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ECL`

ExperimentPNASynthesis

ExperimentPNASynthesis[OligomerModels]⟹Protocol

uses a oligomer OligomerModels to create a Peptide Nucleic Acid (PNA) Synthesis Protocol and associated synthesis cycles methods.

    
Peptide nucleic acids (PNA) are synthetic oligonucleotide analogues of DNA or RNA in which the sugar phosphate backbone is replaced by a pseudo-peptide skeleton to which the nucleobases are linked via a two-atom carboxymethyl spacer. They bind to DNA and RNA with high specificity and selectivity, leading to PNA-RNA and PNA-DNA hybrids being more stable than their corresponding nucleic acid complexes. Because of their high thermal stability and resistance to proteases and nucleases, PNAs are ideal candidates as therapeutic agents and can be used as powerful tools in molecular biology and diagnostics. PNA is chemically synthesized by the condensation reaction of the carboxyl group of one nucleic acid to the amino group of another. This can be achieved with classical solution phase synthesis or solid phase synthesis, which is used in this experiment. In solid phase synthesis, PNA monomers are covalently bound to a solid support material and synthesised step-by-step in a single reaction vessel utilising selective protecting group chemistry. PNA monomers are attached to the solid support from their C terminus. PNA synthesis occurs by coupling the carboxyl group of the incoming amino acid to the N-terminus of the growing PNA chain. This C-to-N synthesis is opposite from protein biosynthesis, during which the N-terminus of the incoming amino acid is linked to the C-terminus of the protein chain (N-to-C). The benefit of the solid support is the isolation of synthesis sites, making interference between growing chains impossible. The use of protecting groups is essential to avoid undesirable side reactions during this process. The most common protecting groups for amino groups used in PNA synthesis are 9-fluorenylmethyloxycarbonyl group (Fmoc), which is used in this experiment, and t-butyloxycarbonyl (Boc). This experiment is very similar to ExperimentPeptideSynthesis and the options are identical. Only some of the options (ActivationSolution, CleavageSolution, DeptectionTime, ActivationTime, CouplingTime, and CleavageTime) are resolved slightly differently. ExperimentMassSpectrometry and ExperimentHPLC with fraction analysis can be run on the results of this experiment to verify the molecular weight and measure percent purity of the product.
    

Experimental Principles

    Figure 1.1: Procedural overview of a PNASynthesis experiment. Step 1: Define the PNA sequence to be synthesized, including any modifications, by providing a Model[Sample], a Model[Molecule,Oligomer], a Sequence (PNA["AGCTA"]), Strand (ToStrand[PNA["AGCTA"]]) or Structure (ToStructure["AGCTA",Polymer->PNA]). Step 2: The first monomer is loaded to the resin Step 3: The monomers are then expanded with a cycle of a) removal of the Fmoc protecting group from the resin linker or the last nucleic acid that is currently on the resin, b) the activation of the monomer and c) the addition on the monomer to the resin or resin with linked strand. Step 4: The PNA is liberated from the resin and side chain protecting groups are remove. Step 5: The PNA is purified by using a solution where the desired PNA strands are insoluble and impurities are soluble. This results in the PNA crashing out of solution. Step 6: The PNA is then resuspended in a resuspension buffer.

Instrumentation

    Symphony X

    Figure 2.1: A system of pre-activation vessels (PV), reaction vessels (RV), amino acid bottles, buffers and solutions, waste and collection vessels (CV) connected by channels. The flow in the channels is controlled by Nitrogen gas and the volume of the liquid deliveries are verified with optical sensors.

Experiment Options

    General

    Instrument

    The model or object instrument to be used for this synthesis.
    Default Value: Model[Instrument, PeptideSynthesizer, Symphony X]
    Pattern Description: An object of type or subtype Model[Instrument, PeptideSynthesizer] or Object[Instrument, PeptideSynthesizer]
    Programmatic Pattern: ObjectP[{Model[Instrument, PeptideSynthesizer], Object[Instrument, PeptideSynthesizer]}]

    SynthesisStrategy

    The type of N-terminal and side chain protecting group scheme used by this synthesis.
    Default Value: Fmoc
    Pattern Description: Fmoc.
    Programmatic Pattern: Fmoc

    Swelling

    SwellSolution

    The model or sample object to be used to swell the resin prior to the start of the synthesis or resin download.
    Default Value: Automatic
    Default Calculation: Automatic will resolve to Model[Sample, "Dichloromethane, Reagent Grade"] if SwellResin has been set to True.
    Pattern Description: An object of type or subtype Object[Sample] or Model[Sample] or a prepared sample or Null.
    Programmatic Pattern: ((ObjectP[{Object[Sample], Model[Sample]}] | _String) | Automatic) | Null

    SwellResin

    Indicates if the resin will be swelled in SwellSolution before the start of a synthesis.
    Default Value: True
    Pattern Description: True or False.
    Programmatic Pattern: BooleanP
    Index Matches to: experiment samples

    SwellTime

    Specifies the amount of time that the resin is swelled for (per cycle).
    Default Value: Automatic
    Default Calculation: Will automatically resolve to 20 Minutes is SwellResin is set to True.
    Pattern Description: Greater than or equal to 0.1 hours and less than or equal to 12 hours or Null.
    Programmatic Pattern: (RangeP[0.1*Hour, 12*Hour] | Automatic) | Null
    Index Matches to: experiment samples

    SwellVolume

    Specifies the volume of SwellSolution that the samples will be swelled with.
    Default Value: Automatic
    Default Calculation: Will automatically resolve to 10 Milliliter if SwellResin is set to True.
    Pattern Description: Greater than or equal to 2.5 milliliters and less than or equal to 25 milliliters or Null.
    Programmatic Pattern: (RangeP[2.5*Milliliter, 25*Milliliter] | Automatic) | Null
    Index Matches to: experiment samples

    NumberOfSwellCycles

    Specifies the number of the cycles of swelling of the resin before the start of a synthesis.
    Default Value: Automatic
    Default Calculation: Will automatically resolve to 3 if SwellResin is set to True.
    Pattern Description: Greater than 0 in increments of 1 or Null.
    Programmatic Pattern: (GreaterP[0, 1] | Automatic) | Null
    Index Matches to: experiment samples

    Washing

    WashSolution

    The model or sample object used to wash the resin in between each reagent addition.
    Default Value: Model[Sample, Dimethylformamide, Reagent Grade]
    Pattern Description: An object of type or subtype Model[Sample] or Object[Sample] or a prepared sample.
    Programmatic Pattern: ObjectP[{Model[Sample], Object[Sample]}] | _String

    WashVolume

    The volume of WashSolution to be used to wash the resin in between each reagent addition.
    Default Value: Automatic
    Default Calculation: Will automatically resolve to 4 Milliliter plus an additional .2 Milliliter for each 1 Micromole of synthesis Scale, rounded up to the nearest .5 Milliliter.
    Pattern Description: Greater than or equal to 1 milliliter and less than or equal to 25 milliliters.
    Programmatic Pattern: RangeP[1*Milliliter, 25*Milliliter] | Automatic
    Index Matches to: experiment samples

