High-Resolution Insight into G-Overhang Architecture

Hänsel, Robert; Löhr, Frank; Trantı́rek, Lukáš; Dötsch, Volker

doi:10.1021/ja312403b

Cited by 107 publications

(118 citation statements)

References 52 publications

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“…In agreement with our interpretation, a recent computational study showed that antiparallel conformation has a lower FRET efficiency than the parallel conformation (27). High-resolution NMR and EPR studies showed that, in K + , human telomeric sequence folds into various hybrid GQ conformations, in addition to the parallel and antiparallel conformations (14,25,30,31). The most stable telomeric GQ conformation strongly depends on the overhang sequence, pH, and ionic conditions (14).…”

Section: Pot1supporting

confidence: 90%

“…High-resolution NMR and EPR studies showed that, in K + , human telomeric sequence folds into various hybrid GQ conformations, in addition to the parallel and antiparallel conformations (14,25,30,31). The most stable telomeric GQ conformation strongly depends on the overhang sequence, pH, and ionic conditions (14). Therefore, we cannot rule out the possibility that the F2 peak may contain both parallel and hybrid conformations with similar distance between the FRET probes.…”

Section: Pot1mentioning

confidence: 95%

“…Recent studies have shown that human telomeres form GQ structures in vivo (12,13) and in cell extracts (14). At physiologically relevant ionic conditions (∼150 mM K + ), GQs are thermodynamically more stable than competing Watson-Crick pairing (15).…”

mentioning

confidence: 99%

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G-quadruplex formation in telomeres enhances POT1/TPP1 protection against RPA binding

Ray

Bandaria

Qureshi

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

137

144

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Human telomeres terminate with a single-stranded 3′ G overhang, which can be recognized as a DNA damage site by replication protein A (RPA). The protection of telomeres (POT1)/POT1-interacting protein 1 (TPP1) heterodimer binds specifically to single-stranded telomeric DNA (ssTEL) and protects G overhangs against RPA binding. The G overhang spontaneously folds into various G-quadruplex (GQ) conformations. It remains unclear whether GQ formation affects the ability of POT1/TPP1 to compete against RPA to access ssTEL. Using single-molecule Förster resonance energy transfer, we showed that POT1 stably loads to a minimal DNA sequence adjacent to a folded GQ. At 150 mM K + , POT1 loading unfolds the antiparallel GQ, as the parallel conformation remains folded. POT1/TPP1 loading blocks RPA's access to both folded and unfolded telomeres by two orders of magnitude. This protection is not observed at 150 mM Na + , in which ssTEL forms only a lessstable antiparallel GQ. These results suggest that GQ formation of telomeric overhangs may contribute to suppression of DNA damage signals.telomere protection | DNA damage response | single molecule imaging H uman telomeres consist of 2,000-30,000 bp of doublestranded TTAGGG repeats and terminate with a 50-to 200-nt-long, single-stranded 3′ G overhang (1). Telomeric termini need to be protected against DNA damage signals to ensure genome integrity. Replication protein A (RPA) nonspecifically binds ssDNA, is highly abundant in eukaryotes, and plays a role in DNA replication and repair (2). RPA binding to ssDNA, including telomeric overhangs, activates the ataxia telangiectasia and Rad3-related checkpoint (2, 3). The protection of telomeres (POT1)/telomere protection protein (TPP1) subunit of the shelterin complex contributes to telomere protection by specifically binding to the G overhang (4, 5). RPA is 1,000-fold more abundant than POT1/TPP1 and has a similar affinity for singlestranded telomeric DNA (ssTEL) (6, 7). Therefore, POT1/TPP1 alone may not be able to effectively compete against RPA binding (8, 9). Efficient protection of ssTEL against RPA binding may require association of POT1/TPP1 to the rest of the shelterin complex along double-stranded telomeric tracts or other telomere-associated proteins (6, 9).Another potentially significant factor that could influence the competition between RPA and POT1/TPP1 is the ability of ssTEL to form G-quadruplex (GQ) structures (10, 11). Recent studies have shown that human telomeres form GQ structures in vivo (12, 13) and in cell extracts (14). At physiologically relevant ionic conditions (∼150 mM K + ), GQs are thermodynamically more stable than competing Watson-Crick pairing (15). These structures were often regarded as obstacles for recruitment of telomerase (16) and translocation of the DNA replication machinery (17), and their unfolding requires helicase activity (17-19) or ssDNA binding proteins (20,21). It remains unclear whether GQ formation of ssTEL plays any role in protection of telomeres. ssTEL sequences fold into parallel...

