Preparation of G-Quartet Structures and Detection by Native Gel Electrophoresis

Moon, Ian K.; Jarstfer, Michael B.

doi:10.1007/978-1-59745-363-9_4

Cited by 12 publications

(6 citation statements)

References 12 publications

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“…Similar results were obtained for UGG hairpin RNA (Figure 3 b, lane 4). The GGG hairpin RNA showed several bands on the gel without NCT6 (Figure 3 b, lane 5), likely due to the formation of G‐clusters 45. Addition of NCT6 to GGG RNA, however, resulted in the appearance of smear bands with a few new distinguishable bands (Figure 3 b, lane 6).…”

Section: Resultsmentioning

confidence: 99%

Formation of a Ligand‐Assisted Complex of Two RNA Hairpin Loops

Hong¹,

Otabe²,

Matsumoto³

et al. 2014

Chemistry A European J

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The hairpin structure is one of the most common secondary structures in RNA and holds a central position in the stream of RNA folding from a non-structured RNA to structurally complex and functional ribonucleoproteins. Since the RNA secondary structure is strongly correlated to the function and can be modulated by the binding of small molecules, we have investigated the modulation of RNA folding by a ligand-assisted formation of loop-loop complexes of two RNA hairpin loops. With a ligand (NCT6), designed based on the ligand binding to the G-G mismatches in double-stranded DNA, we successfully demonstrated the formation of both inter- and intra-molecular NCT6-assisted complex of two RNA hairpin loops. NCT6 selectively bound to the two hairpin loops containing (CGG)3 in the loop region. Native polyacrylamide gel electrophoresis analysis of two doubly-labeled RNA hairpin loops clearly showed the formation of intermolecular NCT6-assisted loop-loop complex. Förster resonance energy-transfer studies of RNA constructs containing two hairpin loops, in which each hairpin was labeled with Alexa488 and Cy3 fluorophores, showed the conformational change of the RNA constructs upon binding of NCT6. These experimental data showed that NCT6 simultaneously bound to two hairpin RNAs at the loop region, and can induce the conformational change of the RNA molecule. These data strongly support that NCT6 functions as molecular glue for two hairpin RNAs.

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Section: Resultsmentioning

confidence: 99%

Formation of a Ligand‐Assisted Complex of Two RNA Hairpin Loops

Hong¹,

Otabe²,

Matsumoto³

et al. 2014

Chemistry A European J

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show abstract

“…A detailed description of most of the methods used for biophysical analysis of such DNA complexes can also be found in the literature. A brief method description can be found in previous reviews, , and here we list several useful methods and protocols: biophysical analysis of DNA triplexes, analysis of DNA melting curves, , biochemical and biophysical analysis of G-quadruplexes, − NMR, crystallographic and mass spectrometry methods for studying G-quadruplexes, and analysis of protein–G-quadruplex interactions …”

Section: Structure and Properties Of Gro Assemblies And The Rationale...mentioning

confidence: 99%

Molecular Engineering of Guanine-Rich Sequences: Z-DNA, DNA Triplexes, and G-Quadruplexes

2013

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“…Intramolecular G-quadruplexes have a compact structure and thus migrate faster through a cation-containing gel than their linear counterparts [8], while intermolecular G-quadruplexes migrate slower due to increased molecular weight [6, 7]. Native gel electrophoresis is also invaluable in enabling purification of G-quadruplexes, an important consideration given the heterogeneity of structures that can form from a single oligonucleotide [121]. …”

Section: Methodologies Used To Study G-quadruplex Structuresmentioning

confidence: 99%

G-Quadruplexes: From Guanine Gels to Chemotherapeutics

Bryan

Baumann

2011

Mol Biotechnol

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G-quartets are square planar arrangements of four guanine bases, which can form extraordinarily stable stacks when present in nucleic acid sequences. Such G-quadruplex structures were long regarded as an in vitro phenomenon, but the widespread presence of suitable sequences in genomes and the identification of proteins that stabilize, modify or resolve these nucleic acid structures have provided circumstantial evidence for their physiological relevance. The therapeutic potential of small molecules that can stabilize or disrupt G-quadruplex structures has invigorated the field in recent years. Here we review some of the key observations that support biological functions for G-quadruplex DNA as well as the techniques and tools that have enabled researchers to probe these structures and their interactions with proteins and small molecules.

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Preparation of G-Quartet Structures and Detection by Native Gel Electrophoresis

Cited by 12 publications

References 12 publications

Formation of a Ligand‐Assisted Complex of Two RNA Hairpin Loops

Formation of a Ligand‐Assisted Complex of Two RNA Hairpin Loops

Molecular Engineering of Guanine-Rich Sequences: Z-DNA, DNA Triplexes, and G-Quadruplexes

G-Quadruplexes: From Guanine Gels to Chemotherapeutics

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