    Deprotection

    DeprotectionSolution

    The model or sample object that represents the deprotection solution that will be used to remove protecting groups from the growing strand during the deprotection step of a synthesis or download resin cycle.
    Default Value: Automatic
    Default Calculation: Will resolve to Model[Sample, StockSolution, "Deprotection Solution (20% piperidine in NMP)"] for Fmoc synthesis and Model[Sample, StockSolution, "95% TFA 5% m-cresol"] for Boc synthesis.
    Pattern Description: An object of type or subtype Model[Sample] or Object[Sample] or a prepared sample.
    Programmatic Pattern: (ObjectP[{Model[Sample], Object[Sample]}] | _String) | Automatic

    InitialDeprotection

    Indicates if an initial deprotection step will be done before the synthesis of the strand begins.
    Default Value: False
    Default Calculation: The initial deprotection will only occur if DownloadResin is set to True as all other cycles already include a deprotection step prior to their coupling steps.
    Pattern Description: True or False.
    Programmatic Pattern: BooleanP
    Index Matches to: experiment samples

    FinalDeprotection

    Indicates if a final deprotection step is will be done as part of the last synthesis cycle prior to the start of cleavage or resin storage.
    Default Value: True
    Pattern Description: True or False.
    Programmatic Pattern: BooleanP
    Index Matches to: experiment samples

    DeprotectionVolume

    The volume of DeprotectionSolution added to each reaction vessel during the deprotection step of a synthesis cycle.
    Default Value: Automatic
    Default Calculation: Automatic will resolve to 3 Milliliter plus an additional .2 Milliliter for each Micromole of synthesis Scale, rounded up to the nearest .5 Milliliter
    Pattern Description: Greater than or equal to 1 milliliter and less than or equal to 25 milliliters.
    Programmatic Pattern: RangeP[1*Milliliter, 25*Milliliter] | Automatic
    Index Matches to: experiment samples

    NumberOfDeprotections

    The number of times that each reaction vessel will be deprotected per deprotection step of a synthesis cycle.
    Default Value: 2
    Pattern Description: Greater than or equal to 1 and less than or equal to 10 in increments of 1.
    Programmatic Pattern: RangeP[1, 10, 1]
    Index Matches to: experiment samples

    NumberOfDeprotectionWashes

    The number of WashSolution washes each reaction vessel will undergo after the deprotection step of the synthesis cycle.
    Default Value: 5
    Pattern Description: Greater than or equal to 1 and less than or equal to 10 in increments of 1.
    Programmatic Pattern: RangeP[1, 10, 1]
    Index Matches to: experiment samples

    DeprotectionTime

    The amount of time that each reaction vessel is exposed to the deprotection solution during each deprotection step of a synthesis cycle.
    Default Value: 7 minutes
    Pattern Description: Greater than or equal to 1 minute and less than or equal to 30 minutes.
    Programmatic Pattern: RangeP[Minute, 30*Minute]
    Index Matches to: experiment samples

    Deprotonation

    DeprotonationSolution

    The model or sample object that represents the DeprotonationSolution that will be used to neutralize the resin prior to the coupling step.
    Default Value: Automatic
    Default Calculation: Will automatically resolve to Model[Sample, StockSolution, "5% DIEA in DCM"] Deprotonation has been set to True.
    Pattern Description: An object of type or subtype Model[Sample] or Object[Sample] or a prepared sample or Null.
    Programmatic Pattern: ((ObjectP[{Model[Sample], Object[Sample]}] | _String) | Automatic) | Null

    Deprotonation

    Indicates if an optional deprotonation step is performed between the deprotection and capping steps of synthesis cycle.
    Default Value: False
    Pattern Description: True or False.
    Programmatic Pattern: BooleanP
    Index Matches to: experiment samples

    DeprotonationVolume

    The volume of DeprotonationSolution added to each reaction vessel during an optional deprotonation step of a synthesis cycle.
    Default Value: Automatic
    Default Calculation: Will automatically resolve to 3 Milliliter plus an additional .2 Milliliter for each 1 Micromole of synthesis Scale, rounded up to the nearest .5 Milliliter.
    Pattern Description: Greater than or equal to 1 milliliter and less than or equal to 25 milliliters or Null.
    Programmatic Pattern: (RangeP[1*Milliliter, 25*Milliliter] | Automatic) | Null
    Index Matches to: experiment samples

    DeprotonationTime

    The amount of time that each reaction vessel is exposed to the DeprotonationSolution during each deprotonation step of a synthesis cycle.
    Default Value: Automatic
    Pattern Description: Greater than or equal to 1 minute and less than or equal to 12 hours or Null.
    Programmatic Pattern: (RangeP[Minute, 12*Hour] | Automatic) | Null
    Index Matches to: experiment samples

    NumberOfDeprotonations

    The number of repetitions of mixing the resin with the DeprotonationSolution during the deprotonation step of a synthesis cycle.
    Default Value: Automatic
    Pattern Description: Greater than or equal to 1 and less than or equal to 10 in increments of 1 or Null.
    Programmatic Pattern: (RangeP[1, 10, 1] | Automatic) | Null
    Index Matches to: experiment samples

    NumberOfDeprotonationWashes

    The number of wash solution washes each reaction vessel undergoes after the deprotonation step.
    Default Value: Automatic
    Pattern Description: Greater than or equal to 1 and less than or equal to 10 in increments of 1 or Null.
    Programmatic Pattern: (RangeP[1, 10, 1] | Automatic) | Null
    Index Matches to: experiment samples

    Capping

    CappingSolution

    The model or sample objects that represents the solution that will be to cap any remaining uncoupled sites from growing further during the synthesis to aid in later purification of the truncations.
    Default Value: Model[Sample, StockSolution, Resin Download Capping Solution]
    Pattern Description: An object of type or subtype Model[Sample] or Object[Sample] or a prepared sample.
    Programmatic Pattern: ObjectP[{Model[Sample], Object[Sample]}] | _String

    NumberOfCappings

    The number of times that each reaction vessel is capped during each capping step of a synthesis cycle.
    Default Value: 1
    Pattern Description: Greater than or equal to 0 and less than or equal to 10 in increments of 1.
    Programmatic Pattern: RangeP[0, 10, 1]
    Index Matches to: experiment samples

    InitialCapping

    Indicates if an initial capping step will be done before the synthesis of the strand begins.
    Default Value: Automatic
    Default Calculation: Will automatically resolve to True of DownloadResin been set to False or False if DownloadResin has been set to True.
    Pattern Description: True or False.
    Programmatic Pattern: BooleanP | Automatic
    Index Matches to: experiment samples

    FinalCapping

    Indicates if a final capping step will be done as part of the last synthesis cycle before the start of cleavage.
    Default Value: False
    Pattern Description: True or False.
    Programmatic Pattern: BooleanP
    Index Matches to: experiment samples

    CappingVolume

    The volume of CappingSolution added to each reaction vessel during the capping step of a main synthesis cycle.
    Default Value: Automatic
    Default Calculation: Will automatically resolve to 3 Milliliter plus an additional .2 Milliliter for each Micromole of synthesis Scale rounded up to nearest .5 Milliliter
    Pattern Description: Greater than or equal to 1 milliliter and less than or equal to 25 milliliters.
    Programmatic Pattern: RangeP[1*Milliliter, 25*Milliliter] | Automatic
    Index Matches to: experiment samples

