Single-Molecule Investigations of G-Quadruplex

2019 ◽  
pp. 275-298 ◽  
Author(s):  
Shankar Mandal ◽  
Mohammed Enamul Hoque ◽  
Hanbin Mao
Keyword(s):  
Single Molecule ◽  
G Quadruplex

scholarly journals Voltammetry and molecular assembly of G-quadruplex DNAzyme on single-crystal Au(111)-electrode surfaces – hemin as an electrochemical intercalator

2016 ◽  
Vol 193 ◽  
pp. 99-112 ◽  
Author(s):  
Ling Zhang ◽  
Jens Ulstrup ◽  
Jingdong Zhang
Keyword(s):  
Single Crystal ◽  
Single Molecule ◽  
Electrode Surface ◽  
Molecular Assembly ◽  
Electrode Surfaces ◽  
Potential Control ◽  
G Quadruplex ◽  
Tunnelling Microscopy ◽  
Dna Quadruplexes

DNA quadruplexes (qs) are a class of “non-canonical” oligonucleotides (OGNs) composed of stacked guanine (G) quartets stabilized by specific cations. Metal porphyrins selectively bind to G-qs complexes to form what is known as DNAzyme, which can exhibit peroxidase and other catalytic activity similar to heme group metalloenzymes. In the present study we investigate the electrochemical properties and the structure of DNAzyme monolayers on single-crystal Au(111)-electrode surfaces using cyclic voltammetry and scanning tunnelling microscopy under electrochemical potential control (in situ STM). The target DNAzyme is formed from a single-strand OGN with 12 guanines and iron(iii) porphyrin IX (hemin), and assembles on Au(111) through a mercapto alkyl linker. The DNAzyme monolayers exhibit a strong pair of redox peaks at 0.0 V (NHE) at pH 7 in acetate buffer, shifted positively by about 50 mV compared to free hemin weakly physisorbed on the Au(111)-electrode surface. The voltammetric hemin signal of DNAzyme is enhanced 15 times compared with that of hemin adsorbed directly on the Au(111)-electrode surface. This is indicative of both the formation of a close to dense DNAzyme monolayer and that hemin is strongly bound to the immobilized 12G-qs in well-defined orientation favorable for interfacial ET with a rate constant of 6.0 ± 0.4 s−1. This is supported by in situ STM which discloses single-molecule G-quartet structures with a size of 1.6 ± 0.2 nm.

Interaction of hnRNP A1 with telomere DNA G-quadruplex structures studied at the single molecule level

2010 ◽  
Vol 39 (9) ◽  
pp. 1343-1350 ◽  
Author(s):  
A. C. Krüger ◽  
M. K. Raarup ◽  
M. M. Nielsen ◽  
M. Kristensen ◽  
F. Besenbacher ◽  
...  
Keyword(s):  
Single Molecule ◽  
Hnrnp A1 ◽  
Single Molecule Level ◽  
G Quadruplex

scholarly journals Characterizing the Binding of G-Quadruplex DNA to Insulin by Single Molecule and Bulk Ensemble Methods

2012 ◽  
Vol 102 (3) ◽  
pp. 75a
Author(s):  
Christine Timmer ◽  
Amanda Witte ◽  
Niecia Flikweert ◽  
Kumar Sinniah
Keyword(s):  
Single Molecule ◽  
Ensemble Methods ◽  
Quadruplex Dna ◽  
G Quadruplex

Assaying the binding strength of G-quadruplex ligands using single-molecule TPM experiments

2013 ◽  
Vol 436 (2) ◽  
pp. 101-108 ◽  
Author(s):  
Shih-Wei Liu ◽  
Jen-Fei Chu ◽  
Cheng-Ting Tsai ◽  
Hung-Chih Fang ◽  
Ta-Chau Chang ◽  
...  
Keyword(s):  
Single Molecule ◽  
Binding Strength ◽  
G Quadruplex

scholarly journals Single Molecule Studies of Physiologically Relevant Telomeric Tails Reveal POT1 Mechanism for Promoting G-quadruplex Unfolding

2010 ◽  
Vol 286 (9) ◽  
pp. 7479-7489 ◽  
Author(s):  
Hong Wang ◽  
Gerald J. Nora ◽  
Harshad Ghodke ◽  
Patricia L. Opresko
Keyword(s):  
Single Molecule ◽  
G Quadruplex ◽  
Single Molecule Studies

scholarly journals Single-molecule imaging reveals a common mechanism shared by G-quadruplex–resolving helicases

2016 ◽  
Vol 113 (30) ◽  
pp. 8448-8453 ◽  
Author(s):  
Ramreddy Tippana ◽  
Helen Hwang ◽  
Patricia L. Opresko ◽  
Vilhelm A. Bohr ◽  
Sua Myong
Keyword(s):  
Secondary Structure ◽  
Substrate Specificity ◽  
Single Molecule ◽  
Genomic Dna ◽  
Rna Helicase ◽  
Resolving Power ◽  
Common Mechanism ◽  
Dna Molecule ◽  
G Quadruplex ◽  
Stable Formation

