Distance measurements between paramagnetic ligands bound to parallel stranded guanine quadruplexes

Donohue, Matthew P.; Szalai, Veronika A.

doi:10.1039/c6cp01121g

Cited by 17 publications

(24 citation statements)

References 81 publications

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“…91,92 This deformation, involving the outermost quadruplexes, explains the experimental data, mentioned in subsection 3.2, indicating a variation in the G-quartet rise when increasing the number of Gquadruplexes. 85 Note that the total rise and twist distributions among all G-quartets shown in Figure 6e,f are smooth Gaussians and overlap each other at various ionic strengths; thus, any indication in the rise and twist of G-quartet variation cannot be detected from here.…”

Section: Results and Discussionmentioning

confidence: 91%

“…Recent experimental measurements by Donohue and Szalai 85 on higher-order quadruplex structure of varying lengths indicate a variation in the distance among adjacent G-quartets as the number of G-quartets is changed. Even if they had analyzed shorter quadruplexes comprising a maximum of ten G-quartets, thus shorter than those studied in the present investigation, the trend that they observed varying the length is possibly of general validity.…”

Section: Results and Discussionmentioning

confidence: 99%

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Coarse-Grained Simulation of Rodlike Higher-Order Quadruplex Structures at Different Salt Concentrations

Rebič

Mocci

Uličný³

et al. 2017

ACS Omega

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We present a coarse-grained (CG) model of a rodlike higher-order quadruplex with explicit monovalent salts, which was developed from radial distribution functions of an underlying reference atomistic molecular dynamics simulation using inverse Monte Carlo technique. This work improves our previous CG model and extends its applicability beyond the minimal salt conditions, allowing its use at variable ionic strengths. The strategies necessary for the model development are clearly explained and discussed. The effects of the number of stacked quadruplexes and varied salt concentration on the elasticity of the rodlike higher-order quadruplex structures are analyzed. The CG model reproduces the deformations of the terminal parts in agreement with experimental observations without introducing any special parameters for terminal beads and reveals slight differences in the rise and twist of the G-quartet arrangement along the studied biopolymer. The conclusions of our study can be generalized for other G-quartet-based structures

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Section: Results and Discussionmentioning

confidence: 91%

Section: Results and Discussionmentioning

confidence: 99%

Coarse-Grained Simulation of Rodlike Higher-Order Quadruplex Structures at Different Salt Concentrations

Rebič

Mocci

Uličný³

et al. 2017

ACS Omega

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“…Gd(III) and Mn(II) tags have been attached to DNA and/or RNA for EPR distance measurements, but these tags are larger than current nitroxide labels. Cu(II)‐Cu(II) distances in DNA have also been reported using Cu(II) binding porphyrins bound to quadraplexes containing multiple G‐quartets (4 guanines that hydrogen bond to each other in a circle via Hoogsteen base pairing) . The latter strategy requires the presence of G‐quartets within the DNA structure.…”

Section: Paramagnetic Metal Ion‐based Spin Labels For Proteins and Fomentioning

confidence: 99%

EPR Distance Measurements as a Tool to Characterize Protein‐DNA Interactions

Sameach

Ruthstein

2019

Israel Journal of Chemistry

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Over recent decades, electron paramagnetic resonance (EPR) spectroscopy has become an essential tool for exploring complex biological systems. Herein, we discuss the potential of pulsed EPR spectroscopy to shed light on the mechanisms of protein-DNA interactions. To this end, we first provide an overview of pulsed EPR methodology (and specifically, double electron electron resonance; DEER), with a focus on the various spin-labeling methods used today both for protein labeling and for DNA labeling. Next, after briefly discussing recent applications of DEER in protein-DNA studies, we introduce a detailed case study, an example of how EPR spectroscopy has been used to resolve the transcription mechanism of the CueR copper regulator.

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“…These tags are typically longer than nitroxide spin labels. Cu 2+ –Cu 2+ DEER distance in DNA has also been reported, using Cu 2+ binding porphyrins bound to quadruplexes containing multiple G‐quartets . This method requires an extremely specific DNA sequence to produce the necessary g‐quadruplex structure.…”

Section: Figurementioning

confidence: 99%

Nucleotide‐Independent Copper(II)‐Based Distance Measurements in DNA by Pulsed ESR Spectroscopy

2017

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A site-specific Cu binding motif within a DNA duplex for distance measurements by ESR spectroscopy is reported. This motif utilizes a commercially available 2,2'-dipicolylamine (DPA) phosphormadite easily incorporated into any DNA oligonucleotide during initial DNA synthesis. The method only requires the simple post-synthetic addition of Cu without the need for further chemical modification. Notably, the label is positioned within the DNA duplex, as opposed to outside the helical perimeter, for an accurate measurement of duplex distance. A distance of 2.7 nm was measured on a doubly Cu -labeled DNA sequence, which is in exact agreement with the expected distance from both DNA modeling and molecular dynamic simulations. This result suggests that with this labeling strategy the ESR measured distance directly reports on backbone DNA distance, without the need for further modeling. Furthermore, the labeling strategy is structure- and nucleotide-independent.

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Distance measurements between paramagnetic ligands bound to parallel stranded guanine quadruplexes

Abstract: Double electron electron resonance utilizing a shaped pump pulse is used to measure end-stacked ligand separation on parallel-stranded guanine quadruplexes.

Cited by 17 publications

References 81 publications

Coarse-Grained Simulation of Rodlike Higher-Order Quadruplex Structures at Different Salt Concentrations

Coarse-Grained Simulation of Rodlike Higher-Order Quadruplex Structures at Different Salt Concentrations

EPR Distance Measurements as a Tool to Characterize Protein‐DNA Interactions

Nucleotide‐Independent Copper(II)‐Based Distance Measurements in DNA by Pulsed ESR Spectroscopy

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