Watchmaker Equinox® Library Amplification Kits
Precision, amplified.
Library amplification is the step where sensitivity is quietly won or lost — every misincorporated base and every over-amplified molecule erodes a rare-variant call. Equinox® Library Amplification Kits are built to protect that step: a uniquely engineered, ultra-high-fidelity proofreading DNA polymerase in an optimised hot-start master mix, formulated for high-efficiency, low-bias amplification of NGS libraries. The result is excellent fidelity, uniform coverage and high library complexity — exactly what rare-variant detection, cfDNA analysis, single-cell work and hybridisation capture demand.
Robust across the inputs and genomes that break other polymerases.
Equinox amplifies efficiently from 0.1 pg to 500 ng of template and across 15–85% GC content, holding coverage even through AT- and GC-rich extremes. A highly effective antibody-based hot start strongly inhibits both polymerase and exonuclease activity until activation, protecting primers and precious low-input samples and suppressing non-specific artefacts — which matters most in automated, low-input library construction.
One platform, three configurations.
The standard Equinox kit (2X master mix) covers most sensitive applications; Equinox HC (4X) adds reaction volume for more dilute inputs; and Equinox Uracil-Tolerant amplifies uracil-containing templates — bisulfite-converted, deaminated or damaged (e.g. FFPE) DNA — without the stalling that defeats ordinary proofreading enzymes. Each is available with or without P5/P7 primers.
- Higher fidelity: up to 40% fewer misincorporations than KAPA HiFi HotStart ReadyMix, including cancer-relevant C>T errors.
- Lower bias: uniform UMI-family coverage and even coverage of complex genomes — sequence less to reach target depth.
- Capture-ready: minimal bias even in the presence of AMPure XP and streptavidin beads, simplifying on-bead amplification.
For Research Use Only. Not for use in diagnostic procedures.
| Parameter | Specification |
| Enzyme | Engineered B-family proofreading DNA polymerase (Uracil-Tolerant variant for modified templates) |
| Format | Hot-start 2X master mix (Equinox), 4X master mix (Equinox HC), 2X (Uracil-Tolerant); master mix includes buffer, enzyme and dNTPs |
| Template input range | 0.1 pg – 500 ng |
| GC compatibility | 15% – 85% |
| Amplicon length | Optimised up to ~1 kb; robustly amplifies up to 10 kb (optimisation recommended >10 kb) |
| Fidelity | ~40% lower overall error rate vs KAPA HiFi HotStart ReadyMix |
| Hot start | Antibody-based; inhibits 5′→3′ polymerase and 3′→5′ exonuclease until activation |
| Activities | 3′→5′ (proofreading) exonuclease; no 5′→3′ exonuclease; temperature-dependent strand displacement; blunt-ended products |
| Bead compatibility | Robust with AMPure XP and Dynabeads™ M-270 streptavidin (on-bead / capture workflows) |
| Sequencing platforms | Illumina and non-Illumina sample-prep workflows |
| Shipping conditions | Ice packs |
| Storage | −20 °C ± 5 °C long-term; 4 °C up to 2 weeks short-term |
| Stability | Up to 20 freeze-thaw cycles |
| Shelf life | 24-rxn: ≥ 6 months · > 24-rxn: ≥ 12 months |
| Quality system | Manufactured under ISO 13485:2016 |
| Configuration | Master mix | Use case |
| Equinox Library Amplification Kit | Equinox® Amplification Master Mix (2X) + P5/P7 Primer Mix (10X, optional) | Sensitive NGS library amplification, default choice |
| Equinox HC (High Concentration) | Equinox® Amplification Master Mix (4X) + P5/P7 (10X, optional) | More dilute inputs — added template volume per reaction |
| Equinox Uracil-Tolerant | Equinox® Uracil-Tolerant Amplification Master Mix (2X) + P5/P7 (10X, optional) | Bisulfite-converted, deaminated or damaged (FFPE) DNA; uracil-containing primers/templates; UDG carry-over prevention |
| Article Number | Description | 24 / 96 / 384 rxn |
| 7K0014-024 / -096 / -384 | Equinox® Library Amplification Kit — incl. P5/P7 Primer Mix (10X) | ✓ / ✓ / ✓ |
| 7K0021-024 / -096 / -384 | Equinox® Library Amplification Kit — w/o primers | ✓ / ✓ / ✓ |
