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Abstract Ring-shaped DNA sliding clamps are essential for DNA replication and genome maintenance. Clamps need to be opened and chaperoned onto DNA by clamp loader complexes (CLCs). Detailed understanding of the mechanisms by which CLCs open and place clamps around DNA remains incomplete. Here, we present a series of six structures of the Escherichia coli CLC bound to an open or closed clamp prior to and after binding to a primer-template DNA, representing the most significant intermediates in the clamp loading process. We show that the ATP-bound CLC first binds to a clamp, then constricts to hold onto it. The CLC then expands to open the clamp with a gap large enough for double-stranded DNA to enter. Upon binding to DNA, the CLC constricts slightly, allowing clamp closing around DNA. These structures provide critical high-resolution snapshots of clamp loading by the E. coli CLC, revealing how the molecular machine works.

This paper questions the side-channel security of central reduction technique, which is widely adapted in efficient implementations of Lattice-Based Cryptography (LBC). We show that the central reduction leads to a vulnerability by creating a strong dependency between the power consumption and the sign of sensitive intermediate values. We exploit this dependency by introducing the novel absolute value prediction function, which can be employed in higher-order non-profiled multi-query Side-Channel Analysis (SCA) attacks. Our results reveal that – compared to classical reduction algorithms – employing the central reduction scheme leads to a two-orders-of-magnitude decrease in the number of required SCA measurements to exploit secrets of masked implementations. We particularly show that our approach is valid for the prime moduli employed by Kyber and Dilithium, the lattice-based post-quantum algorithms selected by NIST. We practically evaluate our introduced approach by performing second-order non-profiled attacks against an open-source masked implementation of Kyber on an ARM Cortex-M4 micro-processor. In our experiments, we revealed the full secret key of the aforementioned masked implementation with only 250 power traces without any forms of profiling or choosing the ciphertexts.

Recombineering is an essential tool for molecular biologists, allowing for the facile and efficient manipulation of bacterial genomes directly in cells without the need for costly and laborious in vitro manipulations involving restriction enzymes. The main workhorses behind recombineering are bacteriophage proteins that promote the single-strand annealing (SSA) homologous recombination pathway to repair double-stranded DNA breaks. While there have been several reviews examining recombineering methods and applications, comparatively few have focused on the mechanisms of the proteins that are the key players in the SSA pathway: a 5′→3′ exonuclease and a single-strand annealing protein (SSAP or “annealase”). This review dives into the structures and functions of the two SSA recombination systems that were the first to be developed for recombineering in E. coli: the RecET system from E. coli Rac prophage and the λRed system from bacteriophage λ. By comparing the structures of the RecT and Redβ annealases, and the RecE and λExo exonucleases, we provide new insights into how the structures of these proteins dictate their function. Examining the sequence conservation of the λExo and RecE exonucleases gives more profound insights into their critical functional features. Ultimately, as recombineering accelerates and evolves in the laboratory, a better understanding of the mechanisms of the proteins behind this powerful technique will drive the development of improved and expanded capabilities in the future.

Teaching computer architecture (Comp-Arch) courses in undergraduate curricula is becoming more of a challenge as most students prefer software-oriented courses. In some computer science/engineering departments, Comp-Arch courses are offered without the lab component due to resource constraints and differing pedagogical priorities. This article demonstrates how students working in teams are motivated to study the Comp-Arch course and how instructors can increase student motivation and knowledge by taking advantage of hands-on practices. The teams are asked to design and implement a 16-bit MIPS-like processor with constraints as a specific instruction set, and limited data and instruction memory. Student projects include following three phases, namely, design, desktop simulator implementation, and verification using hardware description language (HDL). In the design phase, teams develop their Comp-Arch to implement specified instructions. A range of designs resulted, e.g., (a) a processor with extensive user-defined instructions resulting in longer cycle times (b) a processor with a minimal instruction set but with a faster clock cycle time. Next, teams developed a desktop simulator in any programming language to execute instructions on the architecture. Finally, students engage in Verilog Hardware Description Language (HDL) projects to simulate and verify the data-path designed during the initial phase. Student feedback and their current understanding of the project were collected through a questionnaire featuring varying Likert scale questions, some with a ten-point scale, and others with a five-point scale. Results of the survey show that the hands-on approach increases students’ motivation and knowledge in the Comp-Arch course, which is centered around computer system design principles. This approach can also be effectively extended to related courses, such as Microprocessor Design, which delves into the intricacies of creating and implementing microprocessors or central processing units (CPUs) at the hardware level. Furthermore, the present study demonstrates that interactions, specifically through peer reviews and public presentations, between students in each phase increases their knowledge and perspective on designing custom processors.