THE CONJUGATION WORKBENCH / RESEARCH PLANNING

Connect the chemistry.
Keep the assumptions clear.

Plan input amounts, inspect functional-handle compatibility and prepare a reviewable research brief. Calculations describe your inputs, not a successful reaction.

01 / DEFINE THE COMPONENTS

Protein & fluorescent dye

Use non-confidential inputs. A sequence is optional when you supply concentration on a molar basis or know the construct molecular weight. Never infer accessible sites from sequence alone.

Protein or antibodyMature assembly / chain definitionMolar amount denominator

The supplied mass and concentration must describe this same unit. Reactive-site equivalents are not inferred from sequence.

Component name *Amino-acid sequence / single FASTA record (optional)

Standard amino acids support a sequence-only average mass estimate. Ambiguous/nonstandard residues require a supplied mass for mass-based concentration conversion. Tags, glycans and multichain assemblies need construct-specific mass information.

Construct molecular weight

Mass unit

Molecular-weight source / assumptions

A supplied construct mass overrides the sequence estimate. No generic antibody mass is assumed.

Stock concentration *

Concentration unit

Aliquot volume *

Volume unit

Protein / antibody reactive handleProtein handle preparation stateHandle installation position / linker / method

Fluorescent reagent

FLUORESCENT REAGENT CATALOG

Find the exact dye.

Search names, families or catalog identifiers. Choose the reactive derivative you actually have; a family name alone does not establish compatible chemistry.

Search dye name or family

Emission wavelength band

Reactive chemistry

Choose an exact reagent

Selecting a new dye or Custom clears the previous dye's stock inputs and optical constants. Protein inputs stay in place. Filters only browse the catalog.

Custom mode: document the exact derivative. Unknown values remain blank and require review.

Exact dye / derivative name *Reactive derivative / installed handleReagent / DNA handle preparation state

A modification sold as “Azide (NHS Ester)” may leave an azide on the oligo, not a retained reactive NHS ester. Confirm the final installed group.

Reagent stock concentration *

Concentration unit

Exact reagent / modified DNA molecular weight (Da)

Use the supplied construct mass, including the exact reactive derivative or DNA modifications. No mass is guessed from a dye name or modified DNA sequence.

Available stock volume (optional)

Volume unit

Input ratio & formulationReagent input equivalents per selected protein unit *

Your chosen molar feed ratio. This is not measured degree of labeling and is not an experimentally recommended ratio.

Desired label / DNA loading (optional planning goal)

A design goal, separate from input equivalents and measured loading. This value does not change the calculated feed ratio.

Experimentally measured protein recovery (%) (optional)Recovery measurement basis / source

Additional buffer volume

Volume unit

Buffer composition & additives

pH (optional)

Reducing agents

Free amino contaminants or carrier proteins may be presentCosolvent in reagent stock (% v/v) (optional)

Only this stock contribution is modeled; other cosolvent sources and biomolecule tolerance are not assessed.

No reaction is run, no sequence is uploaded and no order is placed.

OPTIONAL / ABSORBANCE ANALYSIS

Estimate labeling from a suitable measured sample.

This calculation uses blank-corrected absorbances and supplied optical coefficients. It does not derive labeling from sequence or input equivalents. Free dye and other absorbing components can invalidate the estimate.

Dye + protein onlySingle dye; no DNA, scattering or other confounding absorbers?Absorbance path conventionFree dye removed and analytical sample suitable?

Blank-corrected A280

Blank-corrected dye absorbance

Protein ε280 (M⁻¹ cm⁻¹)Wavelength of the measured dye absorbance (nm)Wavelength for the supplied dye coefficient / correction set (nm)

These must match. Excitation and absorbance-analysis wavelengths can differ; use the exact derivative calibration set.

Dye ε at measurement wavelength (M⁻¹ cm⁻¹)Dye A280 correction factor

Optical path length (cm)

Sample dilution factor

Protein extinction-coefficient source *Exact dye derivative / coefficient source

Use matched measurements from the same aliquot, dilution and optical path. Exact derivative presets are provided where sourced; unknown coefficients remain blank and must be documented. A280 already normalized to a 1 cm path must use 1 cm here.

DNA SYNTHESIS / QUOTE & FEASIBILITY REVIEW

A synthesis request.
A clear review step.

Specify the DNA construct you want reviewed. Aptaseek can discuss sourcing and coordination after feasibility and commercial terms are agreed. This form creates a local request summary; it does not place a supplier order.

Do not send confidential or proprietary sequences through ordinary email until an appropriate secure process is agreed. No secure intake backend or supplier purchasing integration is connected.

No request sent · No order placed

DNA construct name *Strand formatDNA sequence (5′ → 3′) *

Single DNA or FASTA record. IUPAC ambiguity codes are flagged for review; inline chemical annotations are not accepted as bases.

5′ modification (strand 1)3′ modification (strand 1)Internal modifications / positionsSecond-strand modifications / positions / linker (if applicable)

Requested synthesis scale *

Scale unit

Synthesis scale is not guaranteed delivered yield.

Desired delivered quantity (optional)

Quantity unit

Purification preferenceIntended conjugation handle / position / linkerRequested delivery stateRequested resuspension concentration / bufferPackaging / aliquot preferenceRequested QC / documentationIntended research application *Contact email for the request (optional)

REVIEW BEFORE ANY EXPORT OR EMAIL

You choose what leaves this page.

Calculate an input plan or prepare a synthesis request first. A local download is saved through your browser; opening an email draft transfers its contents to your configured email application. Sending remains your action.

Include the entered sequences in the review preview

Off by default. Sequence-free summaries retain component names and lengths only. FASTA headers are not exported.

I confirm any included sequences are non-confidential and appropriate to share through the chosen route.

I have reviewed this exact summary and its sequence inclusion.

Open reviewed email draft

Nothing has been submitted to Aptaseek or a supplier. Editing inputs invalidates this review.

METHODS, ASSUMPTIONS & REFERENCES

Planning is not validation.

Calculations use your supplied stock values and construct information. Reaction conditions, purification, site accessibility, functional performance and supplier feasibility require separate review. This workbench is for research use only.

Calculation definitions & limits

Amount: nmol = concentration (µM) × volume (µL) / 1000. Reagent amount = protein amount × chosen input equivalents. Reagent volume = required reagent amount / stock molar concentration. Final volume assumes additive volumes.

Mass conversion: µM = stock concentration (mg/mL) × 10⁶ / construct molecular weight (Da). A sequence-only protein mass uses average residue masses plus one water molecule; it excludes modifications, glycans and multichain assembly.

Absorbance: corrected A280 = A280 − correction factor × dye absorbance. Protein concentration = corrected A280 / (protein ε280 × path length). Dye concentration = dye absorbance / (dye ε × path length). DOL estimate = dye concentration / protein concentration. Both concentrations use the same dilution factor; it cancels in the ratio.

No sequence-only pI, extinction coefficient, exposed Lys/Cys count, conjugation site or affinity prediction is made. Ordinary A280 DOL is disabled for DNA-containing modes.

Connect the chemistry.Keep the assumptions clear.

Protein & fluorescent dye

Find the exact dye.

Estimate labeling from a suitable measured sample.

A synthesis request.A clear review step.

You choose what leaves this page.

Planning is not validation.

Aptaseek, on your home screen.

Connect the chemistry.
Keep the assumptions clear.

A synthesis request.
A clear review step.