    CappingTime

    The amount of time that each reaction vessel is exposed to the CappingSolution during each capping step of synthesis cycle.
    Default Value: 7 minutes
    Pattern Description: Greater than or equal to 1 minute and less than or equal to 30 minutes.
    Programmatic Pattern: RangeP[Minute, 30*Minute]
    Index Matches to: experiment samples

    NumberOfCappingWashes

    The number of wash solution washes each reaction vessel undergoes after the capping step of a main synthesis cycle.
    Default Value: 5
    Pattern Description: Greater than or equal to 1 and less than or equal to 10 in increments of 1.
    Programmatic Pattern: RangeP[1, 10, 1]
    Index Matches to: experiment samples

    Download Monomer Activation

    DownloadActivationSolution

    The model of object representing the activation used during the coupling step of resin download.
    Default Value: Automatic
    Default Calculation: Will automatically resolve to value specified by ActivationSolution if DownloadResin is set to True.
    Pattern Description: An object of type or subtype Model[Sample] or Object[Sample] or a prepared sample or Null.
    Programmatic Pattern: ((ObjectP[{Model[Sample], Object[Sample]}] | _String) | Automatic) | Null

    DownloadActivationVolume

    The volume of activator solution added to each preactivation vessel when preactivation monomer for coupling to undownloaded resin.
    Default Value: Automatic
    Pattern Description: Greater than or equal to 1 milliliter and less than or equal to 25 milliliters or Null.
    Programmatic Pattern: (RangeP[1*Milliliter, 25*Milliliter] | Automatic) | Null
    Index Matches to: experiment samples

    DownloadActivationTime

    The amount of time for which the monomer solution will be mixed with the activation solution prior to a resin download cycle.
    Default Value: Automatic
    Default Calculation: Will automatically resolve to 10 minutes if DownloadResin is set to True.
    Pattern Description: Greater than or equal to 1 minute and less than or equal to 30 minutes or Null.
    Programmatic Pattern: (RangeP[Minute, 30*Minute] | Automatic) | Null
    Index Matches to: experiment samples

    DownloadMonomer

    The model or sample object to use for each of the monomers in the download.
    Default Value: Automatic
    Default Calculation: Will automatically resolve to a default monomer solution for the monomer being used to download the resin.
    Pattern Description: An object of type or subtype Model[Sample] or Object[Sample] or a prepared sample or Null.
    Programmatic Pattern: ((ObjectP[{Model[Sample], Object[Sample]}] | _String) | Automatic) | Null
    Index Matches to: experiment samples

    DownloadMonomerVolume

    The volume of download monomer solution added to the preactivation vessel during resin download.
    Default Value: Automatic
    Default Calculation: Will automatically resolve to 1 Milliliter. The entire volume of a DownloadMonomer is delivered in a single shot and can be any amount within the accepted range.
    Pattern Description: Greater than or equal to 1 milliliter and less than or equal to 25 milliliters or Null.
    Programmatic Pattern: (RangeP[1*Milliliter, 25*Milliliter] | Automatic) | Null
    Index Matches to: experiment samples

    SampleStorage

    StorageBuffer

    The sample or model of solution used to store any uncleaved resin samples.
    Default Value: Automatic
    Default Calculation: Will automatically resolve to Model[Sample,"Dimethylformamide, Reagent Grade"] if Cleavage is set to False.
    Pattern Description: An object of type or subtype Model[Sample] or Object[Sample] or a prepared sample or Null.
    Programmatic Pattern: ((ObjectP[{Model[Sample], Object[Sample]}] | _String) | Automatic) | Null

    ResuspensionBuffer

    The sample or model object that represents the object that will be used to resuspend the PNA strands after cleavage from the resin.
    Default Value: Automatic
    Default Calculation: Will automatically resolve to Model[Sample,"Milli-Q water"] if Cleavage is set to True.
    Pattern Description: An object of type or subtype Model[Sample] or Object[Sample] or a prepared sample or Null.
    Programmatic Pattern: ((ObjectP[{Model[Sample], Object[Sample]}] | _String) | Automatic) | Null

    ResuspensionMixUnitOperations

    A complete list of all incubate primitives used to resuspend and mix the strands after trituration. Cannot be provided if the options NumberOfResuspensionMixes,ResuspensionMixTime, and/or ResuspensionMixType are informed.
    Default Value: Automatic
    Default Calculation: These are determined automatically from the Resuspension options if provided.
    Pattern Description: List of one or more unit Operation must match SamplePreparationP entries or Null.
    Programmatic Pattern: ({SamplePreparationP..} | Automatic) | Null
    Index Matches to: experiment samples

    StorageVolume

    The desired volume of solution in which the uncleaved resin will be stored.
    Default Value: Automatic
    Default Calculation: Automatically resolved to Null if all of the resins are cleaved or to 15 Milliliter/Gram with a 5 Milliliter minimum.
    Pattern Description: Greater than or equal to 0.5 milliliters and less than or equal to 25000 milliliters or Null.
    Programmatic Pattern: (RangeP[0.5*Milliliter, 25000*Milliliter] | Automatic) | Null
    Index Matches to: experiment samples

    ResuspensionVolume

    The volume of resuspension buffer that will be used to resuspend the PNA strands after cleavage from the resin.
    Default Value: Automatic
    Default Calculation: Will automatically resolve to 1 milliliter if Cleavage is set to True.
    Pattern Description: Greater than or equal to 0 milliliters and less than or equal to 3 milliliters or Null.
    Programmatic Pattern: (RangeP[0*Milliliter, 3*Milliliter] | Automatic) | Null
    Index Matches to: experiment samples

    NumberOfResuspensionMixes

    The number of times the pelleted strands will be mixed with the resuspension buffer.
    Default Value: Automatic
    Default Calculation: Will automatically resolve to 10 if Cleavage is set to True.
    Pattern Description: Greater than or equal to 1 and less than or equal to 30 in increments of 1 or Null.
    Programmatic Pattern: (RangeP[1, 30, 1] | Automatic) | Null
    Index Matches to: experiment samples

    ResuspensionMixTime

    The length of time for which the pelleted strands will be mixed in resuspension buffer (by sonication or vortexing).
    Default Value: Automatic
    Default Calculation: Will resolve to 5 Minutes if ResuspensionMixType is set to Vortex or Sonicate.
    Pattern Description: Greater than or equal to 1 minute and less than or equal to 12 hours or Null.
    Programmatic Pattern: (RangeP[Minute, 12*Hour] | Automatic) | Null
    Index Matches to: experiment samples

    ResuspensionMixType

    The mix type that should be used to resuspend the cleaved, pelleted strands in ResuspensionBuffer.
    Default Value: Automatic
    Default Calculation: Will automatically resolve to Pipette if Cleavage is set to True.
    Pattern Description: Sonicate, Vortex, or Pipette or Null.
    Programmatic Pattern: ((Sonicate | Vortex | Pipette) | Automatic) | Null
    Index Matches to: experiment samples

