Data storage in DNA is a rapidly evolving technology that could be a transformative solution for the rising energy, materials, and space needs of modern information storage. Given that the information medium is DNA itself, its stability under different storage and processing conditions will fundamentally impact and constrain design considerations and data system capabilities. Here we analyze the storage conditions, molecular mechanisms, and stabilization strategies influencing DNA stability and pose specific design configurations and scenarios for future systems that best leverage the considerable advantages of DNA storage.

The physical architectures of information storage systems often dictate how information is encoded, databases are organized, and files are accessed. Here we show that a simple architecture comprised of a T7 promoter and a single-stranded overhang domain (ss-dsDNA), can unlock dynamic DNA-based information storage with powerful capabilities and advantages. The overhang provides a physical address for accessing specific DNA strands as well as implementing a range of in-storage file operations. It increases theoretical storage densities and capacities by expanding the encodable sequence space and simplifies the computational burden in designing sets of orthogonal file addresses. Meanwhile, the T7 promoter enables repeatable information access by transcribing information from DNA without destroying it. Furthermore, saturation mutagenesis around the T7 promoter and systematic analyses of environmental conditions reveal design criteria that can be used to optimize information access. This simple but powerful ss-dsDNA architecture lays the foundation for information storage with versatile capabilities.

DNA holds significant promise as a data storage medium due to its density, longevity, and resource and energy conservation. These advantages arise from the inherent biomolecular structure of DNA which differentiates it from conventional storage media. The unique molecular architecture of DNA storage also prompts important discussions on how data should be organized, accessed, and manipulated and what practical functionalities may be possible. Here we leverage thermodynamic tuning of biomolecular interactions to implement useful data access and organizational features. Specific sets of environmental conditions including distinct DNA concentrations and temperatures were screened for their ability to switchably access either all DNA strands encoding full image files from a GB-sized background database or subsets of those strands encoding low resolution, File Preview, versions. We demonstrate File Preview with four JPEG images and provide an argument for the substantial and practical economic benefit of this generalizable strategy to organize data.

Queues are commonly used in multithreaded programs for synchronization and communication. However, because software queues tend to be too expensive to support finegrained parallelism, hardware queues have been proposed to reduce overhead of communication between cores. Hardware queues require modifications to the processor core and need a custom interconnect. They also pose difficulties for the operating system because their state must be preserved across context switches. To solve these problems, we propose a hardware-accelerated queue, or HAQu. HAQu adds hardware to a CMP that accelerates operations on software queues. Our design implements fast queueing through an application's address space with operations that are compatible with a fully software queue. Our design provides accelerated and OS-transparent performance in three general ways: (1) it provides a single instruction for enqueueing and dequeueing which significantly reduces the overhead when used in fine-grained threading; (2) operations on the queue are designed to leverage low-level details of the coherence protocol; and (3) hardware ensures that the full state of the queue is stored in the application's address space, thereby ensuring virtualization. We have evaluated our design in the context of application domains: offloading fine-grained checks for improved software reliability, and automatic, fine-grained parallelization using decoupled software pipelining.