Average molecular weight of a DNA base pair

[Paul N Hengen]

Paul N Hengen (pnh at cockleberry.ncifcrf.gov) wrote:

> Many of the biotech. company catalogues (e.g. New England BioLabs, MBI 
> Fermentas) include useful appendices which include as estimate of the 
> molecular weight of single and double stranded DNA (sodium salts).  For 
> double stranded DNA I have seen values of 649, 650 and 660 per bp. Does 
> anyone have an original reference to these numbers, or can derive them 
> from the average molecular weight of a base pair?

: I think they add the 4 bases and divide by 4, then multiply this by the length
: of DNA in bases, a very crude method of calculating the MW of a dsDNA. If you
: know the number of As Cs Gs and Ts, or just the number of GC and AT pairs for
: that matter, you can do a much more accurate determination of MW. The following
: program can help you do it with minimal brain power ;-) If you don't want to
: compile it, just look at the description for the simple math stuff and do it
: on paper.

Sorry for the clutter....

Here is a cleaner version of the program for anyone reading through NetScape:

--

program dnamwt(input, report, output);
(* dnamwt: calculate the molecular weight of a DNA molecule

  Paul N. Hengen and Tom Schneider
  National Cancer Institute
  Laboratory of Mathematical Biology
  NCI/FCRDC Bldg 469. Room 144
  P.O. Box B
  Frederick, MD  21702-1201
  (301) 846-5581 (-5532 for messages)
  e-mail: pnh at ncifcrf.gov and toms at ncifcrf.gov 

 *)

label 1; (* end of program *)

const
(* begin module version *)
version = 1.08; (* of dnamwt.p 1995 July 20
origin 1995 July 14 *)
(* end module version *)

(* begin module describe.dnamwt *)
(*
name
   dnamwt: calculate the molecular weight of a DNA molecule

synopsis
   dnamwt(input: in, report: out, output: out)

files
   input:  user input
   report: output file with calculated weight
   output: output file with calculated weight

description
   This program is used to calculate the molecular weight of DNA

examples

 The molecular weights of the monophosporylated nucleotides are:

 A = 331.2
 C = 307.2
 G = 347.2
 T = 322.2

 When polymerized, each nucleotide will lose a water molecule of 18.0,
 and not considering methylation of any bases, the molecular weight of
 each will be;

 A = 313.2
 C = 289.2
 G = 329.2
 T = 304.2

 But, we'll have to add back two hydroxide ions, one for each strand polymerized,
 which is 17.0 x 2 = 34.0 PLUS 2.0 for the two extra hydrogen ions subtracted earlier.

 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 = #A(313.2) + #C(289.2) + #G(329.2) + #T(304.2) + 18.0

                        PLUS

 MW of strand2 = #A(304.2) + #C(329.2) + #G(289.2) + #T(313.2) + 18.0

 Therefore the overall MW is 

   #A(313.2 + 304.2) + #C(289.2 + 329.2)
 + #G(329.2 + 289.2) + #T(304.2 + 313.2)
 + 36.0
 ---------------------------------------

OR

 #A(617.4) + #C(618.4) + #G(618.4) + #T(617.4) + 36.0

OR

 617.4(#T + #A) + 618.4(#C + #G) + 36.0

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)
 -------------------- (618.4)  +  ------------------------ (617.4) + 36.0
        100                                  100

documentation
   Other sources of information or documents on the program.

see also

author
   Paul N. Hengen and Thomas Dana Schneider

bugs

technical notes

*)
(* end module describe.dnamwt *)

(* begin module dnamwt.const *)
(* molecular weights of all the deoxynucleotides with a single phosphate
   and H2O removed *)

  awt = 313.2;
  cwt = 289.2;
  gwt = 329.2;
  twt = 304.2;

(* end module dnamwt.const *)

var
   report: text; (* file used by this program *)

(* begin module halt *)
procedure halt;
(* stop the program.  the procedure performs a goto to the end of the
   program.  you must have a label:
      label 1;
   declared, and also the end of the program must have this label:
      1: end.
   examples are in the module libraries.
   this is the only goto in the delila system. *)
begin
      writeln(output,' program halt.');
      goto 1
end;
(* end module halt version = 'delmod 6.16 84 mar 12 tds/gds'; *)

(* begin module dnamwt.themain *)
procedure themain(var report: text);
(* the main procedure of the program *)
var
  ano: integer; (* number of a's in the sequence *)
  cno: integer; (* number of c's in the sequence *)
  gno: integer; (* number of g's in the sequence *)
  tno: integer; (* number of t's in the sequence *)
  total: integer; (* total number of bases in the sequence *)

  c: char; (* a character *)
  strand1: real; (* strand 1 molecular weight *)
  strand2: real; (* strand 2 molecular weight *)

procedure getbase(var report: text; xchar: char; var xno: integer);
(* get the number of base x and write it to the report file *)
begin
   write(output,'number of ',xchar,'''s in strand 1 of the sequence: ');
   readln(input, xno);
   writeln(report,'the number of ',xchar,
                  '''s in strand 1 of the sequence is: ',xno:1);
end;

begin
   writeln(output,'dnamwt ',version:4:2);
   rewrite(report);
   writeln(report,'dnamwt ',version:4:2);

   getbase(report,'A',ano);
   getbase(report,'C',cno);
   getbase(report,'G',gno);
   getbase(report,'T',tno);

   strand1 := ano*awt + cno*cwt + gno*gwt + tno*twt + 18.0;
   strand2 := ano*twt + cno*gwt + gno*cwt + tno*awt + 18.0;
   total := ano + cno + gno + tno;
   writeln(report,'total number of bases: ',total);
   writeln(report,'strand 1 molecular weight: ',strand1:4:1,' daltons');
   writeln(report,'strand 2 molecular weight: ',strand2:4:1,' daltons');
   writeln(report,'total molecular weight: ',(strand1+strand2):4:1,' daltons');
   writeln(report,'% GC: ',(100*(gno+cno)/(ano+cno+gno+tno)):4:1);

   (* show the report *)
   writeln(output);
   reset(report);
   while not eof(report) do begin
      while not eoln(report) do begin
         read(report, c);
         write(output, c);
      end;
      readln(report);
      writeln(output);
   end;

end;
(* end module dnamwt.themain *)

begin
   themain(report);
1: end.

--
*******************************************************************************
* Paul N. Hengen, Ph.D.                           /--------------------------/*
* National Cancer Institute                       |Internet: pnh at ncifcrf.gov |*
* Laboratory of Mathematical Biology              |   Phone: (301) 846-5581  |*
* Frederick Cancer Research and Development Center|     FAX: (301) 846-5598  |*
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