Double-stranded flanking ends affect the folding kinetics and conformational equilibrium of G-quadruplexes forming sequences within the promoter of <i>KIT</i> oncogene

Vesco, Guglielmo; Lamperti, Marco; Salerno, Domenico; Marrano, Claudia Adriana; Cassina, Valeria; Rigo, Riccardo; Buglione, Enrico; Bondani, Maria; Nicoletto, Giulia; Mantegazza, Francesco; Sissi, Claudia; Nardo, Luca

doi:10.1093/nar/gkab674

Cited by 9 publications

(8 citation statements)

References 48 publications

(72 reference statements)

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“…Our model predictions of folding patterns are robust as long as K f, N -1 is greater than K f , and K f,N is significantly greater than K f, N -1 . The G-Tracts on the 5′ side (vicinity of ssDNA/dsDNA junction) are significantly less stable due to the flanking duplex regions, similar to a recent observation in KIT promoter ( 37 ). We estimated the folding parameters for these 5′ G-Tracts (K f,1 and K f,2 ) and the cooperativity parameter (K c ) by comparing the patterns observed for the experimentally measured and computationally calculated S-parameters, as described below.…”

Section: Resultssupporting

confidence: 81%

Emerging accessibility patterns in long telomeric overhangs

Shiekh

Mustafa

Kodikara

et al. 2022

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

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We present single-molecule experimental and computational modeling studies investigating the accessibility of human telomeric overhangs of physiologically relevant lengths. We studied 25 different overhangs that contain 4–28 repeats of GGGTTA (G-Tract) sequence and accommodate one to seven tandem G-quadruplex (GQ) structures. Using the FRET-PAINT method, we probed the distribution of accessible sites via a short imager strand, which is complementary to a G-Tract and transiently binds to available sites. We report accessibility patterns that periodically change with overhang length and interpret these patterns in terms of the underlying folding landscape and folding frustration. Overhangs that have [4n]G-Tracts, (12, 16, 20…) demonstrate the broadest accessibility patterns where the peptide nucleic acid probe accesses G-Tracts throughout the overhang. On the other hand, constructs with [4n+2]G-Tracts, (14, 18, 22…) have narrower patterns where the neighborhood of the junction between single- and double-stranded telomeres is most accessible. We interpret these results as the folding frustration being higher in [4n]G-Tract constructs compared to [4n+2]G-Tract constructs. We also developed a computational model that tests the consistency of different folding stabilities and cooperativities between neighboring GQs with the observed accessibility patterns. Our experimental and computational studies suggest the neighborhood of the junction between single- and double-stranded telomeres is least stable and most accessible, which is significant as this is a potential site where the connection between POT1/TPP1 (bound to single-stranded telomere) and other shelterin proteins (localized on double-stranded telomere) is established.

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Section: Resultssupporting

confidence: 81%

Emerging accessibility patterns in long telomeric overhangs

Shiekh

Mustafa

Kodikara

et al. 2022

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

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“…On the 5′ side, our constructs have a ssDNA/dsDNA junction rather than a free end as in ssDNA, which resulted in significantly lower stability for G-Tracts in this region. A similar destabilization due to flanking duplex regions was recently reported for the GQs that form in KIT promoter (53). We estimated the folding parameters associated with the G-Tracts in the vicinity of ssDNA/dsDNA junction ( K f,1 and K f,2 ) and the cooperativity parameter ( K c ) by comparing the patterns observed for the experimentally measured and computationally calculated S-parameters, as described below.…”

Section: Resultssupporting

confidence: 81%

Emerging Accessibility Patterns in Long Telomeric Overhangs

Shiekh¹,

Mustafa²,

Hoque³

et al. 2021

Preprint

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We present single molecule experimental and computational modeling studies investigating the accessibility and folding landscape of human telomeric overhangs of physiologically relevant lengths. The overhangs contain 4-28 repeats of GGGTTA (G-Tract) sequence and accommodate 1-7 tandem G-quadruplex (GQ) structures. Using FRET-PAINT, we probed the distribution of accessible sites via a short imager strand, which is complementary to a G-Tract and transiently binds to unfolded sites. We report accessibility patterns that periodically change with overhang length and provide insights about the underlying folding frustration. Overhangs that have 4n G-Tracts, (12, 16…), demonstrate maximum frustration, while those with 4n+2 G-Tracts, (14, 18…), have minimal frustration. We also developed a computational model that suggests positive folding cooperativity between neighboring GQs is required for persistence of such patterns. Our experimental and computational studies suggest lower folding stability at the junction between single and double stranded telomeric DNA, which has implications for Shelterin complex formation.

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“…Properly designed single-molecule analyses can help to address this issue. In a recent study where FRET analyses were performed, a low sample concentration in solution prevented the occurrence of dimer formation [ 45 ]. As reported in Figure 3 b, two different constructs were designed.…”

Section: Differential Folding Landscapes Of G-quadruplexes At the ...mentioning

confidence: 99%

Polymorphic and Higher-Order G-Quadruplexes as Possible Transcription Regulators: Novel Perspectives for Future Anticancer Therapeutic Applications

2022

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In the past two decades, significant efforts have been put into designing small molecules to target selected genomic sites where DNA conformational rearrangements control gene expression. G-rich sequences at oncogene promoters are considered good points of intervention since, under specific environmental conditions, they can fold into non-canonical tetrahelical structures known as G-quadruplexes. However, emerging evidence points to a frequent lack of correlation between small molecule targeting of G-quadruplexes at gene promoters and the expression of the associated protein, which hampers pharmaceutical applications. The wide genomic localization of G-quadruplexes along with their highly polymorphic behavior may account for this scenario, suggesting the need for more focused drug design strategies. Here, we will summarize the G4 structural features that can be considered to fulfill this goal. In particular, by comparing a telomeric sequence with the well-characterized G-rich domain of the KIT promoter, we will address how multiple secondary structures might cooperate to control genome architecture at a higher level. If this holds true, the link between drug–DNA complex formation and the associated cellular effects will need to be revisited.

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Double-stranded flanking ends affect the folding kinetics and conformational equilibrium of G-quadruplexes forming sequences within the promoter of KIT oncogene

Cited by 9 publications

References 48 publications

Emerging accessibility patterns in long telomeric overhangs

Emerging accessibility patterns in long telomeric overhangs

Emerging Accessibility Patterns in Long Telomeric Overhangs

Polymorphic and Higher-Order G-Quadruplexes as Possible Transcription Regulators: Novel Perspectives for Future Anticancer Therapeutic Applications

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