Create OligoDuplex | Benchling Documentation

curl -X POST https://{tenant_name}.benchling.com/api/v3/oligo-duplex \
     -H "Authorization: Bearer <token>" \
     -H "Content-Type: application/json" \
     -d '{
  "componentMapping": {
    "key": "value"
  },
  "connections": "connections",
  "folderId": "folderId",
  "forwardOffset": 1,
  "name": "name",
  "schemaId": "schemaId"
}'

{
  "__typename": "__typename",
  "authors": "authors",
  "creator": {
    "__typename": "__typename",
    "id": "id"
  },
  "schemaFields": [
    {
      "__typename": "__typename",
      "id": "id",
      "linkedEntityId": "linkedEntityId"
    }
  ],
  "aliases": [
    "aliases"
  ],
  "archiveReason": "archiveReason",
  "archived": true,
  "canonicalHelm": "canonicalHelm",
  "conjugates": [
    {
      "__typename": "__typename",
      "connections": [
        {}
      ],
      "helmReference": "helmReference",
      "nucleotideType": "DNA",
      "polymerType": "polymerType",
      "residues": "residues"
    }
  ],
  "createdAt": "createdAt",
  "customFields": [
    {
      "__typename": "__typename",
      "name": "name",
      "value": "value"
    }
  ],
  "entityRegistryId": "entityRegistryId",
  "folder": {
    "__typename": "__typename",
    "id": "id"
  },
  "forwardOffset": 1,
  "forwardStrand": {
    "__typename": "__typename",
    "connections": [
      {}
    ],
    "entity": {
      "__typename": "__typename",
      "id": "id"
    },
    "helmReference": "helmReference",
    "nucleotideType": "DNA",
    "polymerType": "polymerType",
    "residues": "residues"
  },
  "id": "id",
  "modifiedAt": "modifiedAt",
  "name": "name",
  "originalHelm": "originalHelm",
  "outOfSync": true,
  "outOfSyncReason": "outOfSyncReason",
  "project": {
    "__typename": "__typename",
    "id": "id"
  },
  "registrationOrigin": {
    "__typename": "__typename",
    "originEntry": {
      "__typename": "__typename",
      "id": "id"
    },
    "registeredAt": "registeredAt"
  },
  "registry": {
    "__typename": "__typename",
    "id": "id"
  },
  "reverseStrand": {
    "__typename": "__typename",
    "connections": [
      {}
    ],
    "entity": {
      "__typename": "__typename",
      "id": "id"
    },
    "helmReference": "helmReference",
    "nucleotideType": "DNA",
    "polymerType": "polymerType",
    "residues": "residues"
  },
  "schema": {
    "__typename": "__typename",
    "id": "id"
  },
  "structure": {
    "__typename": "__typename",
    "connections": [
      {}
    ],
    "resolvedAttachments": [
      {}
    ],
    "simplePolymers": [
      {}
    ]
  },
  "typedSchema": {
    "__typename": "__typename",
    "id": "id"
  }
}

Create an oligo duplex. Provide componentMapping, connections, and forwardOffset together.

Authentication

AuthorizationBearer

Bearer authentication of the form Bearer <token>, where token is your auth token.

Request

This endpoint expects an object.

componentMappingmap from strings to stringsRequired

Mapping from schema component names to entity names.

connectionsstringRequired

Connection definitions for the duplex structure, as pipe-delimited entries. Each entry is sourceLabel,targetLabel for a shorthand covalent bond between two small molecules, or sourceLabel,targetLabel,residueIndex:rGroupOrPair-residueIndex:rGroupOrPair for a HELM-style attachment. Labels refer to component names from componentMapping, suffixed with (N) to disambiguate repeated entities (e.g. molecule(2)). For example: oligoName,moleculeName,1:R1-?:?|moleculeName,molecule2Name.

folderIdstringRequired

forwardOffsetintegerRequired

Offset of the forward strand relative to the reverse strand, in residues. For example, -2 means the forward strand begins 2 positions before the reverse strand.

namestringRequired

Name of the item.

schemaIdstringRequired

The ID of the schema to use for the oligo duplex.

aliaseslist of stringsOptional

authorIdslist of stringsOptional

customFieldsmap from strings to objectsOptional

entityRegistryIdstringOptional

Registry ID to assign to the entity. If one is specified, the labeling_strategy must be unspecified.

namingStrategyenumOptional

Strategy to use for labeling the item in the registry. If one is specified, the entity_registry_id must be unspecified.

registryIdstring or nullOptional

A not null value means the entity should be registered. If not null, the value must match the registry of the item's schema.

schemaFieldsmap from strings to objectsOptional

Response

Created

__typenamestringOptional

authorsstring or nullOptionalformat: "uri"

creatorobjectOptional

schemaFieldslist of objects or nullOptional

aliaseslist of strings or nullOptional

archiveReasonstring or nullOptional

archivedbooleanOptional

canonicalHelmstringOptional

conjugateslist of objectsOptional

createdAtstringOptional

customFieldslist of objects or nullOptional

entityRegistryIdstring or nullOptional

The registry-assigned identifier for this item (e.g. its registry ID shown in the UI), present only once the item has been registered. Null if the item is not registered.

folderobject or nullOptional

forwardOffsetinteger or nullOptional

forwardStrandobjectOptional

Represents a nucleic acid strand (DNA or RNA) within a complex polymer structure. Contains the sequence residues and connections to other polymers. The entity field links to a corresponding DnaSequence, RnaSequence, DnaOligo, or RnaOligo. Used as the backbone component in OligoConjugate and as forward/reverse strands in OligoDuplex.

idstringOptional

modifiedAtstringOptional

namestringOptional

Name of the item.

originalHelmstring or nullOptional

outOfSyncbooleanOptional

outOfSyncReasonstring or nullOptional

projectobject or nullOptional

registrationOriginobject or nullOptional

Provenance of this item’s registration — where and when it was registered. Null if unregistered.

registryobject or nullOptional

The Registry this item belongs to, if registered. Null if unregistered.

reverseStrandobjectOptional

schemaobjectOptional

Use typedSchema instead, which returns the per-type schema.

structureobjectOptional

Contains the complete structural definition of an oligo duplex, including its forward and reverse strands, any conjugated molecules and peptides, and the connections between them.

For each simple polymer, restricted read access on the linked entity affects entity only; structural fields on that polymer are still populated for the containing duplex.

typedSchemaobjectOptional

Errors

400

Oligo Duplex Create Request Bad Request Error

403

Oligo Duplex Create Request Forbidden Error

404

Oligo Duplex Create Request Not Found Error

409

Oligo Duplex Create Request Conflict Error

429

Oligo Duplex Create Request Too Many Requests Error

500

Oligo Duplex Create Request Internal Server Error