    ResuspensionMixPrimitives

    A complete list of all incubate primitives used to resuspend and mix the strands after trituration. Cannot be provided if the options NumberOfResuspensionMixes,ResuspensionMixTime, and/or ResuspensionMixType are informed.
    Default Value: Automatic
    Default Calculation: These are determined automatically from the Resuspension options if provided.
    Pattern Description: List of one or more a primitive with head Incubate or Mix entries or Null.
    Programmatic Pattern: ({ResuspensionPrimitiveP..} | Automatic) | Null
    Index Matches to: experiment samples

    Cleavage

    PrimaryResinShrinkSolution

    The model or sample object that represents the methanol used to wash and dry the resin after last coupling step.
    Default Value: Automatic
    Default Calculation: Will automatically resolve to Model[Sample, "Methanol"] if PrimaryResinShrink is set to True.
    Pattern Description: An object of type or subtype Model[Sample] or Object[Sample] or a prepared sample or Null.
    Programmatic Pattern: ((ObjectP[{Model[Sample], Object[Sample]}] | _String) | Automatic) | Null

    SecondaryResinShrinkSolution

    The model or sample object that represents the isopropanol used to wash and dry the resin after last coupling step.
    Default Value: Automatic
    Default Calculation: Will automatically resolve to Model[Sample, "Isopropanol"] if SecondaryResinShrink is set to True.
    Pattern Description: An object of type or subtype Model[Sample] or Object[Sample] or a prepared sample or Null.
    Programmatic Pattern: ((ObjectP[{Model[Sample], Object[Sample]}] | _String) | Automatic) | Null

    CleavageSolution

    The sample or model object that represents the cleavage cocktail that will be used to cleave the PNA strands from the resin.
    Default Value: Automatic
    Default Calculation: Will automatically resolve to Model[Sample,StockSolution,"95%TFA-TIPS-H2O"] if Cleavage is set to True.
    Pattern Description: An object of type or subtype Model[Sample] or Object[Sample] or a prepared sample or Null.
    Programmatic Pattern: ((ObjectP[{Model[Sample], Object[Sample]}] | _String) | Automatic) | Null

    Cleavage

    Indicates if the oligomers will be cleaved from the resin at the end of the synthesis using CleavageSolution. Uncleaved strands will be stored as a resin slurry in StorageBuffer.
    Default Value: True
    Pattern Description: True or False.
    Programmatic Pattern: BooleanP
    Index Matches to: experiment samples

    PrimaryResinShrink

    Indicates if the resin is shrunk with methanol prior to strand cleavage or storage.
    Default Value: True
    Pattern Description: True or False.
    Programmatic Pattern: BooleanP
    Index Matches to: experiment samples

    PrimaryResinShrinkVolume

    The volume of methanol that will be used to wash the resin at the end of the last synthesis cycle.
    Default Value: Automatic
    Pattern Description: Greater than or equal to 1 milliliter and less than or equal to 25 milliliters or Null.
    Programmatic Pattern: (RangeP[Milliliter, 25*Milliliter] | Automatic) | Null
    Index Matches to: experiment samples

    PrimaryResinShrinkTime

    The duration of the resin methanol wash at the end of the last synthesis cycle.
    Default Value: Automatic
    Pattern Description: Greater than or equal to 1 minute and less than or equal to 12 hours or Null.
    Programmatic Pattern: (RangeP[Minute, 12*Hour] | Automatic) | Null
    Index Matches to: experiment samples

    SecondaryResinShrink

    Indicates if the resin is shrunk with isopropanol prior to strand cleavage or storage.
    Default Value: True
    Pattern Description: True or False.
    Programmatic Pattern: BooleanP
    Index Matches to: experiment samples

    SecondaryResinShrinkVolume

    The volume of isopropanol that will be used to wash the resin at the end of the last synthesis cycle.
    Default Value: Automatic
    Pattern Description: Greater than or equal to 1 milliliter and less than or equal to 25 milliliters or Null.
    Programmatic Pattern: (RangeP[Milliliter, 25*Milliliter] | Automatic) | Null
    Index Matches to: experiment samples

    SecondaryResinShrinkTime

    The duration of the resin isopropanol wash at the end of the last synthesis cycle.
    Default Value: Automatic
    Pattern Description: Greater than or equal to 1 minute and less than or equal to 12 hours or Null.
    Programmatic Pattern: (RangeP[Minute, 12*Hour] | Automatic) | Null
    Index Matches to: experiment samples

    CleavageVolume

    The volume of cleavage cocktail that will be used to cleave the PNA strands from the resin.
    Default Value: Automatic
    Default Calculation: Will resolve to 5 Milliliter if Cleavage is set to True.
    Pattern Description: Greater than or equal to 2.5 milliliters and less than or equal to 25 milliliters or Null.
    Programmatic Pattern: (RangeP[2.5*Milliliter, 25*Milliliter] | Automatic) | Null
    Index Matches to: experiment samples

    CleavageTime

    The length of time for which the strands will be cleaved in cleavage solution.
    Default Value: Automatic
    Default Calculation: Will resolve to 30 Minutes per cleavage cycle if Cleavage is set to True.
    Pattern Description: Greater than or equal to 1 minute and less than or equal to 12 hours or Null.
    Programmatic Pattern: (RangeP[Minute, 12*Hour] | Automatic) | Null
    Index Matches to: experiment samples

    NumberOfCleavageCycles

    The number of times the PNA strands on the resin will be incubated with the cleavage cocktail.
    Default Value: Automatic
    Default Calculation: Will automatically resolve to 3 if Cleavage is set to True.
    Pattern Description: Greater than or equal to 1 and less than or equal to 10 in increments of 1 or Null.
    Programmatic Pattern: (RangeP[1, 10, 1] | Automatic) | Null
    Index Matches to: experiment samples

    Trituration

    TriturationSolution

    The sample or model object that represents the solution that will be used to triturate the PNA strands after cleavage from the resin.
    Default Value: Automatic
    Default Calculation: Will automatically resolve to Model[Sample,"Diethyl ether"] if Cleavage is set to True.
    Pattern Description: An object of type or subtype Model[Sample] or Object[Sample] or a prepared sample or Null.
    Programmatic Pattern: ((ObjectP[{Model[Sample], Object[Sample]}] | _String) | Automatic) | Null

    TriturationVolume

    The volume of ether that will be used to triturate the PNA strands after cleavage from the resin.
    Default Value: Automatic
    Default Calculation: Will automatically resolve to 35 milliliter if Cleavage is set to True.
    Pattern Description: Greater than or equal to 1 milliliter and less than or equal to 35 milliliters or Null.
    Programmatic Pattern: (RangeP[Milliliter, 35*Milliliter] | Automatic) | Null

    NumberOfTriturationCycles

    The number of times the cleaved PNA strands will be TriturationSolution with ether.
    Default Value: Automatic
    Default Calculation: Will automatically resolve to 3 if Cleavage is set to True.
    Pattern Description: Greater than or equal to 1 and less than or equal to 10 in increments of 1 or Null.
    Programmatic Pattern: (RangeP[1, 10, 1] | Automatic) | Null