| 7K0094-096 / -384 | Equinox® HC Library Amplification Kit — incl. P5/P7 Primer Mix (10X) | — / ✓ / ✓ |
| 7K0065-096 / -384 | Equinox® HC Library Amplification Kit — w/o primers | — / ✓ / ✓ |
| 7K0023-024 / -096 / -384 | Equinox® Uracil-Tolerant Amplification Kit — incl. P5/P7 Primer Mix (10X) | ✓ / ✓ / ✓ |
| 7K0028-024 / -096 / -384 | Equinox® Uracil-Tolerant Amplification Kit — w/o primers | ✓ / ✓ / ✓ |
| Non-hot-start formulations and custom fills/labels available on request. Equinox HC is not offered in a 24-rxn size. | ||
| Topic | Detail |
| Primers | Forward/reverse at equal concentration, 0.5–2 µM final (0.5 µM yields ~500 ng library; use 2 µM for higher yield) |
| Primer protection | 3′-end phosphorothioate bonds strongly recommended for specificity/yield |
| Annealing temperature | 60 °C with Watchmaker FL-UDI + standard P5/P7; 55 °C with Watchmaker Stubby UDI |
| Extension | 30 s sufficient up to ~500 bp mode size; longer for longer inserts |
| Modified bases | Use the Uracil-Tolerant kit for uracil/modified templates; Cy3/Cy5, 5′Bromo-dU, 2′-OMe/2′-F and reversible terminators likely work (larger mods less efficient) |
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Tell us your library workflow, inputs and platform, and we'll help you choose the right Equinox configuration — with evaluation samples, cycling guidance and local logistics.
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High-stringency amplification across DNA, RNA and epigenetic workflows
Low-frequency variant detection
High fidelity and even coverage protect sensitive calls from FFPE and cfDNA, where false variants are costly.
Hybridisation capture
Low bias even in the presence of streptavidin and AMPure beads simplifies on-bead amplification and reduces dropout.
Single-cell & low-input
A strong hot start safeguards primers and minimal templates, sustaining sensitivity in automated, low-input builds.
WGS & complex genomes
Uniform coverage across 15–85% GC reduces the sequencing needed to reach target depth on demanding genomes.
Amplicon, RNA-seq, ChIP/ATAC
A dependable amplification step across DNA, RNA and epigenetic library workflows, Illumina and non-Illumina alike.
Methyl-seq (Uracil-Tolerant)
The Uracil-Tolerant kit amplifies bisulfite-converted DNA with high yield and minimal bias for epigenetic applications.
Three configurations, one high-fidelity platform
Same engineered polymerase — pick the format your workflow needs
Equinox (2X)
The default ultra-high-fidelity master mix for sensitive NGS library amplification across inputs and GC content. Available with or without primers.
Equinox HC (4X)
A high-concentration master mix that frees up reaction volume for more dilute templates — more mass per reaction, equivalent performance. (96- and 384-rxn.)
Equinox Uracil-Tolerant (2X)
Amplifies uracil-containing templates — bisulfite-converted, deaminated or damaged (FFPE) DNA — without the stalling that defeats ordinary proofreading enzymes.
- ULTRA-HIGH-FIDELITY LIBRARY AMPLIFICATION
- UP TO 40% FEWER POLYMERASE ERRORS
- UNIFORM COVERAGE ACROSS 15–85% GC
- INPUTS FROM 0.1 pg TO 500 ng
- LOW-BIAS, ON-BEAD CAPABLE
- URACIL-TOLERANT OPTION FOR METHYL-SEQ
- ULTRA-HIGH-FIDELITY LIBRARY AMPLIFICATION
- UP TO 40% FEWER POLYMERASE ERRORS
- UNIFORM COVERAGE ACROSS 15–85% GC
- INPUTS FROM 0.1 pg TO 500 ng
- LOW-BIAS, ON-BEAD CAPABLE
- URACIL-TOLERANT OPTION FOR METHYL-SEQ
Fidelity that protects rare-variant calls
~40% lower error rate, with C>T errors suppressed
In sensitive sequencing, a polymerase error is indistinguishable from a real variant until it costs you a false call. Measured across more than nine million base-incorporation events, Equinox delivered a ~40% lower overall error rate than KAPA HiFi HotStart ReadyMix, with a marked reduction in C>T substitutions specifically. That subtype matters twice over: it arises from spontaneous deamination of methylated cytosine, and it is among the most common true mutation types in cancer — so suppressing it sharpens confidence in the variants that count.
