Manual


Nucleotide Sequence Molecular Weight Calculator:

This program allows you to calculate the molecular weight of DNA and RNA sequence files which are written in the Genbank format (text format). The program can be used to calculate single- or double stranded sequences, or the molecular weight of the complement of a sequence. You can select the 3' and 5' terminus chemistry, and add common counterions in molar ratios to each residue.

You can download DNA/RNA sequences directly into the calculator from Genbank. Clicking on the "Download Sequence" button will connect you to the Entrez database for downloading Genbank sequence files.

If you would like to import your own sequence, you need to make sure that the file is in the proper Genbank format.

Example sequence:

DEFINITION  exon from: Gallus gallus egg white lysozyme gene, partial cds.
ORIGIN
   1 agtcccgctg tgtgtacgac actggcaaca tgaggtcttt gctaatcttg gtgctttgct
  61 tcctgcccct ggctgctctg gggaaagtct ttggacgatg tgagctggca gcggctatga
 121 agcgtcacgg acttgataac tatcggggat acagcctggg aaact
  //

The following four fields are required:

Field 1: "DEFINITION"
This field has to be spelled in upper case and everything following it on the same line will be printed as the sequence title in the program.

Field 2: "ORIGIN"
This field has to be spelled in upper case and should be the only word in this line. This word indicates that the next line will contain the beginning of the actual sequence.

Field 3: The actual sequence (multiline). The sequence elements (a, g, c, t, u) can be spelled in upper or lower case, and can contain spaces. Each line with sequence data needs to contain exactly one string, separated by white space, in front of the actual sequence data. This is ordinarily the position of the first residue listed in that line.

Field 4: The sequence terminator "//". This terminator symbol should be on a separate line following the last sequence line. Any information past the terminator symbol is ignored.

Amy other information contained in the file is ignored.

The program uses the following algorithm (Ref.: Steve Hardies, University of Texas Health Science Center at San Antonio, Dept. of Biochemistry):

Natural isotope adjusted MWs

C	12.011
N	14.0067
O	15.9994
H	1.00794
P	30.9738

Adenine C5N5H5
Guanine C5N5OH5
Thymine C5N2O2H6
Cytosine C4N3OH5
Uracil  C4N2O2H4

ribose C5O5H10
deoxyribose C5O4H10

phosphate PO4

Adding the base to the ribose involves loss of 1 H2O 
Bonding the phosphate to either 5' or 3' OH causes loss of 1 HO

An internal ribonucleotide is then calculated as base+ribose+phosphate
-H2O - 2 OH.

MW of an internal ribonucleotide:

rAMP - 313.21
rCMP - 289.19
rUMP - 290.17
rGMP - 329.21
rTMP - 304.63

to make deoxy, subtract 16.00
to make terminal 3'OH add 17.01
to make terminal 3' phosphate  add 94.97
to make terminal 5' phosphate - no change
to make terminal 5' OH substract 77.96

Does not account for the 2nd dissociable H of the terminal phosphate, which 
has a pK somewhere around neutrality. It would be 7.2 for a free phosphate.


www contact: Borries Demeler

This document is part of the UltraScan Software Documentation distribution.
Copyright 1998 - 2001, The University of Texas Health Science Center at San Antonio.

The latest version of this document can always be found at:

    http://www.ultrascan.uthscsa.edu

Last modified on December 27, 2000.