Structure and hydrodynamics of a DNA G-quadruplex with a cytosine bulge

Meier, Markus; Moya‐Torres, Aniel; Krahn, Natalie; McDougall, Matthew; Orriss, George L.; McRae, Ewan K.S.; Booy, Evan P.; McEleney, Kevin; Patel, Trushar R.; McKenna, Sean Andrew; Stetefeld, Jörg

doi:10.1093/nar/gky307

Cited by 52 publications

(70 citation statements)

References 68 publications

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“…Projections or bulges in the G-quadruplex G-tract core have been reported in a range of G-quadruplex topologies (Fig. 3A) [139][140][141][142][143][144][145][146][147][148]. Their presence is context dependent with the nature of adjacent guanine stretches (with their unique range of c torsion angles) greatly influencing bulged G-tract usage [140,141,147].…”

Section: G-tetrads: Canonical and Noncanonicalmentioning

confidence: 99%

The diverse structural landscape of quadruplexes

et al. 2019

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G‐quadruplexes are secondary structures formed in G‐rich sequences in DNA and RNA. Considerable research over the past three decades has led to in‐depth insight into these unusual structures in DNA. Since the more recent exploration into RNA G‐quadruplexes, such structures have demonstrated their in cellulo existence, function and roles in pathology. In comparison to Watson‐Crick‐based secondary structures, most G‐quadruplexes display highly redundant structural characteristics. However, numerous reports of G‐quadruplex motifs/structures with unique features (e.g. bulges, long loops, vacancy) have recently surfaced, expanding the repertoire of G‐quadruplex scaffolds. This review addresses G‐quadruplex formation and structure, including recent reports of non‐canonical G‐quadruplex structures. Improved methods of detection will likely further expand this collection of novel structures and ultimately change the face of quadruplex‐RNA targeting as a therapeutic strategy.

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Section: G-tetrads: Canonical and Noncanonicalmentioning

confidence: 99%

The diverse structural landscape of quadruplexes

et al. 2019

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“…We utilized the B21 beamline at Diamond Light Source (Didcot, Oxfordshire, UK) to collect small-angle X-ray scattering (HPLC-SAXS) data as previously described [40]. Making use of an in-line Agilent 1200 (Agilent Technologies, Stockport, UK) HPLC connected to a flow cell, each purified RNA, 50 µL of~2.0 mg mL −1 was injected into a buffer equilibrated Shodex KW403-4F (Showa Denko America Inc., New York, NY, USA) size exclusion column at a flow rate of 0.160 mL per minute.…”

Section: Small-angle X-ray Scattering (Saxs)mentioning

confidence: 99%

Nanoscale Structure Determination of Murray Valley Encephalitis and Powassan Virus Non-Coding RNAs

Mrozowich

Henrickson

Demeler

et al. 2020

Viruses

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Viral infections are responsible for numerous deaths worldwide. Flaviviruses, which contain RNA as their genetic material, are one of the most pathogenic families of viruses. There is an increasing amount of evidence suggesting that their 5' and 3' non-coding terminal regions are critical for their survival. Information on their structural features is essential to gain detailed insights into their functions and interactions with host proteins. In this study, the 5' and 3' terminal regions of Murray Valley encephalitis virus and Powassan virus were examined using biophysical and computational modeling methods. First, we used size exclusion chromatography and analytical ultracentrifuge methods to investigate the purity of in-vitro transcribed RNAs. Next, we employed small-angle X-ray scattering techniques to study solution conformation and low-resolution structures of these RNAs, which suggest that the 3' terminal regions are highly extended as compared to the 5' terminal regions for both viruses. Using computational modeling tools, we reconstructed 3-dimensional structures of each RNA fragment and compared them with derived small-angle X-ray scattering low-resolution structures. This approach allowed us to reinforce that the 5' terminal regions adopt more dynamic structures compared to the mainly double-stranded structures of the 3' terminal regions.

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“…The cells were washed and resuspended in staining buffer containing 0.2% (w/v) propidium iodide for dead cell discrimination followed by flow analysis. FcγRIIIa allotyping was performed using a comparative analysis of cells stained with the V158‐specific Ab MEM‐154 and the allotype nonspecific Ab 3G8 according to a published method . All labeled Abs were from BD Biosciences except for the anti‐CD3 Ab, clone UCHT‐1 (Bio‐Rad).…”

Section: Methodsmentioning

confidence: 99%

“…FccRIIIa allotyping was performed using a comparative analysis of cells stained with the V158-specific Ab MEM-154 and the allotype nonspecific Ab 3G8 according to a published method. 33 All labeled Abs were from BD Biosciences except for the anti-CD3 Ab, clone UCHT-1 (Bio-Rad). Data were analyzed using FlowJo software (version 7.6.5; BD Biosciences).…”

Section: Flow Cytometrymentioning

confidence: 99%

Modulating antibody‐dependent cellular cytotoxicity of epidermal growth factor receptor‐specific heavy‐chain antibodies through hinge engineering

et al. 2019

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Human IgG1 and IgG3 antibodies (Abs) can mediate Ab‐dependent cellular cytotoxicity (ADCC), and engineering of the Ab Fc (point mutation; defucosylation) has been shown to affect ADCC by modulating affinity for FcRγIIIa. In the absence of a CH1 domain, many camelid heavy‐chain Abs (HCAbs) naturally bear very long and flexible hinge regions connecting their VHH and CH2 domains. To better understand the influence of hinge length and structure on HCAb ADCC, we produced a series of hinge‐engineered epidermal growth factor receptor (EGFR)‐specific chimeric camelid VHH‐human Fc Abs and characterized their affinities for recombinant EGFR and FcRγIIIa, their binding to EGFR‐positive tumor cells, and their ability to elicit ADCC. In the case of one chimeric HCAb (EG2‐hFc), we found that variants bearing longer hinges (IgG3 or camelid hinge regions) showed dramatically improved ADCC in comparison with a variant bearing the human IgG1 hinge, in similar fashion to a variant with reduced CH2 fucosylation. Conversely, an EG2‐hFc variant bearing a truncated human IgG1 upper hinge region failed to elicit ADCC. However, there was no consistent association between hinge length and ADCC for four similarly engineered chimeric HCAbs directed against distinct EGFR epitopes. These findings demonstrate that the ADCC of some HCAbs can be modulated simply by varying the length of the Ab hinge. Although this effect appears to be heavily epitope‐dependent, this strategy may be useful to consider during the design of VHH‐based therapeutic Abs for cancer.

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Structure and hydrodynamics of a DNA G-quadruplex with a cytosine bulge

Cited by 52 publications

References 68 publications

The diverse structural landscape of quadruplexes

The diverse structural landscape of quadruplexes

Nanoscale Structure Determination of Murray Valley Encephalitis and Powassan Virus Non-Coding RNAs

Modulating antibody‐dependent cellular cytotoxicity of epidermal growth factor receptor‐specific heavy‐chain antibodies through hinge engineering

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