Low-bias amplification, cleaner UMIs, less sequencing
Uniform UMI families mean more error-correctable reads
Unique molecular indices only help if amplification is even. Biased "jackpotting" over-amplifies a few molecules, leaving others as singletons that can't be error-corrected — and forcing extra sequencing to recover coverage. Equinox amplifies UMI families uniformly: more than 75% of all read families (and over 90% of families at 25–75% GC) fall within 3× of the mean family depth. More error-correctable molecules, better sensitivity, and lower sequencing cost for the same answer.
Engineered for on-bead hybridisation capture
Minimal bias, even in the presence of magnetic beads
Capture workflows increasingly amplify directly on beads to cut handling — but most polymerases bias coverage when AMPure or streptavidin beads are present. Equinox holds coverage uniform with both AMPure XP and Dynabeads™ M-270 streptavidin, and on an extreme AT-rich/GC-rich microbial mix (Plasmodium falciparum and Pseudomonas aeruginosa) showed lower AT-dropout than KAPA HiFi — superior recovery of the hardest sequences. The practical upshot: simpler on-bead protocols with less locus dropout.
Equinox Uracil-Tolerant: amplify bisulfite-converted & damaged DNA
A proofreading polymerase that doesn't stall on uracil
Most B-family proofreading polymerases stall when they meet a uracil or other modified base — a real problem for epigenetics, where bisulfite conversion fills the template with them. Equinox Uracil-Tolerant DNA Polymerase is engineered to read straight through, amplifying uracil-containing templates with high yield and minimal bias. Use it for bisulfite-converted DNA, deaminated or damaged (FFPE) inputs, uracil-containing primers, and UDG-based carry-over prevention. It is the amplification chemistry behind Watchmaker methyl-seq workflows (and, in DHU-tolerant form, behind TAPS+).
COMPLETE YOUR NGS PIPELINE
Tailored Solutions for Challenging Applications
A great result relies on more than just a single high-quality reagent. Visit our Solutions page to see how we integrate cutting-edge technologies, like Watchmaker Genomics, into end-to-end workflows designed to maximize your laboratory’s efficiency and sequencing yield.
Technical insights & configuration selection
Practical guidance on choosing and running Equinox amplification.
Use the standard Equinox (2X) for most sensitive NGS library amplification. Choose Equinox HC (4X) when inputs are dilute and you need more template volume per reaction (it performs equivalently at 1×). Choose Equinox Uracil-Tolerant for bisulfite-converted, deaminated or damaged (FFPE) DNA and uracil-containing templates/primers.
0.1 pg to 500 ng of template, across 15–85% GC, for amplicons optimised up to ~1 kb (robustly up to 10 kb with optimisation).
An engineered B-family proofreading DNA polymerase, supplied as a hot-start master mix (buffer, enzyme and dNTPs included). An antibody strongly inhibits both polymerase and 3′→5′ exonuclease activity until activation; non-hot-start formats are available on request.
Lower misincorporation means fewer false variants. Equinox reduces overall error rate ~40% vs KAPA HiFi HotStart ReadyMix, including C>T errors that otherwise mimic real cancer mutations — improving sensitivity in rare-variant and cfDNA work.
Yes. Equinox maintains uniform coverage in the presence of AMPure XP and Dynabeads™ M-270 streptavidin beads, simplifying hybridisation-capture and on-bead protocols.
Equal forward/reverse primers at 0.5–2 µM final (0.5 µM yields ~500 ng library); 3′ phosphorothioate-protected primers are recommended. Anneal at 60 °C with FL-UDI/standard P5–P7 or 55 °C with stubby UDI; 30 s extension up to ~500 bp. See the User Guide for full cycling.
Use the Uracil-Tolerant kit for modified templates. Fluorescent labels (Cy3/Cy5), 5′Bromo-dU, 2′-OMe/2′-F and reversible terminators are likely to work; larger or backbone modifications are less efficient.
Yes. Watchmaker's quality management system is certified to ISO 13485:2016.