G-Quadruplex conformational change driven by pH variation with potential application as a nanoswitch

Yan, Yi Yong; Tan, Jia Heng; Lu, Yu; Yan, Siu‐Cheong; Wong, Kwok Yin; Li, Ding; Gu, Lian Quan; Huang, Zifang

doi:10.1016/j.bbagen.2013.06.019

Cited by 31 publications

(18 citation statements)

References 50 publications

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“…This change in conformation can be attributed to rearrangement of the G-quadruplex loop at very low pH. 37 …”

Section: Resultsmentioning

confidence: 98%

Tunable Loading of Oligonucleotides with Secondary Structure on Gold Nanoparticles through a pH-Driven Method

Dam¹,

Lee²,

Lee³

et al. 2015

Bioconjugate Chem.

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This paper describes how pH can be used to control covalent attachment of oligonucleotides with secondary structure on gold nanoparticles (AuNPs). The highest loading of thiolated nucleic acids occurred at low pH (pH = 1.7) due to reduced repulsion between the negatively charged oligonucleotides and the AuNP surface. The packing of oligonucleotides at low pH decreased (single-stranded ≫ duplex > quadruplex) as the spatial footprint of secondary structure increased. As the pH increased, a decrease in the number of DNA strands grafted to the AuNPs was observed. Notably, the loading density depended on the flexibility and spatial organization of the secondary structures at all pH conditions. At the lowest pH tested, circular dichroism analysis revealed that G-quadruplex aptamers underwent a structural change (from parallel to antiparallel or vice versa), although the biological activity of the aptamer-loaded AuNPs was still maintained. We anticipate that pH-tuning can result in quantitative loading of oligonucleotides on various types of AuNPs with different shapes and surface capping layers.

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“…This change in conformation can be attributed to rearrangement of the G-quadruplex loop at very low pH. 37 …”

Section: Resultsmentioning

confidence: 98%

Tunable Loading of Oligonucleotides with Secondary Structure on Gold Nanoparticles through a pH-Driven Method

Dam¹,

Lee²,

Lee³

et al. 2015

Bioconjugate Chem.

View full text Add to dashboard Cite

show abstract

“…The height of DPV response reached a plateau when cytosine methylation in CpG island was close to saturation at 120 min. Afterwards, to obtain the response of MB, which was closed in the MSNs by the G-quadruplex [31], the PBS (0.1 M, pH 9.0) was dripped on the surface of the electrode after methylation and HpaII cleavage. With the increasing of the soak time, the DPV response increased, which was presented in Fig.…”

Section: Assay Of M Sssi Mtase Activitymentioning

confidence: 99%

“…It is a polymorphous structure [29] which can vary in different environment [30]. The DNA of repetitive G (guanine) tracts will transfer from single-stranded to four-stranded structure at a certain pH [31] or a certain concentration of salt [30], such as K + , Na + and NH 4 + . And the structure will turn over when the conditions change again.…”

Section: Introductionmentioning

confidence: 99%

G-quadruplex functionalized nano mesoporous silica for assay of the DNA methyltransferase activity

Pei

Pang

Yin

et al. 2015

Analytica Chimica Acta

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“…Compared to the traditional nucleotides, G-quadruplex, which formed from guanine-rich oligonucleotide sequences, has attracted a growing interest in application of nanodevice and molecular switching 22 23 24 25 26 . To date, G-quadruplex involved switching systems based on the characterized signal of G-quadruplex 27 28 29 , or mediated by iron 30 31 32 33 34 35 or fluorescent probe 36 37 38 39 40 have been reported. These works showed the G-quadruplex had great potential in construction of molecular device.…”

mentioning

confidence: 99%

G-quadruplex induced chirality of methylazacalix[6]pyridine via unprecedented binding stoichiometry: en route to multiplex controlled molecular switch

Guan

Shen

Xiang

et al. 2015

Sci Rep

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Nucleic acid based molecular device is a developing research field which attracts great interests in material for building machinelike nanodevices. G-quadruplex, as a new type of DNA secondary structures, can be harnessed to construct molecular device owing to its rich structural polymorphism. Herein, we developed a switching system based on G-quadruplexes and methylazacalix[6]pyridine (MACP6). The induced circular dichroism (CD) signal of MACP6 was used to monitor the switch controlled by temperature or pH value. Furthermore, the CD titration, Job-plot, variable temperature CD and 1H-NMR experiments not only confirmed the binding mode between MACP6 and G-quadruplex, but also explained the difference switching effect of MACP6 and various G-quadruplexes. The established strategy has the potential to be used as the chiral probe for specific G-quadruplex recognition.

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G-Quadruplex conformational change driven by pH variation with potential application as a nanoswitch

Cited by 31 publications

References 50 publications

Tunable Loading of Oligonucleotides with Secondary Structure on Gold Nanoparticles through a pH-Driven Method

Tunable Loading of Oligonucleotides with Secondary Structure on Gold Nanoparticles through a pH-Driven Method

G-quadruplex functionalized nano mesoporous silica for assay of the DNA methyltransferase activity

G-quadruplex induced chirality of methylazacalix[6]pyridine via unprecedented binding stoichiometry: en route to multiplex controlled molecular switch

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