title: Structural and mechanical properties of individual human telomeric G-quadruplexes in molecularly crowded solutions.
abstract: Recent experiments provided controversial observations that either parallel or non-parallel G-quadruplex exists in molecularly crowded buffers that mimic cellular environment. Here, we used laser tweezers to mechanically unfold structures in a human telomeric DNA fragment, 5'-(TTAGGG)4TTA, along three different trajectories. After the end-to-end distance of each unfolding geometry was measured, it was compared with PDB structures to identify the best-matching G-quadruplex conformation. This method is well-suited to identify biomolecular structures in complex settings not amenable to conventional approaches, such as in a solution with mixed species or at physiologically significant concentrations. With this approach, we found that parallel G-quadruplex coexists with non-parallel species (1:1 ratio) in crowded buffers with dehydrating cosolutes [40% w/v dimethyl sulfoxide (DMSO) or acetonitrile (ACN)]. In crowded solutions with steric cosolutes [40% w/v bovine serum albumin (BSA)], the parallel G-quadruplex constitutes only 10% of the population. This difference unequivocally supports the notion that dehydration promotes the formation of parallel G-quadruplexes. Compared with DNA hairpins that have decreased unfolding forces in crowded (9 pN) versus diluted (15 pN) buffers, those of G-quadruplexes remain the same (20 pN). Such a result implies that in a cellular environment, DNA G-quadruplexes, instead of hairpins, can stop DNA/RNA polymerases with stall forces often <20 pN.
authors: Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA.
authors: Soma
authors: S
authors: Dhakal
authors: Yunxi
authors: Y
authors: Cui
authors: Deepak
authors: D
authors: Koirala
authors: Chiran
authors: C
authors: Ghimire
authors: Saurabh
authors: S
authors: Kushwaha
authors: Zhongbo
authors: Z
authors: Yu
authors: Philip M
authors: PM
authors: Yangyuoru
authors: Hanbin
authors: H
authors: Mao
mesh_terms: D000097:Acetonitriles / Q000737:chemistry; D002021:Buffers; D004121:Dimethyl Sulfoxide / Q000737:chemistry; D054856:G-Quadruplexes; D006801:Humans; D016615:Telomere / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D000097:Acetonitriles; D002021:Buffers; D004121:Dimethyl Sulfoxide; C032159:acetonitrile
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