Zymo Research ZR-96 Oligo Clean & Concentrator™ D4063 | 4×96 Prep Plate Format, Oligonucleotide Cleanup ≥16 nt

The Zymo Research ZR-96 Oligo Clean & Concentrator™ D4063 is a 4×96-preparation 96-well plate format oligonucleotide cleanup kit — designed for the rapid, high-throughput purification of oligonucleotides ≥16 nt from enzymatic reactions using Zymo-Spin™ I-96 Plate technology. There is no need for organic denaturants or chloroform. The kit features Zymo-Spin plate technology and employs a single-buffer system that allows for efficient oligonucleotide adsorption to the matrix of each well in the Zymo-Spin™ I-96 Plate. Oligonucleotide is washed and concentrated into a small volume of water (≥10 µl). Purified oligonucleotide is suitable for hybridization, gel shift assays, enzymatic reactions, ligation, sequencing, microarray analysis, etc. Effectively removes unincorporated nucleotides, short oligos, dyes, enzymes, and salts. >90% recovery of ssDNA oligonucleotides. 4 plates (4×96 preps) — 384 total wells. Catalog # D4063. The 2×96-preparation version is available as D4062.

High-Throughput 96-Well Plate Format — 96 Samples Per Plate, 384 Per Kit The defining format distinction of the D4063 is its 96-well plate architecture — processing up to 96 oligonucleotide samples simultaneously per plate, 4 plates per kit, 384 total samples per kit. The plate format is specifically designed for high-throughput oligonucleotide synthesis facilities, core laboratories processing large batches of oligos simultaneously, and any workflow where individual spin column cleanup of 96+ samples would be prohibitively time-consuming. For high-throughput oligo purification where speed and throughput are the primary constraints, the D4063 96-well plate format reduces cleanup time per sample by an order of magnitude compared to individual spin column formats.

D4063 vs. D4062 — Choosing the Right Kit Size:

Oligonucleotide Cleanup ≥16 nt — Size Limits and Compatibility Size Limits — For oligonucleotides ≥16 nt, up to 23 kb. The ZR-96 Oligo Clean & Concentrator™ recovers oligonucleotides from 16 nt — the minimum length reliably retained on the Zymo-Spin I-96 plate matrix — through large DNA up to 23 kb. Sample Sources include enzymatic reaction mixtures containing oligonucleotides ≥16 nt (radioactive-, biotin-, DIG-labeled, etc.). The kit is specifically designed for:

• Oligonucleotide synthesis reactions — removal of failed sequences, protecting groups, and synthesis byproducts
• Radioactively labeled oligos — cleanup of ³²P, ³³P, and ³⁵S-labeled oligonucleotide probes
• Biotin-labeled oligonucleotides — cleanup of biotinylated probes and primers
• DIG-labeled oligonucleotides — cleanup of digoxigenin-labeled probes
• Fluorescently labeled oligos — removal of unincorporated fluorescent dyes
• PCR primers — cleanup from enzymatic reactions
• Any oligo-containing enzymatic reaction — removal of enzymes, salts, unincorporated nucleotides, and short fragments

>90% Recovery — High-Efficiency Oligonucleotide Purification >90% recovery of ssDNA oligonucleotides. The ZR-96 Oligo Clean & Concentrator™ achieves >90% recovery of ssDNA oligonucleotides from enzymatic reactions — a performance benchmark that is maintained consistently across all 96 wells of each plate and across all 4 plates in the D4063 kit. For oligonucleotide synthesis and labeling workflows where oligo yield and recovery directly affect downstream assay performance, the consistently high recovery of the D4063 ensures maximum oligo yield from every purification.

10µg ssDNA/RNA or 5µg dsDNA Per Well — Per-Well Binding Capacity Binding Capacity — 10 µg ssDNA/RNA or 5 µg dsDNA per well. The per-well binding capacity of the Zymo-Spin™ I-96 Plate accommodates the full range of standard oligonucleotide reaction scales — from small-scale single-tube synthesis reactions through large-scale parallel synthesis in 96-well format. The differential capacity for ssDNA/RNA (10µg) vs. dsDNA (5µg) reflects the binding chemistry of the silica matrix for single-stranded vs. double-stranded nucleic acids.

