CRISPR-Cas systems, as adaptive immune systems in prokaryotes, have revolutionized genome editing with programmable nucleic acid sequence recognition. However, inserting large DNA fragments at a desired position remains challenging. Recently discovered mobile genetic elements, termed CRISPR-associated transposons (CASTs), have sparked substantial interest due to their potential to facilitate DNA insertion applications. CASTs insert DNA fragments through an RNA-guided mechanism using multiple conserved components: a CRISPR effector, a transposase (TnsB or TnsA/TnsB), a AAA+ regulator (TnsC), and target-site associated protein (TniQ). The most well-characterized CAST subtypes, type V-K and I-F3 elements, primarily differ by the associated CRISPR effectors. The V-K subtype uses Cas12k, while the I-F3 uses the multi-subunit Cascade complex. This dissertation outlines our progress in characterizing the molecular basis of RNA-guided DNA integration facilitated by the two distinct CAST subtypes. The initial three chapters focus on the V-K CAST from Scytonema hofmanni (ShCAST). The first chapter describes ATP-dependent filament formation of TnsC on a double-stranded DNA and the interaction between TnsC filament and TniQ at the target site. We also reveal that TnsB disassembles the TnsC filaments by promoting ATP hydrolysis of TnsC, explaining how untargeted transpositions and duplicated transpositions may be prevented. The second chapter discusses how the transposase TnsB uses its C-terminal helix to interact with the TnsC filaments. We found that while this helix is crucial, it isn’t solely sufficient to trigger TnsC filament disassembly, suggesting unidentified secondary interactions. We also visualize the structure of the TnsB strand-transfer complex that forms an inter-twined symmetric tetramer. This structure describes how TnsB recognizes the transposon end sequence and catalyzes the strand-transfer reaction. In chapter three, we have reconstituted the multi-subunit integration complex that represents the product of RNA-guided transposition and determined its structure using cryo-EM. In this structure, the CRISPR effector Cas12k forms a complex with bacterial host protein S15 and TniQ, creating a complete R-loop with the target DNA. TnsC mini-filament bridges the target-site recognition module with the transposase TnsB, making novel asymmetric interactions with the target DNA. Finally, we show interactions between TnsB and the C-terminal face of TnsC, which contribute to the stimulation of TnsC ATPase activity. Chapter four explores how type I-F3b CAST has adapted during its co-option of the Cascade CRISPR effector for target-site recognition. Using cryo-EM, we visualized the structure of the Cascade-TniQ complex of I-F3b CAST from Aeromonas salmonicida. Extensive cryo-EM data analysis reveals two major states that represent partial and complete R-loop conformation, highlighting the crucial roles of TniQ and a Cas8/5 helix bundle in licensing the target site for transposition. We further investigate the role of TniQ in recognizing the crRNA sequence and the molecular basis of the flexible PAM requirements for target recognition. Our structural characterization of CASTs substantially advances our understanding of how these transposition systems operate and presents avenues to improve CAST transposition for precision genome-editing applications.