A Novel DNA Synthesis Platform Design with High-Throughput Paralleled Addressability and High-Density Static Droplet Confinement

Abstract

Using DNA as the next-generation medium for data storage offers unparalleled advantages in terms of data density, storage duration, and power consumption as compared to existing data storage technologies. To meet the high-speed data writing requirements in DNA data storage, this paper proposes a novel design for an ultra-high-density and high-throughput DNA synthesis platform. The presented design mainly leverages two functional modules: a dynamic random-access memory (DRAM)-like integrated circuit (IC) responsible for electrode addressing and voltage supply, and the static droplet array (SDA)-based microfluidic structure to eliminate any reaction species diffusion concern in electrochemical DNA synthesis. Through theoretical analysis and simulation studies, we validate the effective addressing of 10 million electrodes and stable, adjustable voltage supply by the integrated circuit. We also demonstrate a reaction unit size down to 3.16 × 3.16 μm², equivalent to 10 million/cm², that can rapidly and stably generate static droplets at each site, effectively constraining proton diffusion. Finally, we conducted a synthesis cycle experiment by incorporating fluorescent beacons on a microfabricated electrode array to examine the feasibility of our design.

Keywords: DNA data storage; DNA synthesis; DRAM; microfluidics; static droplet.

Figure 1

Schematic illustration of the overall design of a DNA synthesis chip and the synthesis process: (a) the DRAM-like IC and the SDA-based microfluidic structure. The enlarged view in the red dotted line box is (b) The electrode–IC connection. (c) The reagent forms independent droplets in a microfluidic structure and the IC selectively energizes sites to induce electrochemical reactions. The enlarged view in the red dotted line box is (d) The DMT at the oligonucleotide terminals is removed upon activation at selected sites and the protons are restricted in the droplet.

Figure 2

(a) The overall design architecture of the DRAM-like IC. (b) The basic unit of the DRAM-like IC consists of a transistor connected to a capacitor. (c) The column addressing circuit consists of 128 5-to-25 decoders.

Figure 3

The post-simulation waveform: (a) The selected electrode (orange) is charged to 3 V in 80 ns and unselected electrodes (brown) are kept at 0 V with row/column addressing (cyan and magenta) input set at 5 V. (b) A relatively stable voltage output is maintained by the electrode through charge-discharge cycling, with a period of 6 ms indicated by the red dotted line. (c) Different charging times for different stabilization voltages. (d) The DRAM-like IC can precisely control the magnitude of the stable voltage within the 0–3 V range.

Figure 4

(a) The SDA-based microfluidic structure restricting the diffusion of protons in a high-density oligonucleotide synthesis array. (b) The enlarged view of capillary valve unit indicated by red dotted line including the bypass channel, capillary valve, and chamber (the reaction site). (c) The schematic of two-phase flow simulation results: the aqueous phase forms independent droplets in the reaction site driven by the oil phase. (d) The variation in the average areas of the aqueous phase within the chambers in the same column.

Figure 5

(a) The patterned Ti/Au microelectrode arrays on the silicon dioxide wafer. (b) The Ti/Au microelectrode arrays chip obtained by slicing the patterned silicon dioxide wafer. (c) The functionalized microelectrode array chip was aligned and attached to the PDMS microfluidic channel. (d) Cy3 synthetic reagents were injected into the microfluidic channel using a precision syringe pump (LongerPump LSP02-2A). (e) The chip and microfluidic channel were clamped together using customized PMMA fixtures and bolts. (f) Enlarged view of the chip in the blue dotted line box is during reagent injection.

Figure 6

(a) Scheme of the electrografting and Cy3 phosphoramidite chemistry. (b) Cyclic voltammogram (CV) of 4-aminophenylethanol grafting on the Ti/Au electrode. (c) Microscopic photograph of the gold electrode array with Cy3 selectively synthesized on the (d) circular or (e) straight electrodes.