DNA G-quadruplexes are uniquely stable in the presence of denaturants and monovalent cations

Hoog, Tanner G.; Pawlak, Matthew R.; Bachan, Benjamin F.; Engelhart, Aaron E.

doi:10.1016/j.bbrep.2022.101238

Cited by 4 publications

(3 citation statements)

References 27 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…G-quadruplex (G4) structures have been employed in a range of synthetic biology applications, including sensing of diverse ligands for readout of metabolic states, [3][4][5][6] forming nucleic acid-based nanomachines, 7,8 , and biomimetic cofactor binding that enables catalysis of a wide range of electron transfer reactions. [9][10][11][12] Monitoring the polymorphism and folding states of G-rich sequences is key to understanding their function. A variety of techniques have been employed for such monitoring, including high-resolution structural techniques such as NMR and crystallography, [13][14][15][16] as well as higher-throughput spectroscopic techniques, including circular dichroism and FRET.…”

Section: Introductionmentioning

confidence: 99%

Quencher-free fluorescence monitoring of G-quadruplex folding

Parada,

Hoog,

Adamala

et al. 2024

Preprint

Self Cite

View full text Add to dashboard Cite

Guanine-rich sequences exhibit a high degree of polymorphism and can form single-stranded, Watson-Crick duplex, and four-stranded G-quadruplex structures. These sequences have found a wide range of uses in synthetic biology applications, arising in part from their structural plasticity. High-throughput, low-cost tools for monitoring the folding and unfolding transitions of G-rich sequences would provide an enabling technology for accelerating prototyping of synthetic biological systems and for accelerating design-build-test cycles. Here, we show that unfolding transitions of a range of G-quadruplex-forming DNA sequences can be monitored in a FRET-like format using DNA sequences that possess only a single dye label, with no quencher. These quencher-free assays can be performed at low cost, with both cost and lead times ca. 1 order of magnitude lower than FRET-labeled strands. Thus, quencher-free secondary structure monitoring promises to be a valuable tool for testing and development of synthetic biology systems employing G-quadruplexes.

show abstract

Section: Introductionmentioning

confidence: 99%

Quencher-free fluorescence monitoring of G-quadruplex folding

Parada,

Hoog,

Adamala

et al. 2024

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

“…1 ). While G-quadruplex was initially found in vitro , growing evidence suggests that this unusual nucleic acid construct is also generated in living cells on a genome-wide scale [ [4] , [5] , [6] ]. These guanine-rich repetitive sequences are likely to stack on one another to form guanine planes termed G-tetrads.…”

Section: Introductionmentioning

confidence: 99%

Structural insights and shedding light on preferential interactions of dietary flavonoids with G-quadruplex DNA structures: A new horizon

Bag¹,

Burman²,

Bhowmik³

2023

Heliyon

View full text Add to dashboard Cite

“…[20][21][22] Unlike numerous studies which have been done to understand the mechanism by which urea affects protein stability, only a few studies have dealt with the effect of urea on nucleic acids. In addition, most of them reported on the stability of helical DNA and RNA, [23][24][25][26][27] while the influence of urea on the conformational equilibrium of G-quadruplexes has been almost neglected. 19,28 Since G4 structure has some common features with globular proteins, such as the spherical shape with the central cavity and less charge with respect to other nucleic acid structures, urea may interact with G4 in a manner different from that with helical DNA and RNA structures.…”

Section: Introductionmentioning

confidence: 99%

SERS evidence of urea‐disordered G‐quadruplex structure

Petrović

Saftić

Kenđel

et al. 2023

J Raman Spectroscopy

View full text Add to dashboard Cite

Structural changes of the human telomeric d(TTAGGG)4 sequence (Tel24) in the presence of sodium ions and urea were studied using SERS spectroscopy. The SERS spectra indicated that Tel24 (4 × 10−5 mol/l) formed an anti‐parallel G‐quadruplex in a medium containing Na+ ions (100 mmol/l), which was disrupted by the subsequent addition of urea (7.2 mol/l). Intensity ratios of SERS bands originating from breathing vibrations of adenine (~730 cm−1) and guanine (~660 cm−1) rings clearly pointed to the urea‐induced unfolding of G‐quadruplex. In addition, SERS bands assigned to guanine implied the breaking of Hoogsteen hydrogen bonds, most likely due to the bonding of guanine bases with the urea molecules. Considering various experimental conditions applied, the structure‐related SERS response was more pronounced in the silver than in the gold colloid as well as upon NIR (785 nm) rather than Vis (532 nm) laser excitation. The CD spectra of the same colloidal samples supported structural changes of Tel24 obtained by SERS.

show abstract

DNA G-quadruplexes are uniquely stable in the presence of denaturants and monovalent cations

Cited by 4 publications

References 27 publications

Quencher-free fluorescence monitoring of G-quadruplex folding

Quencher-free fluorescence monitoring of G-quadruplex folding

Structural insights and shedding light on preferential interactions of dietary flavonoids with G-quadruplex DNA structures: A new horizon

SERS evidence of urea‐disordered G‐quadruplex structure

Contact Info

Product

Resources

About