    TriturationTime

    The length of time for which the cleaved strands will be incubated in ether.
    Default Value: Automatic
    Default Calculation: Will automatically resolve to 5 minutes if Cleavage is set to True.
    Pattern Description: Greater than or equal to 1 minute and less than or equal to 12 hours or Null.
    Programmatic Pattern: (RangeP[Minute, 12*Hour] | Automatic) | Null

    TriturationTemperature

    The temperature at which the cleaved strands will be incubated while in ether.
    Default Value: Automatic
    Default Calculation: Will automatically resolve to -80 Celsius if Cleavage is set to True.
    Pattern Description: -80 degrees Celsius or Null.
    Programmatic Pattern: (-80*Celsius | Automatic) | Null

    Monomer Activation

    Monomers

    The model or sample object to use for each of the monomers in the synthesis.
    Default Value: Automatic
    Default Calculation: Automatic will resolved to default options for all monomers needed for the synthesis.
    Pattern Description: List of one or more {Monomer Sequence, Model} entries.
    Programmatic Pattern: {{SequenceP, ObjectP[{Model[Sample], Object[Sample]}] | _String}..} | Automatic

    RecoupMonomers

    Indicates if any left over monomer solutions will be stored or discarded at the conclusion of a synthesis.
    Default Value: False
    Pattern Description: True or False.
    Programmatic Pattern: BooleanP

    ActivationVolume

    The volume of ActivationSolution added to each preactivation vessel.
    Default Value: Automatic
    Default Calculation: Will resolve automatically to .2 Milliliter per Micromole of synthesis scale Scale, rounded up to the nearest .5 Milliliter.
    Pattern Description: Greater than or equal to 1 milliliter and less than or equal to 25 milliliters.
    Programmatic Pattern: RangeP[1*Milliliter, 25*Milliliter] | Automatic
    Index Matches to: experiment samples

    MonomerVolume

    The volume of monomer solution added for each reaction vessel to the preactivation vessel for a micromole scale synthesis.
    Default Value: Automatic
    Default Calculation: Will resolve automatically to .2 Milliliter per Micromole of synthesis Scale, rounded up to the nearest .5 Milliliter.
    Pattern Description: Greater than or equal to 1 milliliter and less than or equal to 25 milliliters.
    Programmatic Pattern: RangeP[1*Milliliter, 25*Milliliter] | Automatic
    Index Matches to: experiment samples

    ActivationSolution

    The model or object representing the mix of preactivation and base solutions used to activate the monomers prior to coupling during a synthesis cycle.
    Default Value: Model[Sample, StockSolution, 90 mM HBTU in NMP w/ 130 mM DIPEA]
    Pattern Description: An object of type or subtype Model[Sample] or Object[Sample] or a prepared sample.
    Programmatic Pattern: ObjectP[{Model[Sample], Object[Sample]}] | _String

    MonomerPreactivation

    Determines if the monomer will be preactivated directly on the resin, in a separate reaction vessel or not at all.
    Default Value: ExSitu
    Default Calculation: The maximum number of oligomers that can be concurrently synthesis depends on this option. Each ex situ preactivation requires an additional position on the instrument that could be otherwise used for synthesis when no preactivation or in situ preactivation is used.
    Pattern Description: ExSitu or InSitu or Null.
    Programmatic Pattern: PreactivationTypeP | Null
    Index Matches to: experiment samples

    ActivationTime

    The duration of the preactivation mixing.
    Default Value: 1 minute
    Pattern Description: Greater than or equal to 1 minute and less than or equal to 30 minutes.
    Programmatic Pattern: RangeP[Minute, 30*Minute]
    Index Matches to: experiment samples

    Protocol

    Scale

    The scale at which the oligomers will be synthesized.
    Default Value: 5 micromoles
    Pattern Description: Greater than or equal to 5 micromoles and less than or equal to 100 micromoles in increments of 2.5 micromoles.
    Programmatic Pattern: RangeP[5*Micromole, 100*Micromole, 2.5*Micromole]
    Index Matches to: experiment samples

    TargetLoading

    The desired target loading of the resin to be used for the synthesis.
    Default Value: 90 micromoles per gram
    Pattern Description: Greater than or equal to 60 micromoles per gram and less than or equal to 200 micromoles per gram.
    Programmatic Pattern: Alternatives[RangeP[60*(Micromole/Gram), 200*(Micromole/Gram)]]
    Index Matches to: experiment samples

    Resin

    The model or sample object of resin to be used as the solid support for the synthesis.
    Default Value: Automatic
    Default Calculation: Will resolve automatically to the undownloaded Resin Model[Sample, "Rink Amide AM resin"] if DownloadResin is set to True. If DownloadResin is set to False, the user is required to specify an appropriate downloaded resin.
    Pattern Description: An object of type or subtype Model[Sample] or Object[Sample] or a prepared sample.
    Programmatic Pattern: (ObjectP[{Model[Sample], Object[Sample]}] | _String) | Automatic
    Index Matches to: experiment samples

    DownloadResin

    Indicates if an undownloaded resin will be used and resin download will be performed as the first cycle of the synthesis.
    Default Value: True
    Pattern Description: True or False.
    Programmatic Pattern: BooleanP
    Index Matches to: experiment samples

    Download Deprotection

    DownloadDeprotectionVolume

    The volume of deprotection solution added to each reaction vessel during a resin download cycle.
    Default Value: Automatic
    Default Calculation: Automatic will resolve to 3 Milliliter plus an additional .5 Milliliter for each 2.5 umol scale for PeptideSynthesizer syntheses.
    Pattern Description: Greater than or equal to 1 milliliter and less than or equal to 25 milliliters or Null.
    Programmatic Pattern: (RangeP[1*Milliliter, 25*Milliliter] | Automatic) | Null
    Index Matches to: experiment samples

    DownloadDeprotectionTime

    The amount of time that each reaction vessel is exposed to the deprotection solution during each deprotection step of a resin download cycle.
    Default Value: Automatic
    Default Calculation: Will automatically resolve to the same value as DeprotectionTime is DownloadResin is set to True.
    Pattern Description: Greater than or equal to 1 minute and less than or equal to 30 minutes or Null.
    Programmatic Pattern: (RangeP[Minute, 30*Minute] | Automatic) | Null
    Index Matches to: experiment samples

    NumberOfDownloadDeprotections

    The number of times that each reaction vessel will be deprotected per deprotection step of a synthesis cycle.
    Default Value: Automatic
    Pattern Description: Greater than or equal to 1 and less than or equal to 10 in increments of 1 or Null.
    Programmatic Pattern: (RangeP[1, 10, 1] | Automatic) | Null
    Index Matches to: experiment samples

    NumberOfDownloadDeprotectionWashes

    The number of wash solution washes each reaction vessel undergoes after the deprotection step of the synthesis cycle.
    Default Value: Automatic
    Pattern Description: Greater than or equal to 1 and less than or equal to 10 in increments of 1 or Null.
    Programmatic Pattern: (RangeP[1, 10, 1] | Automatic) | Null
    Index Matches to: experiment samples

