• Silent mutation
  • The function of Silent Mutation allows you to change restriction properties of the current DNA sequence without changing the coding amino acid sequence. This function searches for a potential region that can be altered to create or destroy restriction enzyme sites.

    1.Choose Restriction | Silent Mutation to open the Silent Mutation dialog box. This command is activated when the current channel contains a DNA sequence.

    2.Select a restriction enzyme file. “restrict.enz” is the default enzyme file in DNAMAN.

    3.Select the one of the Cutter options.

    4.Define the region you want to be analyzed in the Seq box.

    5.Click the Seq button to confirm the both ends of the selected region and the coding amino acid sequence in Reading frame 1.

    *If you are interested the Reading frame 2, increase the one base of the start point in the Seq box.

    *If you are interested the Reading frame 3, increase the two bases of the start point in the Seq box.

    6.Click the OK button to perform analysis and display the results in a text window.

    Analysis results:

    Silent mutation analysis is performed on the following three sequences to find different restriction sites.

    WT:Wild type sequence

    RT1:Degenerated sequence 1 from the amino acid sequence translated from WT sequence in reading frame 1.

    RT2:Degenerated sequence 2 from the amino acid sequence translated from WT sequence in reading frame 1.

    RT1 and RT2 are degenerated sequences according to the universal genetic code. Most amino acids can be reverse-translated to one triplet using IUPAC code, but two triplets must be used for Leu, Arg and Ser. Thus, RT1 represents one reverse translated sequence and RT2 represents another one.

    Analysis results show all possible restriction sites in the three sequences. By comparing the difference of restriction sites among WT, RT1 and RT2, you can find suitable positions to generate a silent mutation.

    Example:

    W.T. TTTGACTGCC ACTTCCTCGA TGAAGGTTTT 30
    RT1  TTYGAYTGYC AYTTYCTNGA YGARGGNTTY 30
    RT2  TTYGAYTGYC AYTTYTTRGA YGARGGNTTY 30
    
    TCTAGA XbaI 
    W.T.: 
    RT1 : 15 
    RT2 :

    The DNA sequence in RT1 at the position 15 is YCTNGA. According the IUPAC code, the YCTNGA represents the ambiguous sequences of

    TCTAGA,CCTAGA

        TCTCGA,    CCTCGA
        TCTGGA,    CCTGGA
        TCTTGA,    CCTTGA.

    You can create a mutant by changing your original sequence “CCTCGA” at the position 15 to “TCTAGA”. It will produce a restriction site of XbaI at that location without altering the coding amino acid sequence.