DNA nanotechnology provides a versatile foundation for designing programmable self-assembling structures, but optimal control over such molecular systems remains a challenge. This paper introduces a novel Multi-Quantum Agent System (MQAS) to coordinate and enhance DNA self-assembly processes. The proposed model integrates quantum-enhanced agents, classical sensing, reinforcement learning, and DNA nanostructure environments. By leveraging quantum circuits for decision-making and entangled communication for coordination, MQAS agents can dynamically interact with the DNA assembly grid to guide structure formation. We detail the system architecture, agent behavior, quantum learning mechanisms, and simulation environment, and compare our framework to classical multi-agent DNA systems. Experimental scenarios and future directions demonstrate the potential of MQAS to advance programmable matter and synthetic biology.