    DownloadDeprotonationVolume

    The volume of DeprotonationSolution added to each reaction vessel during a deprotonation step of a resin download cycle.
    Default Value: Automatic
    Pattern Description: Greater than or equal to 1 milliliter and less than or equal to 25 milliliters or Null.
    Programmatic Pattern: (RangeP[1*Milliliter, 25*Milliliter] | Automatic) | Null
    Index Matches to: experiment samples

    DownloadDeprotonationTime

    The amount of time for which the resin will be mixed with DeprotonationSolution for each deprotonation step of a resin download cycle.
    Default Value: Automatic
    Pattern Description: Greater than or equal to 1 minute and less than or equal to 30 minutes or Null.
    Programmatic Pattern: (RangeP[Minute, 30*Minute] | Automatic) | Null
    Index Matches to: experiment samples

    NumberOfDownloadDeprotonations

    The number of repetitions of mixing the resin with the DeprotonationSolution during a resin download cycle.
    Default Value: Automatic
    Default Calculation: Will automatically resolve to 2 if DownloadResin has been set to True.
    Pattern Description: Greater than or equal to 1 and less than or equal to 10 in increments of 1 or Null.
    Programmatic Pattern: (RangeP[1, 10, 1] | Automatic) | Null
    Index Matches to: experiment samples

    NumberOfDownloadDeprotonationWashes

    The number of washes each reaction vessel will undergo after a deprotonation step during a resin download cycle.
    Default Value: Automatic
    Default Calculation: Will automatically resolve to 5 if DownloadResin has been set to True.
    Pattern Description: Greater than or equal to 1 and less than or equal to 10 in increments of 1 or Null.
    Programmatic Pattern: (RangeP[1, 10, 1] | Automatic) | Null
    Index Matches to: experiment samples

    Download Capping

    DownloadCappingVolume

    The volume of CappingSolution added to each reaction vessel during the capping step of of a resin download cycle.
    Default Value: Automatic
    Default Calculation: Will automatically resolve to 3 Milliliter plus an additional .2 Milliliter per each umol of Scale.
    Pattern Description: Greater than or equal to 1 milliliter and less than or equal to 25 milliliters or Null.
    Programmatic Pattern: (RangeP[1*Milliliter, 25*Milliliter] | Automatic) | Null
    Index Matches to: experiment samples

    DownloadCappingTime

    The amount of time for which the resin will be shaken with CappingSolution per capping step of a resin download cycle.
    Default Value: Automatic
    Default Calculation: Will automatically resolve to 15 minutes if DownloadResin is set to True.
    Pattern Description: Greater than or equal to 1 minute and less than or equal to 12 hours or Null.
    Programmatic Pattern: (RangeP[Minute, 12*Hour] | Automatic) | Null
    Index Matches to: experiment samples

    NumberOfDownloadCappings

    The number of times that each reaction vessel is capped during each capping step of a resin download cycle.
    Default Value: Automatic
    Pattern Description: Greater than or equal to 1 and less than or equal to 10 in increments of 1 or Null.
    Programmatic Pattern: (RangeP[1, 10, 1] | Automatic) | Null
    Index Matches to: experiment samples

    NumberOfDownloadCappingWashes

    The number of wash solution washes each reaction vessel undergoes after the capping step of a resin download cycle.
    Default Value: Automatic
    Pattern Description: Greater than or equal to 1 and less than or equal to 10 in increments of 1 or Null.
    Programmatic Pattern: (RangeP[1, 10, 1] | Automatic) | Null
    Index Matches to: experiment samples

    Coupling

    CouplingTime

    The amount of time that each reaction vessel is exposed to the coupling solution during each coupling step of a synthesis cycle.
    Default Value: 30 minutes
    Pattern Description: Greater than or equal to 1 minute and less than or equal to 12 hours.
    Programmatic Pattern: RangeP[Minute, 12*Hour]
    Index Matches to: experiment samples

    NumberOfCouplingWashes

    The number of wash solution washes each reaction vessel undergoes after the coupling step of a synthesis cycle.
    Default Value: 5
    Pattern Description: Greater than or equal to 1 and less than or equal to 10 in increments of 1.
    Programmatic Pattern: RangeP[1, 10, 1]
    Index Matches to: experiment samples

    DoubleCoupling

    Specifies the cycle at which monomers are double coupled. All couplings will be performed twice following the cycle number specified.
    Default Value: 99
    Pattern Description: Greater than or equal to 1 in increments of 1 or Null.
    Programmatic Pattern: GreaterEqualP[1, 1] | Null
    Index Matches to: experiment samples

    Download Coupling

    DownloadCouplingTime

    The amount of time for which the resin mixed be mixed with coupling solution during a coupling step of a resin download cycle.
    Default Value: Automatic
    Default Calculation: Automatically resolved to 60 Minutes
    Pattern Description: Greater than or equal to 1 minute and less than or equal to 12 hours or Null.
    Programmatic Pattern: (RangeP[Minute, 12*Hour] | Automatic) | Null
    Index Matches to: experiment samples

    NumberOfDownloadCouplingWashes

    The number of wash solution washes each reaction vessel undergoes after the coupling step of a resin download cycle.
    Default Value: Automatic
    Default Calculation: Automatically resolved to 5.
    Pattern Description: Greater than or equal to 1 and less than or equal to 10 in increments of 1 or Null.
    Programmatic Pattern: (RangeP[1, 10, 1] | Automatic) | Null
    Index Matches to: experiment samples

    Post Experiment

    SamplesOutStorageCondition

    The non-default conditions under which any new samples generated by this experiment should be stored after the protocol is completed. If left unset, the new samples will be stored according to their Models' DefaultStorageCondition.
    Default Value: Null
    Pattern Description: {AmbientStorage, EnclosedAmbientStorage, Refrigerator, Freezer, DeepFreezer, CryogenicStorage, YeastIncubation, YeastShakingIncubation, BacterialIncubation, BacterialShakingIncubation, MammalianIncubation, ViralIncubation, CrystalIncubation, AcceleratedTesting, IntermediateTesting, LongTermTesting, UVVisLightTesting} or Disposal or Null.
    Programmatic Pattern: (Alternatives[SampleStorageTypeP | Disposal]) | Null
    Index Matches to: experiment samples

Protocol Options

    Organizational Information

    Template

    A template protocol whose methodology should be reproduced in running this experiment. Option values will be inherited from the template protocol, but can be individually overridden by directly specifying values for those options to this Experiment function.
    Default Value: Null
    Pattern Description: An object of type or subtype Object[Protocol] or an object of type or subtype of Object[Protocol] with UnresolvedOptions, ResolvedOptions specified or Null.
    Programmatic Pattern: (ObjectP[Object[Protocol]] | FieldReferenceP[Object[Protocol], {UnresolvedOptions, ResolvedOptions}]) | Null

    Name

    A object name which should be used to refer to the output object in lieu of an automatically generated ID number.
    Default Value: Null
    Pattern Description: A string or Null.
    Programmatic Pattern: _String | Null

