Characterization of the Search Complex and Recognition Mechanism of the AlkD-DNA Glycosylase

Investigation of the Flipping Dynamics of 1, N6-Ethenoadenine in Alkyladenine DNA Glycosylase

Alkyladenine DNA glycosylase (AAG) is an essential enzyme responsible for maintaining genome integrity by repairing several DNA lesions damaged by alkylation or deamination. Understanding how it can recognize and excise the lesions thus lays the foundation for therapeutic treatment against lesion-associated diseases or cancers. However, the molecular details of how the lesion can be distinguished from the matched base by AAG and how it enters the cleavage site, ready for excision, are not fully elucidated. In this study, we have revealed the molecular details of the flipping dynamics of 1, N6-ethenoadenine (εA) not only in the form of free double-stranded DNA (dsDNA) but also in the form of the AAG-dsDNA complex. Our MD simulations and PMF calculations have shown that the flipping of εA and dA is thermodynamically disfavored in the free dsDNA, even though εA has a lower flipping energy barrier than dA. By sharp contrast, the flipping of εA is thermodynamically favored in AAG with an obvious free energy drop, while dA is equally stabilized before and after the flipping. Moreover, a comparison of the PMFs in the forms of free dsDNA and the AAG-dsDNA complex has pinpointed the role of AAG in discriminating εA against dA and facilitating the flipping of εA. Besides, the flipping process is simulated along the major and minor grooves, and our results have additionally demonstrated that the flipping is not directional in the free dsDNA while flipping along the major groove is kinetically more favorable than the minor groove in the AAG-dsDNA complex. Overall, our study has offered molecular insights into the flipping dynamics of εA and revealed its discrimination mechanism by AAG, which is expected to guide further enzyme engineering for therapeutic applications.

Activatable Self-Dissociation of Watson-Crick Structures with Fluorescent Nucleotides for Sensing Multiple Human Glycosylases at Single-Cell Level

Nucleobase oxidation and alkylation can destroy Watson-Crick base-pairing to challenge the genomic integrity. Human 8-oxoguanine glycosylase 1 (hOGG1) and alkyladenine glycosylase (hAAG) are evolved to counter these two cytotoxic lesions through base-excision repair, and their deregulations are implicated with multifactorial diseases and cancers. Herein, we demonstrate activatable self-dissociation of Watson-Crick structures with fluorescent nucleotides for sensing multiple human glycosylases at single-cell level. The presence of hOGG1 and hAAG catalyzes 8-oxoG and deoxyinosine removal in functional probe 1 to release two trigger probes (1 and 2). Then, trigger probes hybridize with functional probe 2 to activate the autocatalytic degradation of functional probes 2 (Cycle I) and 3 (Cycle II), replicating abundant trigger probes (1-4) and releasing two fluorophores (2-aminopurine (2-AP) and pyrrolo-dC (P-dC)). New trigger probes (1, 2) and (3, 4), in turn, hybridize with free functional probes 2 and 3, repeating Cycles I and II turnovers. Through multicycle self-dissociation of Watson-Crick structures, 2-AP and P-dC are exponentially accumulated for the simultaneous quantification of hOGG1 and hAAG. This nanodevice exhibits high sensitivity with a detection limit of 2.9 × 10^-3 U/mL for hOOG1 and 1.5 × 10^-3 U/mL for hAAG, and it can measure enzymatic kinetics, identify potential inhibitors, discriminate glycosylases between cancer and normal cell lines, and even quantify glycosylase activities in a single HeLa cell. Moreover, this assay may be rapidly and isothermally performed in one tube with only one tool enzyme in a quencher-free manner, promising a simple and powerful platform for multiple human glycosylase detection.

Non-flipping DNA glycosylase AlkD scans DNA without formation of a stable interrogation complex

The multi-step base excision repair (BER) pathway is initiated by a set of enzymes, known as DNA glycosylases, able to scan DNA and detect modified bases among a vast number of normal bases. While DNA glycosylases in the BER pathway generally bend the DNA and flip damaged bases into lesion specific pockets, the HEAT-like repeat DNA glycosylase AlkD detects and excises bases without sequestering the base from the DNA helix. We show by single-molecule tracking experiments that AlkD scans DNA without forming a stable interrogation complex. This contrasts with previously studied repair enzymes that need to flip bases into lesion-recognition pockets and form stable interrogation complexes. Moreover, we show by design of a loss-of-function mutant that the bimodality in scanning observed for the structural homologue AlkF is due to a key structural differentiator between AlkD and AlkF; a positively charged β-hairpin able to protrude into the major groove of DNA.

Target search and recognition mechanisms of glycosylase AlkD revealed by scanning FRET-FCS and Markov state models

DNA glycosylase repairs DNA damage to maintain the genome integrity, and thus it is essential for the survival of all organisms. However, it remains a long-standing puzzle how glycosylase diffuses along the genomic DNA to locate the sparse and aberrant lesion sites efficiently and accurately in the genome containing numerous base pairs. Previously, only the high-speed–low-accuracy search mode has been characterized experimentally, while the low-speed–high-accuracy mode is undetectable. Here, we observed the low-speed mode of glycosylase AlkD translocating, and further dissected its molecular mechanisms. To achieve this, we developed an integrated platform by combining scanning FRET-FCS with Markov state model. We expect that this platform can be widely applied to investigate other glycosylases and DNA-binding proteins.

DNA glycosylase is responsible for repairing DNA damage to maintain the genome stability and integrity. However, how glycosylase can efficiently and accurately recognize DNA lesions across the enormous DNA genome remains elusive. It has been hypothesized that glycosylase translocates along the DNA by alternating between a fast but low-accuracy diffusion mode and a slow but high-accuracy mode when searching for DNA lesions. However, the slow mode has not been successfully characterized due to the limitation in the spatial and temporal resolutions of current experimental techniques. Using a newly developed scanning fluorescence resonance energy transfer (FRET)–fluorescence correlation spectroscopy (FCS) platform, we were able to observe both slow and fast modes of glycosylase AlkD translocating on double-stranded DNA (dsDNA), reaching the temporal resolution of microsecond and spatial resolution of subnanometer. The underlying molecular mechanism of the slow mode was further elucidated by Markov state model built from extensive all-atom molecular dynamics simulations. We found that in the slow mode, AlkD follows an asymmetric diffusion pathway, i.e., rotation followed by translation. Furthermore, the essential role of Y27 in AlkD diffusion dynamics was identified both experimentally and computationally. Our results provided mechanistic insights on how conformational dynamics of AlkD–dsDNA complex coordinate different diffusion modes to accomplish the search for DNA lesions with high efficiency and accuracy. We anticipate that the mechanism adopted by AlkD to search for DNA lesions could be a general one utilized by other glycosylases and DNA binding proteins.