Single-Buffer System — Simple, Rapid, No Organic Solvents There is no need for organic denaturants or chloroform. The kit features Zymo-Spin plate technology and employs a single-buffer system that allows for efficient oligonucleotide adsorption. The single-buffer design of the ZR-96 Oligo Clean & Concentrator™ eliminates the buffer selection and optimization steps required by competing oligo cleanup methods — a single Oligo Binding Buffer addition to the sample initiates binding, followed by wash and elution. No organic solvent handling, no hazardous waste, and no pH adjustment steps are required.

≥10µL Elution — Concentrated Oligonucleotide Recovery Elution Volume — ≥10 µl. Oligonucleotide is washed and concentrated into a small volume of water (≥10 µl). The ≥10µL minimum elution volume concentrates purified oligonucleotides from enzymatic reaction volumes into a small, analysis-ready volume — compatible with direct use in downstream hybridization, PCR, ligation, sequencing, and microarray applications without further concentration steps.

High Purity — A260/A280 and A260/A230 >1.8 Purity — A260/A280 & A260/A230 >1.8. DNA/RNA is ready for hybridization, sequencing, ligation, PCR and etc. The high purity of oligonucleotides recovered by the D4063 meets the quality standards required for all standard downstream oligo applications — including sequencing, microarray hybridization, and enzymatic reactions sensitive to salt or enzyme carryover.

Elution Plates Included — Complete Plate-to-Plate Workflow Elution Plates: 4 included. Collection Plates: 8 included. 96-Well Cover Foil: 4 included. The D4063 includes all plates required for the complete cleanup workflow — Zymo-Spin I-96 binding plates, collection plates for flow-through capture, elution plates for eluate collection, and cover foil for plate sealing — providing a fully self-contained plate-to-plate purification system requiring no additional labware beyond a plate centrifuge.

Room Temperature Storage — All Kit Components Store all kit components at room temperature. Note: Ethanol must be added to DNA Wash Buffer concentrate prior to use as indicated on the label.

Complete Kit Contents — D4063 (4×96 Preps):

Complete ZR-96 Oligo Clean & Concentrator™ Family:

Compatible Replacement — Cross-Reference Guide

The Zymo Research ZR-96 Oligo Clean & Concentrator™ D4063 is a comparable alternative to 96-well plate format oligonucleotide cleanup kits from several major manufacturers:

• Qiagen QIAquick 96 PCR Purification Kit (28181) — 96-well format DNA cleanup
• NEB Monarch PCR & DNA Cleanup Kit — spin column format (no 96-well equivalent)
• Macherey-Nagel NucleoSpin 96 PCR — 96-well plate PCR cleanup format

The D4063 specifically targets oligonucleotides ≥16 nt in a 96-well plate format — more specialized than standard PCR cleanup plates. These products may differ in protocol, yield, and performance characteristics.

Key Features

• Zymo Research ZR-96 Oligo Clean & Concentrator™ — Catalog # D4063
• 4×96 prep plate format — 384 total wells, 4 Zymo-Spin™ I-96 Plates
• High-throughput oligonucleotide cleanup — 96 samples simultaneously per plate
• Oligonucleotide size range: ≥16 nt to 23 kb
• Binding capacity: 10µg ssDNA/RNA or 5µg dsDNA per well
• >90% recovery of ssDNA oligonucleotides
• ≥10µL minimum elution volume
• Single-buffer system — no organic solvents, no chloroform
• Effectively removes unincorporated nucleotides, short oligos, dyes, enzymes, and salts
• Compatible with radioactive-, biotin-, DIG-, and fluorescent-labeled oligonucleotides
• A260/A280 and A260/A230 >1.8 — high-purity eluate
• Complete plate system included — binding plates, collection plates, elution plates, cover foil
• Room temperature storage — all components
• Ethanol must be added to DNA Wash Buffer concentrate before use
• 1-year kit component integrity guarantee
• 2×96 prep version: D4062

Supported Applications High-throughput oligonucleotide synthesis cleanup, parallel purification of radioactively labeled probes, biotin-labeled oligonucleotide cleanup, DIG-labeled probe purification, fluorescent label removal from labeled oligos, PCR primer cleanup from enzymatic reactions, core laboratory oligo purification services, microarray probe cleanup, hybridization probe preparation, sequencing primer cleanup, and any high-throughput molecular biology workflow requiring simultaneous purification of 96 oligonucleotide samples ≥16 nt per plate in a 96-well format.

Technical Specifications