lig program

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Documentation for the lig program is below, with links to related programs in the "see also" section.

{version = 1.28; (* of lig 1999 Aug 20}

(* begin module describe.lig *)
(*
name
   lig: DNA ligation theory

synopsis
   lig(input: in, list: out, output: out)

files
   input: user commands
   list: a 'hard copy' of the inputs and the outputs
   output: ligation predictions

description
   This program computes the results of a ligation reaction
   for insertion of a linker onto both ends of a linearized plasmid.
   The user gives
      the size of a plasmid in KB,
      the pico moles or micrograms of plasmid (you get to chose)
      the size of an insert in KB,
      the pico moles of or micrograms of insert
      the volume of the reaction in micro liters
   The program calculates whether circular or linear molecules are favored
   for the plasmid alone and with the insert.  The logic is:
   1.  The plasmid alone should circularize.
   2.  The plasmid with the insert should be linear.
   Thus, as the ligation proceeds, the first thing that happens is that
   the plasmid and insert ligate together (2 above).  Then the concentration of
   ends is lower, and circularization will be favored (1 above).
   Obviously this is all really rule of thumb, but it does seem to work
   in my experience.

documentation
   A. Dugaiczyk, H. W. Boyer and H. M. Goodman
   J. Mol. Biol. 96: 171-184 (1975)
   'Ligation of EcoRI Endonuclease-generated DNA fragements
    into Linear and Circular Structures'

author
   Thomas Dana Schneider

examples

| % lig
| lig 1.27
| plasmid size in kb: 4
| for the input plasmid, do you want to give ug or pMOL (u or p):u
| ug input plasmid: 1
| that is    0.37500 pMol
|
| for the input linker, do you want to give ug or pMOL (u or p):u
| ug linker: 1
| linker size in kb: 0.025
| that is   60.00000 pMol
| volume in microliters: 60
|
| for the plasmid alone
| critical [dna] = 0.0323 (g/l = micrograms/microliter)
| above this concentration: linears below: circles of the plasmid
| actual concentration of 1.000 micrograms of dna: 0.0167 (g/l)
| CIRCULAR MOLECULES FAVORED  (j/i =  1.939E+00)
|
| for the plasmid mixed with linkers:
| ratio of linker molecules to plasmid:  1.600E+02
| j =  1.521E+13 (ends / mil)  effective concentration of plasmid ends
| i =  6.097E+17 (ends / mil)  total ends
| LINEAR MOLECULES FAVORED  (j/i =  2.494E-05)

This example shows that when the plasmid is mixed with linkers one would get
them to ligate together to form linears.  Then the concentration drops so
that the plasmid is effectively alone, and one would form circles.  This
would insert the linker into the plasmid - exactly what one wants!

bugs
   none known

*)
(* end module describe.lig *)
{This manual page was created by makman 1.45}