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Section: Pot1supporting

confidence: 90%

Section: Pot1mentioning

confidence: 95%

See 1 more Smart Citation

G-quadruplex formation in telomeres enhances POT1/TPP1 protection against RPA binding

Ray

Bandaria

Qureshi

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

137

144

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“…A later in vitro study brought additional evidence of folding into two and three contiguous G4s [30]. Recently, structural investigations by nuclear magnetic resonance of individually labeled G4 units provided some insights into the conformations of the different G4 units in a tandem context [31,32].…”

Section: Introductionmentioning

confidence: 99%

Understanding the stability of DNA G-quadruplex units in long human telomeric strands

Bugaut

Alberti

2015

Biochimie

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Human telomeric DNA is composed of GGGTTA repeats. The presence of consecutive guanines makes the telomeric G-strand prone to fold into contiguous (or tandem) G-quadruplexes (G4s). The aim of this study was to provide a clarified picture of the stability of telomeric tandem G4 structures as a function of the number of G4 units and of boundary sequences, and an understanding of the diversity of their melting behaviors in terms of the single G4 units composing them. To this purpose we undertook an UV-spectroscopic investigation of the structure and stability of telomeric repeats potentially able to fold into up to four contiguous G4s, flanked or not by TTA sequences at their 5' and 3' extremities. We explain why the stability of (GGGTTA)4m-1GGG structures (m = 2, 3, 4 …) decreases with increasing the number m of G4 units, whereas the stability of TTA-(GGGTTA)4m-1GGG-TTA structures does not. Our results support that the inner G4 units have similar stabilities, whereas the stabilities of the terminal G4 units are modulated by their flanking nucleotides: in a TTA-(GGGTTA)4m-1GGG-TTA tandem context, the terminal G4 units are roughly as stable as the inner G4 units; while in a (GGGTTA)4m-1GGG tandem context, the G4 at the 5' extremity is more stable than the G4 at the 3' extremity, which in turn is more stable than an inner G4. Our study provides new information about the global and local stability of telomeric tandem G4 structures under near physiological conditions.

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“…Contrarily, a growing number of evidences indicate that the parallel form of telomeric DNA might not be biologically relevant target as it requires dehydrated conditions to exist. [25][26][27] Recent findings suggest that hybrid-1, hybrid-2 and 2-tetrads antiparallel basket topologies are the biologically relevant quadruplex structures for the telomeric DNA. 26,[28][29][30] Major folding differences between parallel-promoter quadruplexes and telomeric quadruplexes can be exploited for the design of topology-specific ligands.…”

Section: Introductionmentioning

confidence: 99%

Topology Specific Stabilization of Promoter over Telomeric G-Quadruplex DNAs by Bisbenzimidazole Carboxamide Derivatives

et al. 2014

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Various potential G-quadruplex forming sequences present in the genome offer a platform to modulate their function by means of stabilizing molecules. Though G-quadruplex structures exhibit diverse structural topologies, the presence of G-quartets as a common structural element makes the design of topology specific ligands a daunting task. To address this, the subtle structural variations of loops and grooves present in the quadruplex structures can be exploited. To this end, we report the design and synthesis of quadruplex stabilizing agents based on bisbenzimidazole carboxamide derivatives of pyridine, 1,8-naphthyridine, and 1,10-phenanthroline. The designed ligands specifically bind to and stabilize promoter quadruplexes having parallel topology over any of the human telomeric quadruplex topologies (parallel, hybrid, or antiparallel) and duplex DNAs. CD melting studies indicate that ligands could impart higher stabilization to c-MYC and c-KIT promoter quadruplexes (up to 21 °C increment in Tm) than telomeric and duplex DNAs (ΔTm ≤ 2.5 °C). Consistent with a CD melting study, ligands bind strongly (Kb = ∼10(4) to 10(5) M(-1)) to c-MYC quadruplex DNA. Molecular modeling and dynamics studies provide insight into how the specificity is achieved and underscore the importance of flexible N-alkyl side chains attached to the benzimidazole-scaffold in recognizing propeller loops of promoter quadruplexes. Overall, the results reported here demonstrate that the benzimidazole scaffold represents a potent and powerful side chain, which could judiciously be assembled with a suitable central core to achieve specific binding to a particular quadruplex topology.

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High-Resolution Insight into G-Overhang Architecture

Cited by 107 publications

References 52 publications

G-quadruplex formation in telomeres enhances POT1/TPP1 protection against RPA binding

G-quadruplex formation in telomeres enhances POT1/TPP1 protection against RPA binding

Understanding the stability of DNA G-quadruplex units in long human telomeric strands

Topology Specific Stabilization of Promoter over Telomeric G-Quadruplex DNAs by Bisbenzimidazole Carboxamide Derivatives

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