molecular weight of oligos

[Paul N Hengen]

 In article <3u5mss$j93 at is.bbsrc.ac.uk> Your Name
 <your.name at bbsrc.ac.uk> writes:

| Does anyone know of a gcg programme which will calculate
| the molecular weight of DNA fragments?

Dear "Your Name":

Huh?? Why do you need a program in the GCG package to do this???
This should be very easy to do on your pocket calculator...

T = 322.2
A = 331.2
C = 307.2
G = 347.2
 
If you only know the sequence of one strand, and want to know 
the molecular weight of the entire double-stranded DNA: 
 
MW of strand1 = #T(322.2) + #A(331.2) + #C(307.2) + #G(347.2)
 
                        PLUS
 
MW of strand2 = #T(331.2) + #A(322.2) + #C(347.2) + #G(307.2)
 
Therefore the overall MW is 
 
   #T(322.2 + 331.2) + #A(331.2 + 322.2)
 + #C(307.2 + 347.2) + #G(347.2 + 307.2)
 --------------------------------------- 
 
OR
 
#T(653.4) + #A(653.4) + #C(654.4) + #G(654.4) 
 
OR 
 
653.4(#T + #A) + 654.4(#C + #G)   
 
OR
 
If you know the %GC of the single stranded sequence, 
MW in daltons for the double stranded DNA would be = 
 
(%GC * total length)             (100-%GC * total length)
-------------------- (654.4)  +  ------------------------ (653.4)
       100                                  100

Of course if I made a mistake somewhere down the line, I should return to
first year chemistry class ;-) Please send me if I've goofed. Well... if
you really want a program to do this kind of thing, I've just put together a
program where all these calculations are done for you.  You can download the
pascal source code for dnamwt.p by anonymous ftp from ftp.ncifcrf.gov as the
file pub/delila/dnamwt.p

or use the URL http://www-lmmb.ncifcrf.gov/~toms/delila/delilaprograms.html

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* Paul N. Hengen, Ph.D.                           /--------------------------/*
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