Structural polymorphism of the four-repeat Oxytricha nova telomeric DNA sequences

Abu-Ghazalah, Rashid M.; Macgregor, Robert B.

doi:10.1016/j.bpc.2009.01.013

Cited by 13 publications

(19 citation statements)

References 42 publications

(68 reference statements)

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“…36–38 Of the three 5’-GMP salts studied, only in concentrated Rb 2 (5’-GMP) in the 5–20 °C range did we observe the typical CD spectrum for antiparallel stacking (opposite polarity) of G-quartets, although it was somewhat red-shifted ((−) 277, (+)311 nm) (Fig. 8).…”

Section: Discussionmentioning

confidence: 97%

“…In some cases, it is possible to detect a mixture of structures or conformers existing simultaneously in a solution by comparison of the CD spectrum with those of known conformations. 32,38–42 For example, Lee et al showed that d[G 4 T 4 ] n in the presence of 200 mM Na + had an antiparallel conformation, but in the presence of 200 mM K + it was a mixture of a parallel and antiparallel conformations. 41 …”

Section: Introductionmentioning

confidence: 99%

“…31,37,38 That is, some of the bases were stacked with the same polarity, also known as head-tail stacking, and others were stacked with opposite polarities (head-head stacking). Masiero et al have shown that the observed CD spectra are dependent on the polarities of the base stacking rather than whether the associated strands are aligned parallel or antiparallel.…”

Section: Introductionmentioning

confidence: 99%

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Circular Dichroism Study of Supramolecular Assemblies of Guanosine 5′-Monophosphate

Panda

Walmsley

2011

J. Phys. Chem. B

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Concentration and temperature dependent studies of the circular dichroism of dianionic guanosine 5’-monophosphate (5’-GMP), where the cation was Na+, K+, or Rb+ ion, were done to obtain information regarding the nature of the self-assembled 5’-GMP species in aqueous solution, including G-quartets and other structures. Concentrations in the 0.05 M – 0.85 M range and temperatures in the 5–50 °C range were used. At the highest concentrations and 5 °C, Na2(5’-GMP) and K2(5’-GMP) formed a cholesteric phase, but Rb2(5’-GMP) did not. Evidence for antiparallel base stacking (stacked with opposite polarity; head to head) was observed for Rb2(5’-GMP), but not for the Na+ or K+ salts. This structure, believed to be G-quartets, had a melting temperature of 15 °C and dissociated into a second associated species as the temperature increased. The latter was present to the greatest extent at ~40 °C and it is characterized by a prominent negative CD band at 306 nm, which may be indicative of an X-DNA type of structure (an expanded G-quartet) or base-stacked monomers or dimers. The same negative band appeared at 310 nm in the CD spectra of K2(5’-GMP) and Na2(5’-GMP), but was much less intense in the latter case. K2(5’-GMP) also formed a non-cholesteric phase containing at least two different species, one more stable at low temperatures and the other more stable at higher temperatures, similar to Rb2(5’-GMP). 1H NMR spectroscopy was used to assist in the interpretation of the CD spectra.

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Section: Discussionmentioning

confidence: 97%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Circular Dichroism Study of Supramolecular Assemblies of Guanosine 5′-Monophosphate

Panda

Walmsley

2011

J. Phys. Chem. B

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“…They have been found to be regulatory elements in the human genome implicated in key functions such as telomere maintenance and genome transcription regulation, replication and repair (17). G4 structures have also been identified in fungi (18)(19)(20)(21), bacteria (22)(23)(24)(25)(26) and parasites (27)(28)(29)(30)(31)(32). Their occurrence are known in many viruses that afflict humans as well.…”

Section: Introductionmentioning

confidence: 99%

Exploring G and C-quadruplex structures as potential targets against the severe acute respiratory syndrome coronavirus 2

Belmonte-Reche

Serrano

González

et al. 2020

Preprint

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In this paper we report the analysis of the 2019-nCoV genome and related viruses using an upgraded version of the open-source algorithm G4-iM Grinder. This version improves the functionality of the software, including an easy way to determine the potential biological features affected by the candidates found. The quadruplex definitions of the algorithm were optimized for 2019-nCoV. Using a lax quadruplex definition ruleset, which accepts amongst other parameters two residue G- and C-tracks, hundreds of potential quadruplex candidates were discovered. These sequences were evaluated by their in vitro formation probability, their position in the viral RNA, their uniqueness and their conservation rates (calculated in over three thousand different COVID-19 clinical cases and sequenced at different times and locations during the ongoing pandemic). These results were compared sequentially to other Coronaviridae members, other Group IV (+)ssRNA viruses and the entire realm. Sequences found in common with other species were further analyzed and characterized. Sequences with high scores unique to the 2019-nCoV were studied to investigate the variations amongst similar species. Quadruplex formation of the best candidates was then confirmed experimentally. Using NMR and CD spectroscopy, we found several highly stable RNA quadruplexes that may be suitable theranostic targets against the 2019-nCoV.

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“…Increasing repeat numbers can affect G-quadruplex formation by telomere repeats and slipped DNAs and R-loops by (CAG)/ (CTG) and (CGG)/(CCG) repeats (22)(23)(24)(25)(26). Here we analyzed increasing r(GGGGCC) n repeat lengths of n ϭ 4, 6, and 8 units (Fig.…”

Section: Ion Dependence Of the Slow Migrating R(ggggcc)mentioning

confidence: 99%

The Disease-associated r(GGGGCC) Repeat from the C9orf72 Gene Forms Tract Length-dependent Uni- and Multimolecular RNA G-quadruplex Structures

Reddy

Zamiri

Stanley

et al. 2013

Journal of Biological Chemistry

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295

314

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Structural polymorphism of the four-repeat Oxytricha nova telomeric DNA sequences

Cited by 13 publications

References 42 publications

Circular Dichroism Study of Supramolecular Assemblies of Guanosine 5′-Monophosphate

Circular Dichroism Study of Supramolecular Assemblies of Guanosine 5′-Monophosphate

Exploring G and C-quadruplex structures as potential targets against the severe acute respiratory syndrome coronavirus 2

The Disease-associated r(GGGGCC) Repeat from the C9orf72 Gene Forms Tract Length-dependent Uni- and Multimolecular RNA G-quadruplex Structures

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