G-quadruplex (GQ) is a four stranded DNA secondary structure that arises from a guanine rich sequence. Stable formation of GQ in genomic DNA can be counteracted by the resolving activity of specialized helicases including RNA helicase AU (associated with AU rich elements) (RHAU) (G4 resolvase 1), Bloom helicase (BLM), and Werner helicase (WRN). However, their substrate specificity and the mechanism involved in GQ unfolding remain uncertain. Here, we report that RHAU, BLM, and WRN exhibit distinct GQ conformation specificity, but use a common mechanism of repetitive unfolding that leads to disrupting GQ structure multiple times in succession. Such unfolding activity of RHAU leads to efficient annealing exclusively within the same DNA molecule. The same resolving activity is sufficient to dislodge a stably bound GQ ligand, including BRACO-19, NMM, and Phen-DC3. Our study demonstrates a plausible biological scheme where different helicases are delegated to resolve specific GQ structures by using a common repetitive unfolding mechanism that provides a robust resolving power.

scholarly journals Single-Molecule Manipulation of the Duplex Formation and Dissociation at the G-Quadruplex/i-Motif Site in the DNA Nanostructure

ACS Nano ◽  
2015 ◽  
Vol 9 (10) ◽  
pp. 9922-9929 ◽  
Author(s):  
Masayuki Endo ◽  
Xiwen Xing ◽  
Xiang Zhou ◽  
Tomoko Emura ◽  
Kumi Hidaka ◽  
...  
Keyword(s):  
Single Molecule ◽  
Dna Nanostructure ◽  
G Quadruplex ◽  
Motif Site ◽  
Duplex Formation ◽  
Single Molecule Manipulation

scholarly journals The Binding of G‐Quadruplex DNA to Insulin: From Single Molecule to Bulk‐Methods

2012 ◽  
Vol 26 (S1) ◽  
Author(s):  
Kumar Sinniah ◽  
Susanna Lynch ◽  
Christine Timmer ◽  
Amanda Witte
Keyword(s):  
Single Molecule ◽  
Quadruplex Dna ◽  
G Quadruplex

scholarly journals A mechanism for the extension and unfolding of parallel telomeric G-quadruplexes by human telomerase at single-molecule resolution

2020 ◽  
Author(s):  
Bishnu P. Paudel ◽  
Aaron Lavel Moye ◽  
Hala Abou Assi ◽  
Roberto El-Khoury ◽  
Scott B. Cohen ◽  
...  
Keyword(s):  
Single Molecule ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Quadruplex Structure ◽  
G Quadruplex ◽  
Nucleotide Addition ◽  
Small Molecule Ligands ◽  
Large Conformational Change ◽  
Human Telomerase ◽  
Linear Product

AbstractTelomeric G-quadruplexes (G4) were long believed to form a protective structure at telomeres, preventing their extension by the ribonucleoprotein telomerase. Contrary to this belief, we have previously demonstrated that parallel-stranded conformations of telomeric G4 can be extended by human and ciliate telomerase. However, a mechanistic understanding of the interaction of telomerase with structured DNA remained elusive. Here, we use single-molecule fluorescence resonance energy transfer (smFRET) microscopy and bulk-phase enzymology to propose a mechanism for the resolution and extension of parallel G4 by telomerase. Binding is initiated by the RNA template of telomerase interacting with the G-quadruplex; nucleotide addition then proceeds to the end of the RNA template. It is only through the large conformational change of translocation following synthesis that the G-quadruplex structure is completely unfolded to a linear product. Surprisingly, parallel G4 stabilization with either small molecule ligands or by chemical modification does not always inhibit G4 unfolding and extension by telomerase. These data reveal that telomerase is a parallel G-quadruplex resolvase.

scholarly journals Single-molecule fluorescence studies on cotranscriptional G-quadruplex formation coupled with R-loop formation

2020 ◽  
Vol 48 (16) ◽  
pp. 9195-9203
Author(s):  
Gunhyoung Lim ◽  
Sungchul Hohng
Keyword(s):  
Gene Regulation ◽  
Single Molecule ◽  
Genome Instability ◽  
Feedback Mechanism ◽  
Rnase H ◽  
Formation Mechanisms ◽  
Loop Formation ◽  
Single Molecule Fluorescence ◽  
Fluorescence Studies ◽  
G Quadruplex

Abstract G-quadruplex (GQ) is formed at various regions of DNA, including telomeres of chromosomes and regulatory regions of oncogenes. Since GQ is important in both gene regulation and genome instability, the biological and medical implications of this abnormal DNA structure have been intensively studied. Its formation mechanisms, however, are not clearly understood yet. We report single-molecule fluorescence experiments to monitor the cotranscriptional GQ formation coupled with R-loop formation using T7 RNA polymerase. The GQ is formed very rarely per single-round transcription. R-loop formation precedes and facilitates GQ formation. Once formed, some GQs are extremely stable, resistant even to RNase H treatment, and accumulate in multiple-round transcription conditions. On the other hand, GQ existing in the non-template strand promotes the R-loop formation in the next rounds of transcription. Our study clearly shows the existence of a positive feedback mechanism of GQ and R-loop formations, which may possibly contribute to gene regulation and genome instability.

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