Example Calls

    Resin

    The resin that will be used for the synthesis can be controlled via the Resin option. If you would like to use a resin that is pre-downloaded with a monomer, indicate that via the option DownloadResin->False and specify which Resin to use. For example, here we perform one synthesis with a regular resin (where the first monomer will be downloaded onto the resin), and another synthesis with a resin that already contains the first monomer:

    Modifications

    Any modifications that will be used for the synthesis can be directly added to the strand Model. For any novel modifications, you can directly specify the monomer solution with the Monomers Option. For example, here we perform one synthesis with a common modification (automatically selecting the Monomer), and another synthesis with a novel modification that has a monomer solution specified:

    Cleavage and Sample Storage

    By default, the synthesized strands are cleaved from the resin at the end of the synthesis and then resuspended in distilled water. If desired, it is possible to keep the strands on the resin by specifying Cleavage -> False, in which case the uncleaved strands will be stored as a resin slurry in storage buffer. The parameters for these manipulations (such as the buffer and buffer amount) are controlled via the set of Resuspension and Storage options, respectively. In the following example, the first synthesized PNA is being cleaved in 2.5 mL of cleavage solution and then resuspended in 1 mL of resuspension solution, while the second strand is kept uncleaved and is stored as a slurry in 2 mL of storage solution:
    ExperimentPNASynthesis offers flexibility in the way that the cleaved and dried PNA pellet is resuspended in the final resuspension solution. The type of mixing can be specified by ResuspensionMixType as either Pipette, Sonicate or Vortex. NumberOfResuspensionMixes and ResuspensionMixTime provide control over the duration of the mixing. If more thorough mixing is desired, sequential mixing steps can be provided by a list of instruction primitives for each strand. In the following example, the PNA pellet is first resuspended by pipetting up and down 10 times, followed by a 5 minutes sonication and vortexing step to ensure full solubilization of the PNA

Warnings and Errors

    Messages  (112)

    DownloadedResinNeeded  (1)

    If DownloadResin is set to False, the Resin specified by the user cannot be undownloaded:

    IncompatibleResuspensionMixPrimitives  (1)

    Returns an error if resuspension mixing primitives are not properly defined:

    InsufficientSolventVolume  (1)

    Throws an error if we use more of a solvent than fits into the solvent container under the deck:

    MismatchedResinAndStrand  (1)

    The specified downloaded Resin has to match the sequence of the 3' bases in the strand to be synthesized:

    NumberOfInputs  (1)

    Throws an error if the number of oligomer(s) being synthesized in one protocol is outside the capability of the instrument:

    PolymerType  (1)

    Throws an error if a strand of a type other than PNA is being synthesized:

    RequiredOption  (1)

    Download related options cannot be set to Null, if DownloadResin has been set to True::

    ResinNeeded  (1)

    If DownloadResin is set to False, an appropriate downloaded Resin has to be specified by the user via the Option Resin:

    SwellResinNeeded  (1)

    If DownloadResin is set to True and SwellResin is False, an error will be thrown:

    TooManyMonomers  (1)

    Throws an error if a strand is being synthesized that requires more monomers than fit on the deck:

    UnavailableDownloadMonomer  (1)

    DownloadMonomer automatic resolution will fail when a novel download monomer is used and therefore must explicity specified:

    UnavailableMonomer  (1)

    Monomers automatic resolution will fail when novel monomers are used and therefore monomer solutions must be explicitly specified:

    UnneededCleavageOptions  (3)

    Cleavage related options should only be specified if Cleavage has been set to True:

    ResuspensionMixPrimitives should only be specified if Cleavage has been set to True:

    ResuspensionMixType should only be specified if Cleavage has been set to True:

    UnneededDeprotonationOptions  (1)

    Deprotonation related options should only be specified if DownloadResin or Deprotonation has been set to True:

    UnneededDownloadResinOptions  (1)

    Download related options should only be specified if DownloadResin has been set to True::

    UnneededResuspensionOptions  (1)

    ResuspensionMixPrimitives and resuspension mixing options cannot be defined simultaneously:

    UnneededShrinkOptions  (1)

    PrimaryResinShrink related options should only be specified if PrimaryResinShrink has been set to True:

    UnneededStorageOptions  (1)

    Storage related options cannot be set to Null, if Cleavage has been set to False:

    UnneededSwellOptions  (1)

    Swell related options should only be specified if SwellResin has been set to True:

    WrongResin  (1)

    If DownloadResin is set to True, Resin cannot be specified to a downloaded resin (Object/Model[Sample]) since the first step in the synthesis will be the download of the resin:

    CleavageSolution  (2)

    CleavageSolution cannot be set to Null, if Cleavage has been set to True:

    CleavageSolution should only be specified if Cleavage has been set to True:

    CleavageTime  (2)

    CleavageTime cannot be set to Null, if Cleavage has been set to True:

    CleavageTime should only be specified if Cleavage has been set to True:

    CleavageVolume  (2)

    CleavageVolume cannot be set to Null, if Cleavage has been set to True:

    CleavageVolume should only be specified if Cleavage has been set to True:

    DeprotonationSolution  (3)

    DeprotonationSolution cannot be set to Null if Deprotonation has been set to True:

    DeprotonationSolution cannot be set to Null if DownloadResin has been set to True:

    DeprotonationSolution should only be specified if DownloadResin or Deprotonation has been set to True:

    DeprotonationTime  (2)

    DeprotonationTime cannot be set to Null, if Deprotonation has been set to True:

    DeprotonationTime should only be specified if Deprotonation has been set to True:

    DeprotonationVolume  (2)

    DeprotonationVolume cannot be set to Null, if Deprotonation has been set to True:

    DeprotonationVolume should only be specified if Deprotonation has been set to True:

    DownloadActivationSolution  (2)

    DownloadActivationSolution cannot be set to Null, if DownloadResin has been set to True:

    DownloadActivationSolution should only be specified if DownloadResin has been set to True:

    DownloadActivationTime  (2)

    DownloadActivationTime cannot be set to Null, if DownloadResin has been set to True:

    DownloadActivationTime should only be specified if DownloadResin has been set to True:

    DownloadActivationVolume  (2)

    DownloadActivationVolume cannot be set to Null, if DownloadResin has been set to True:

    DownloadActivationVolume should only be specified if DownloadResin has been set to True:

    DownloadCappingTime  (2)

    DownloadCappingTime cannot be set to Null, if DownloadResin has been set to True:

    DownloadCappingTime should only be specified if DownloadResin has been set to True:

    DownloadCappingVolume  (2)

    DownloadCappingVolume cannot be set to Null, if DownloadResin has been set to True:

    DownloadCappingVolume should only be specified if DownloadResin has been set to True:

    DownloadCouplingTime  (2)

    DownloadCouplingTime cannot be set to Null, if DownloadResin has been set to True:

    DownloadCouplingTime should only be specified if DownloadResin has been set to True:

    DownloadDeprotectionTime  (2)

    DownloadDeprotectionTime cannot be set to Null if DownloadResin has been set to True:

    DownloadDeprotectionTime should only be specified if DownloadResin has been set to True:

    DownloadDeprotectionVolume  (2)

