Photocrosslinking of human telomeric G-quadruplex loops by anti cyclobutane thymine dimer formation

Abstract

The unusual structural forms of telomere DNA, which protect the ends of chromosomes during replication, may render it vulnerable to unprecedented photodamage, possibly involving nonadjacent bases that are made proximate by folding. The G-quadruplex for the human telomere sequence consisting of a repeating d(T-TAGGG) is one unusual form. Tel22, d[AGGG(TTAGGG)3], forms a basket structure in the presence of Na ؉ and may form multiple equilibrating structures in the presence of K ؉ with hybrid-type structures predominating. UVB irradiation of d[AGGG(TTAGGG)3] in the presence of Na ؉ results in a cis,syn thymine dimer between two adjacent Ts in a TTA loop and a mixture of nonadjacent anti thymine dimers between various loops. Irradiation in the presence of K ؉ , however, produces, in addition to these same products, a large amount of specific anti thymine dimers formed between either T in loop 1 and the central T in loop 3. These latter species were not observed in the presence of Na ؉ . Interloop-specific anti thymine dimers are incompatible with hybrid-type structures, but could arise from a chair or basket-type structure or from triplex intermediates involved in interconverting these structures. If these unique nonadjacent anti thymine dimer photoproducts also form in vivo, they would constitute a previously unrecognized type of DNA photodamage that may interfere with telomere replication and present a unique challenge to DNA repair. Furthermore, these unusual anti photoproducts may be used to establish the presence of G-quadruplex or quadruplex-like structures in vivo.mass spectrometry ͉ photochemistry ͉ nonadjacent dimer ͉ DNA ͉ UV T elomeres are repetitive sequences at the ends of chromosomes that function in concert with telomerase and a number of other proteins to protect the ends of chromosomes from shortening during successive rounds of replication (1-3). The human telomere sequence consists of repeating d(TTAGGG) that may fold into various repeating G-quadruplex structures. Short fragments of the human telomere sequence can exist in a myriad of structures that depend on their sequence and on the cations present (4-7). To date, basket (8, 9), parallel (10), and (3 ϩ 1) structures including hybrid-1 and hybrid-2 (11-14) type G-quadruplex forms have been determined by NMR and crystallography. The oligodeoxynucleotide, d[AGGG(TTAGGG) 3 ] (Tel22), adopts a basket structure in solutions containing Na ϩ (8), whereas in the presence of K ϩ , the predominant intracellular cation, the hybrid-type structures are favored over the basket (11, 13) and/or chair (15) structures (Fig. 1).Recently, we discovered that a highly unusual interstrand-type nonadjacent, anti thymine photodimer (Fig. 2B), previously only found in dried or ethanolic solutions of UVC irradiated DNA (16), can form in aqueous solution. Irradiation of d(GTATCAT-GAGGTGC) with UVB light produced a high yield of cis,anti thymine photodimer between T2 and T7 under slightly acidic conditions (17). This anti photodimer must originate from some folded structur...

Folding and Unfolding Pathways of the Human Telomeric G-Quadruplex

“…In addition to the spectroscopic evidence cited above supporting the assignment of an antiparallel chair structure to I 2 and a triplex structure to I 3 , the studies of Su et al [46] provide direct chemical evidence for the coexistence of chair forms as well as triplex forms for Tel22 in 150 mM KCl at 4 °C. In these studies, the authors identified the sequential positions of thymine photodimers which can only form from when proximate thymine residues are excited by UV irradiation.…”

“…12) which could take place in a single step. It is noteworthy that photocrosslinking studies of Su et al [46] provide direct evidence for the presence of chair, basket and/or triple helical structures for Tel22 in K + solutions.…”

“…Ambrus et al[39] also suggested a role for a triplex intermediate in the transition from the basket topology in Na + to the hybrid topology in K + . In addition, UV photocrosslinking studies of Tel22 in K + solution provide evidence for the presence of antiparallel chair conformation and possibly triple helical structures in a dynamic equilibrium [46]. …”

Folding and misfolding pathways of G-quadruplex DNA

“…The nature of these states is however still debated. The folding pathway may include a collapse of the unfolded species into hairpin-like structures with G:G base pairs (44–47), which then fold into an antiparallel G-quadruplex (37,48), then interconvert progressively into triplexes intermediates (49–51) before folding properly into a G-quadruplex (37). This model is sequential, and therefore does not consider side-reactions in the mechanism, i.e.…”

Photoinduced Damage to Cellular DNA: Direct and Photosensitized Reactions†

“…Structural parameters have also to be taken into account, such as the nucleosome positioning that modulates the photoreactivity and therefore the ratio formation between 6-4PPs and CPDs (69). Evidence has also been provided for the enhanced efficiency of photoreactions in telomeres (70) with the possible formation of interstrand lesions in the quadruplex region (71).…”