Base Flipping Free Energy Profiles for Damaged and Undamaged DNA

Zheng, Han; Cai, Yuqin; Ding, Shuang; Tang, Ying; Kropachev, Konstantin; Zhou, Yanzi; Wang, Lihua; Wang, Shenglong; Geacintov, Nicholas E.; Zhang, Yingkai; Broyde, Suse

doi:10.1021/tx1003613

Cited by 32 publications

(47 citation statements)

References 17 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Furthermore, UvrB is believed to interact with the damaged substrate through base stacking with a tyrosine residue at the base of the beta-hairpin and through a base flipping event [25], and the yeast homologue of human XPC-RAD23B [23] also utilizes base-flipping interactions with the protein. Base flipping free energy profiles and repair susceptibility of damaged DNA are currently under investigation [71]. …”

Section: Discussionmentioning

confidence: 99%

Probing for DNA damage with β-hairpins: Similarities in incision efficiencies of bulky DNA adducts by prokaryotic and human nucleotide excision repair systems in vitro

et al. 2011

Self Cite

View full text Add to dashboard Cite

Nucleotide excision repair (NER) is an important prokaryotic and eukaryotic defense mechanism that removes a large variety of structurally distinct lesions in cellular DNA. While the proteins involved are completely different, the mode of action of these two repair systems is similar, involving a cut-and-patch mechanism in which an oligonucleotide sequence containing the lesion is excised. The prokaryotic and eukaryotic NER damage-recognition factors have common structural features of β-hairpin intrusion between the two DNA strands at the site of the lesion. In the present study, we explored the hypothesis that this common β-hairpin intrusion motif is mirrored in parallel NER incision efficiencies in the two systems. We have utilized human HeLa cell extracts and the prokaryotic UvrABC proteins to determine their relative NER incision efficiencies. We report here comparisons of relative NER efficiencies with a set of stereoisomeric DNA lesions derived from metabolites of benzo[a]pyrene and equine estrogens in different sequence contexts, utilizing 21 samples. We found a general qualitative trend towards similar relative NER incision efficiencies for ~ 65% of these substrates; the other cases deviate mostly by ~ 30% or less from a perfect correlation, although several more distant outliers are also evident. This resemblance is consistent with the hypothesis that lesion recognition through β-hairpin insertion, a common feature of the two systems, is facilitated by local thermodynamic destabilization induced by the lesions in both cases. In the case of the UvrABC system, varying the nature of the UvrC endonuclease, while maintaining the same UvrA/B proteins, can markedly affect the relative incision efficiencies. These observations suggest that, in addition to recognition involving the initial modified duplexes, downstream events involving UvrC can also play a role in distinguishing and processing different lesions in prokaryotic NER.

show abstract

Section: Discussionmentioning

confidence: 99%

Probing for DNA damage with β-hairpins: Similarities in incision efficiencies of bulky DNA adducts by prokaryotic and human nucleotide excision repair systems in vitro

et al. 2011

Self Cite

View full text Add to dashboard Cite

show abstract

“…The opening times for more stable, undamaged/matched DNA are expected to be much longer than for mismatch DNA (55). Although the 1D diffusion constants of Rad4/XPC on DNA are yet to be reported, studies have revealed microsecond-regime residence times per DNA site for a wide range of DNA-binding proteins (7)(8)(9)(10)(11)(12)(13).…”

Section: Significancementioning

confidence: 99%

Twist-open mechanism of DNA damage recognition by the Rad4/XPC nucleotide excision repair complex