    DownloadDeprotectionVolume cannot be set to Null if DownloadResin has been set to True:

    DownloadDeprotectionVolume should only be specified if DownloadResin has been set to True:

    DownloadDeprotonationTime  (2)

    DownloadDeprotonationTime cannot be set to Null, if DownloadResin has been set to True:

    DownloadDeprotonationTime should only be specified if DownloadResin has been set to True:

    DownloadDeprotonationVolume  (2)

    DownloadDeprotonationVolume cannot be set to Null, if DownloadResin has been set to True:

    DownloadDeprotonationVolume should only be specified if DownloadResin has been set to True:

    DownloadMonomer  (2)

    DownloadMonomer cannot be set to Null, if DownloadResin has been set to True::

    DownloadMonomer should only be specified if DownloadResin has been set to True::

    DownloadMonomerVolume  (1)

    DownloadMonomerVolume should only be specified if DownloadResin has been set to True:

    NumberOfCleavageCycles  (2)

    NumberOfCleavageCycles cannot be set to Null, if Cleavage has been set to True:

    NumberOfCleavageCycles should only be specified if Cleavage has been set to True:

    NumberOfDeprotonations  (2)

    NumberOfDeprotonations cannot be set to Null, if Deprotonation has been set to True:

    NumberOfDeprotonations should only be specified if Deprotonation has been set to True:

    NumberOfDeprotonationWashes  (2)

    NumberOfDeprotonationWashes cannot be set to Null, if Deprotonation has been set to True:

    NumberOfDeprotonationWashes should only be specified if Deprotonation has been set to True:

    NumberOfDownloadCappings  (2)

    NumberOfDownloadCappings cannot be set to Null, if DownloadResin has been set to True:

    NumberOfDownloadCappings should only be specified if DownloadResin has been set to True:

    NumberOfDownloadCappingWashes  (2)

    NumberOfDownloadCappingWashes cannot be set to Null, if DownloadResin has been set to True:

    NumberOfDownloadCappingWashes should only be specified if DownloadResin has been set to True:

    NumberOfDownloadCouplingWashes  (2)

    NumberOfDownloadCouplingWashes cannot be set to Null, if DownloadResin has been set to True:

    NumberOfDownloadCouplingWashes should only be specified if DownloadResin has been set to True:

    NumberOfDownloadDeprotections  (2)

    NumberOfDownloadDeprotections cannot be set to Null, if DownloadResin has been set to True:

    NumberOfDownloadDeprotections should only be specified if DownloadResin has been set to True:

    NumberOfDownloadDeprotectionWashes  (2)

    NumberOfDownloadDeprotectionWashes cannot be set to Null, if DownloadResin has been set to True:

    NumberOfDownloadDeprotectionWashes should only be specified if DownloadResin has been set to True:

    NumberOfDownloadDeprotonations  (2)

    NumberOfDownloadDeprotections should only be specified if DownloadResin has been set to True:

    NumberOfDownloadDeprotonations cannot be set to Null, if DownloadResin has been set to True:

    NumberOfDownloadDeprotonationWashes  (2)

    NumberOfDownloadDeprotonationWashes cannot be set to Null, if DownloadResin has been set to True:

    NumberOfDownloadDeprotonationWashes should only be specified if DownloadResin has been set to True:

    NumberOfSwellCycles  (1)

    NumberOfSwellCycles should only be specified if SwellResin has been set to True:

    NumberOfTriturationCycles  (2)

    NumberOfTriturationCycles allows specification number of times the cleaved PNA strands should be triturated with TriturationSolution:

    NumberOfTriturationCycles cannot be set to Null, if Cleavage has been set to True:

    PrimaryResinShrinkSolution  (2)

    PrimaryResinShrinkSolution cannot be set to Null, if PrimaryResinShrink has been set to True:

    PrimaryResinShrinkSolution should only be specified if PrimaryResinShrink has been set to True:

    PrimaryResinShrinkTime  (2)

    PrimaryResinShrinkTime cannot be set to Null, if PrimaryResinShrink has been set to True:

    PrimaryResinShrinkTime should only be specified if PrimaryResinShrink has been set to True:

    PrimaryResinShrinkVolume  (2)

    PrimaryResinShrinkVolume cannot be set to Null, if PrimaryResinShrink has been set to True:

    PrimaryResinShrinkVolume should only be specified if PrimaryResinShrink has been set to True:

    ResuspensionBuffer  (2)

    ResuspensionBuffer cannot be set to Null, if Cleavage has been set to True:

    ResuspensionBuffer should only be specified if Cleavage has been set to True:

    ResuspensionVolume  (2)

    ResuspensionVolume cannot be set to Null, if Cleavage has been set to True:

    ResuspensionVolume should only be specified if Cleavage has been set to True:

    SecondaryResinShrinkSolution  (2)

    SecondaryResinShrinkSolution cannot be set to Null, if SecondaryResinShrink has been set to True:

    SecondaryResinShrinkSolution should only be specified if SecondaryResinShrink has been set to True:

    SecondaryResinShrinkTime  (2)

    SecondaryResinShrinkTime cannot be set to Null, if SecondaryResinShrink has been set to True:

    SecondaryResinShrinkTime should only be specified if SecondaryResinShrink has been set to True:

    SecondaryResinShrinkVolume  (2)

    SecondaryResinShrinkVolume cannot be set to Null, if SecondaryResinShrink has been set to True:

    SecondaryResinShrinkVolume should only be specified if SecondaryResinShrink has been set to True:

    StorageBuffer  (2)

    StorageBuffer cannot be set to Null, if Cleavage has been set to False:

    StorageBuffer should only be specified if Cleavage has been set to False:

    StorageVolume  (2)

    StorageVolume cannot be set to Null, if Cleavage has been set to False:

    StorageVolume should only be specified if Cleavage has been set to False:

    SwellSolution  (1)

    SwellSolution should only be specified if SwellResin has been set to True:

    SwellTime  (1)

    SwellTime should only be specified if SwellResin has been set to True:

    SwellVolume  (1)

    SwellVolume should only be specified if SwellResin has been set to True:

    TriturationSolution  (2)

    TriturationSolution cannot be set to Null, if Cleavage has been set to True:

    TriturationSolution should only be specified if Cleavage has been set to True:

    TriturationTemperature  (2)

    TriturationTemperature cannot be set to Null, if Cleavage has been set to True:

    TriturationTemperature should only be specified if Cleavage has been set to True:

    TriturationTime  (2)

    TriturationTime cannot be set to Null, if Cleavage has been set to True:

    TriturationTime should only be specified if Cleavage has been set to True:

    TriturationVolume  (2)

    TriturationVolume cannot be set to Null, if Cleavage has been set to True:

    TriturationVolume should only be specified if Cleavage has been set to True:

Possible Issues

    No yield

    For a difficult strands the chemical steps, including resin swelling, resin downloading, coupling, cleavage and resuspension, used to synthesize a strand can be controlled with the Primatives and ResuspensionMixPrimitives options.

    Too many side products

    Side products can be reduced by increasing the number washes between steps.
Last modified on Mon 8 Sep 2025 11:09:20

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