2015 ◽  
Vol 39 (11) ◽  
pp. 8752-8762 ◽  
Author(s):  
Gaofeng Liu ◽  
Zhiwen Li ◽  
Junfei Zhu ◽  
Yang Liu ◽  
Ying Zhou ◽  
...  
Keyword(s):  
Dna Duplexes ◽  
Base Pairing ◽  
Dna Duplex ◽  
Base Pairs ◽  
Thermal Stabilities

Parallel and anti-parallel T–Hg–T base pairs have different thermal stabilities and conformational influences on DNA duplex structures.

Silver(I)‐Ion‐Mediated Cytosine‐Containing Base Pairs: Metal Ion Specificity for Duplex Stabilization and Susceptibility toward DNA Polymerases

ChemBioChem ◽  
2019 ◽  
Vol 21 (4) ◽  
pp. 517-522 ◽  
Author(s):  
Tatsuya Funai ◽  
Megumi Aotani ◽  
Risa Kiriu ◽  
Junko Nakamura ◽  
Yuki Miyazaki ◽  
...  
Keyword(s):  
Metal Ion ◽  
Dna Polymerases ◽  
Base Pairs ◽  
Ion Specificity

scholarly journals Metal-mediated base pairs in parallel-stranded DNA

2017 ◽  
Vol 13 ◽  
pp. 2671-2681 ◽  
Author(s):  
Jens Müller
Keyword(s):  
Nucleic Acid ◽  
Complex Formation ◽  
Transition Metal Ions ◽  
Dna Duplexes ◽  
Base Pairs ◽  
Experimental Conditions ◽  
Site Specific ◽  
Glycosidic Bonds ◽  
Double Helices ◽  
Significant Extension

In nucleic acid chemistry, metal-mediated base pairs represent a versatile method for the site-specific introduction of metal-based functionality. In metal-mediated base pairs, the hydrogen bonds between complementary nucleobases are replaced by coordinate bonds to one or two transition metal ions located in the helical core. In recent years, the concept of metal-mediated base pairing has found a significant extension by applying it to parallel-stranded DNA duplexes. The antiparallel-stranded orientation of the complementary strands as found in natural B-DNA double helices enforces a cisoid orientation of the glycosidic bonds. To enable the formation of metal-mediated base pairs preferring a transoid orientation of the glycosidic bonds, parallel-stranded duplexes have been investigated. In many cases, such as the well-established cytosine–Ag(I)–cytosine base pair, metal complex formation is more stabilizing in parallel-stranded DNA than in antiparallel-stranded DNA. This review presents an overview of all metal-mediated base pairs reported as yet in parallel-stranded DNA, compares them with their counterparts in regular DNA (where available), and explains the experimental conditions used to stabilize the respective parallel-stranded duplexes.

scholarly journals Bending of DNA duplexes with mutation motifs

DNA Research ◽  
2019 ◽  
Vol 26 (4) ◽  
pp. 341-352
Author(s):  
Michal Růžička ◽  
Přemysl Souček ◽  
Petr Kulhánek ◽  
Lenka Radová ◽  
Lenka Fajkusová ◽  
...  
Keyword(s):  
De Novo ◽  
Excision Repair ◽  
Dna Duplexes ◽  
De Novo Mutations ◽  
Base Pairs ◽  
Inherited Disorders ◽  
Cpg Dinucleotides ◽  
Human Genes ◽  
Base Excision ◽  
Dynamics Simulations

Abstract Mutations can be induced by environmental factors but also arise spontaneously during DNA replication or due to deamination of methylated cytosines at CpG dinucleotides. Sites where mutations occur with higher frequency than would be expected by chance are termed hotspots while sites that contain mutations rarely are termed coldspots. Mutations are permanently scanned and repaired by repair systems. Among them, the mismatch repair targets base pair mismatches, which are discriminated from canonical base pairs by probing altered elasticity of DNA. Using biased molecular dynamics simulations, we investigated the elasticity of coldspots and hotspots motifs detected in human genes associated with inherited disorders, and also of motifs with Czech population hotspots and de novo mutations. Main attention was paid to mutations leading to G/T and A+/C pairs. We observed that hotspots without CpG/CpHpG sequences are less flexible than coldspots, which indicates that flexible sequences are more effectively repaired. In contrary, hotspots with CpG/CpHpG sequences exhibited increased flexibility as coldspots. Their mutability is more likely related to spontaneous deamination of methylated cytosines leading to C > T mutations, which are primarily targeted by base excision repair. We corroborated conclusions based on computer simulations by measuring melting curves of hotspots and coldspots containing G/T mismatch.

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