Velmurugu

Chen

Sevilla

et al. 2016

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

125

View full text Add to dashboard Cite

DNA damage repair starts with the recognition of damaged sites from predominantly normal DNA. In eukaryotes, diverse DNA lesions from environmental sources are recognized by the xeroderma pigmentosum C (XPC) nucleotide excision repair complex. Studies of Rad4 (radiation-sensitive 4; yeast XPC ortholog) showed that Rad4 "opens" up damaged DNA by inserting a β-hairpin into the duplex and flipping out two damage-containing nucleotide pairs. However, this DNA lesion "opening" is slow (~5-10 ms) compared with typical submillisecond residence times per base pair site reported for various DNA-binding proteins during 1D diffusion on DNA. To address the mystery as to how Rad4 pauses to recognize lesions during diffusional search, we examine conformational dynamics along the lesion recognition trajectory using temperaturejump spectroscopy. Besides identifying the~10-ms step as the ratelimiting bottleneck towards opening specific DNA site, we uncover an earlier~100-to 500-μs step that we assign to nonspecific deformation (unwinding/"twisting") of DNA by Rad4. The β-hairpin is not required to unwind or to overcome the bottleneck but is essential for full nucleotide-flipping. We propose that Rad4 recognizes lesions in a step-wise "twist-open" mechanism, in which preliminary twisting represents Rad4 interconverting between search and interrogation modes. Through such conformational switches compatible with rapid diffusion on DNA, Rad4 may stall preferentially at a lesion site, offering time to open DNA. This study represents the first direct observation, to our knowledge, of dynamical DNA distortions during search/interrogation beyond base pair breathing. Submillisecond interrogation with preferential stalling at cognate sites may be common to various DNA-binding proteins.DNA damage recognition | time-resolved fluorescence spectroscopy | temperature-jump perturbation | DNA unwinding dynamics | xeroderma pigmentosum E ssential genetic mechanisms, such as replication, transcription, recombination, and repair, all require recognition of specific DNA sequences or structures by specialized proteins. How DNA-binding proteins search for and identify their target sites embedded in a vast excess of nontarget sites, especially if using only thermal energy, is a fundamental question in biology. Several lines of evidence indicate that proteins use some combination of 3D diffusion in the bulk solution and 1D diffusion while nonspecifically bound to DNA, and use this "facilitated diffusion" as a means to search efficiently in genomic DNA for their targets (1-7). Direct observations of proteins diffusing on nonspecific DNA have revealed residence times per base pair site ranging from 50 ns to 300 μs (7-13). On the other end, highresolution structures and thermodynamic studies on a wide range of specific protein-DNA complexes have revealed significant distortions in otherwise B-form DNA duplex structures and concerted rearrangements in the bound protein to accommodate the deformed DNA; this "induced-fit" mechanism has emerged as a general pr...

show abstract

“…Such differences result in different protein/DNA recognition and repair activities (see 3.4). Thermal destabilization was also observed using 14R(+)-transanti-DB [a,l]P-N 2 -dG adduct (Zheng et al, 2010) or 14S(-)-trans-anti-DB [a,l]P-N 6 -dA adducts whereas 14R(+) isomer stabilizes the ds-DNA (Cai et al, 2011). The hormone-derived genotoxic compound, 4-OHEN, derives from equilin and equilenin, two equine oestrogens present in hormone substitution therapies used to prevent the uncomfortable effects of menopauses but are also thought to increase breast cancer incidence in the population of hormonally-treated women (Rossouw et al, 2002).…”

Section: Carcinogens As Dna Destabilizing Agentsmentioning

confidence: 91%

“…This results in a base-flipping where the (+)-anti-B[a]P-N 2 -dG bulky adduct is located in the minor groove and the opposite cytosine is positioned in the major groove (Cosman et al, 1993). The precise orientation of this highly carcinogenic 10S(+)-trans-anti-B[a]P-N 2 -dG adduct depends on the sequence surrounding the target guanine (Cai et al, 2010). DNA is untwisted at 5'-CGG*C sites where a large bend is induced in the DNA helix, but not at 5'-CG*GC sequences where, conversely, DNA helix is destabilized in its portion orientated 5' to the lesion (Rodríguez et al, 2007).…”

Section: Carcinogens As Dna Destabilizing Agentsmentioning

confidence: 99%

DNA Helix Destabilization by Alkylating Agents: From Covalent Bonding to DNA Repair

Lenglet¹,

Depauw²,

Mendy-Belaiche³

et al. 2011

Selected Topics in DNA Repair

View full text Add to dashboard Cite

Base Flipping Free Energy Profiles for Damaged and Undamaged DNA

Cited by 32 publications

References 17 publications

Probing for DNA damage with β-hairpins: Similarities in incision efficiencies of bulky DNA adducts by prokaryotic and human nucleotide excision repair systems in vitro

Probing for DNA damage with β-hairpins: Similarities in incision efficiencies of bulky DNA adducts by prokaryotic and human nucleotide excision repair systems in vitro

Twist-open mechanism of DNA damage recognition by the Rad4/XPC nucleotide excision repair complex

DNA Helix Destabilization by Alkylating Agents: From Covalent Bonding to DNA Repair

Contact Info

Product

Resources

About