Many laboratories synthesize and store a large number of oligoes for the use of DNA sequencing, blotting, PCR, etc. Without proper management, it may be difficult to handle the information of these oligoes. DNAMAN provides an oligo database manager that can help you effectively organize and use these oligoes.
Choosing the Primer | Oligo Database | Manager command opens a Database Manager dialog box where all the oligo databases are listed.
Clicking any database name displays the following information of the selected database on the top of the dialog box:
- File name,
- Number of records,
- Type of database,
- Date of last update
You may create a new oligo database, delete an existing database or change the password of the selected database by using corresponding buttons in the dialog box.
Creating a new oligo database
You may create a new oligo database by giving a file name and password. Clicking the New button opens a New Database dialog box. You should type in 8 or fewer characters as a filename. DNAMAN will automatically add the olig database extension: odb.
You can attach a password to the database to protect it. DNAMAN will ask for the password when anyone wants to modify (add or remove records, delete database) the database. However, anyone can freely retrieve information of records in the database without password.
The database is not protected if you do not enter any letter in the password box. In this case, all users can modify the database.
Changing password
DNAMAN allows you to change the password of a database.
1.Choosing Primer | Oligo Database | Manager opens the dialog box.
2.Clicking the database selects it as the default database.
3.Clicking the Password button opens a Password dialog box.
4.DNAMAN will ask you for the old password, the new password and confirmation of the new password. The new password will be effective only if the old password is confirmed.
5.Click OK to validate your change.
The changing password function allows you switch your database from protection to non-protection, or other way around.
Deleting database
If you want to erase an oligo database, you should first select the database as the default database by following the step 1 and 2 described in the Changing password section. Click the Delete button to delete the database.
If the database is protected by a password, DNAMAN will ask you for the password.
The basic functions of editing include adding or deleting oligo records and modifying the record information. Choosing the Primer | Oligo Database | Edit Record. command brings up the Oligo Database dialog box.
First, you should select the database you want to edit by clicking the database filename listed in the Database box. The information of the number of records and the date of the last update is displayed on the top of the dialog box.
DNAMAN lists the information of a record to seven fields: Name, Source, Memo, Length, GC content, Melting temperature and Sequence. If you have a large number of records in a database, you may use the first four fields as the sorting keys to selectively display the records in the Record List box.
You may query a list of record by setting the parameter for oligo length. There are three options:
EnterClick the Show button
23listing the oligoes with a length of 23,
>23listing the oligoes with a length greater than 23,
<23listing the oligoes with a length smaller than 23.
Adding oligo record
Clicking the Add button in the Oligo Database dialog box adds a “NEW” record in the oligo list. All the seven fields are empty in the new record. You should fill out the information of the Name, Source and Memo boxes. The maximum length of each box is 69 characters. The maximum length of an oligonucleotide is 200 bases.
After entering the oligo sequence, click on the Save button. The name of the new record appears in the oligo list. According to the oligo sequence, DNAMAN calculates the length, GC content and melting temperature and displays the information in the Length, GC% and Tm boxes. The thermo Tm is calculated using the following formula:
Tm=dH/(dS-Rln(Cd))-273.15+16.6*(log10(Cs))
Where dH is the enthalpy, dS is the entropy, R is 1.987 cal K-1 mol-1 , Cd is the DNA concentration (50 nM is used), and Cs is the salt concentration (50 mM).
Deleting oligo record
In the oligo list, click on the record name you want to delete. Press the Delete button to remove the oligo record from this database. DNAMAN will ask you for the password, if the database is protected.
Modifying record information
You may edit the information of an oligo record in the database. The fields of “Name”, “Source”, “Memo”, and “Sequence” are editable, but those of “Length”, “Tm”, and “GC%” are not. After editing, you should click on the Save button to save the changed information immediately. If you go to another record of the database without saving, the changed information will be lost. If the sequence is modified, DNAMAN will recalculate and display the length, GC% and Tm of the oligo.