MolWeight
for iPhone and iPad Touch

MolWeight is a simple tool for scientists and science students that allows calculation of the molecular weight and other key properties of peptides and oligonucleotides from their sequences. In addition, a calculator is provided for determining the molecular weight of any substance from its chemical formula.

Features:
- Calculate molecular weight, molar extinction coefficient, melting temperature and GC content for DNA or RNA
- Calculate molecular weight, molar extinction coefficient and isoelectric point for peptides
- Choose between common terminal modifications for oligonucleotides and peptides
- Calculate formula weights using average or monoisotopic atomic masses

MolWeight is easy to use. Just enter your sequence using one-letter codes and the molecular properties are recalculated as you type. MolWeight performs accurate weight calculations and estimates other properties using high-quality, fully documented algorithms. Bring your calculations into the lab where you need them!

MolWeight is available now on the iPhone App Store.

New features in Version 1.1:

- Abbreviations for common organic substituents now can be used in chemical formulas.
- Percent composition information has been simplified and now lists elements in their standard order.
- A bug which allowed invalid element symbols to be accepted in chemical formulas has been fixed.


Using MolWeight

When you start the program, you will see four buttons at the bottom of the screen. The first three of these allow you to select between calculations for oligonucleotides, for peptides and for generic molecules specified by their chemical formula. The fourth, "Info" button provides basic information about how to you use the program and what algorithms are employed.

Oligonucleotide Calculations

Tap on the large, central text box to begin entering the nucleotide sequence. Use the keyboard to enter the sequence using the one-letter codes A, C, G, T and U. These can be entered in upper or lower case. All other keyboard input is ignored and will not appear on screen. The calculated values are updated as you type.

You can select between single- or double-stranded DNA or RNA using the buttons directly below the sequence box.

Alternative chemical groups on the 5' and 3' termini of the molecule can be selected from popup lists. Synthetic oligonucleotides and DNA strands obtained by primer extension typically lack a 5' phosphate group and thus have a free 5’-hydroxyl. DNA obtained by the action of restriction enzymes usually is 5'-phosphorylated. Cellular RNA transcripts have a triphosphate on their 5' terminus prior to any post-transcriptional modification.

A larger set of 5’ and 3’ terminal modifications will be available soon in a program update.

Peptide Calculations

Tap on the central text box to begin entering the peptide sequence. Use the keyboard to enter the sequence using one-letter amino acid codes. The twenty standard amino acids can be used:

A => Alanine
C => Cysteine
D => Aspartic acid
E => Glutamic acid
F => Phenylalanine
G => Glycine
H => Histidine
I => Isoleucine
K => Lysine
L => Leucine
M => Methionine
N => Asparagine
P => Proline
Q => Glutamine
R => Arginine
S => Serine
T => Threonine
V => Valine
W => Tryptophan
Y => Tyrosine

Any other keyboard input that does not correspond to one of these codes is ignored, and will not appear on screen.

Using the switches below the sequence box, you can toggle between standard chain termini and N-terminal acetyl or C-terminal amide modifications.

Formula Weight Calculations

Enter element symbols using a combination of upper and lower case letters. For example:

NaCl = sodium chloride
CO = carbon monoxide
Co = cobalt

Elements 1-116 and 118 are recognized, along with deuterium (symbol "D").

To indicate multiple atoms, enter a number after the atomic symbol, for example:

H2O = water
C2H2 = acetylene

Parentheses may be used to group atoms. Up to four levels of nested parentheses can be used:

Al2(SO4)3 = aluminum sulfate
CuSO4(H2O)5 = copper sulfate pentahydrate

The molecular mass can be calculated using either average or monoisotopic atomic masses. Average masses are appropriate for most common calculations. The monoisotopic mass represents the mass of the most common single isotope for each element.

Help/Information

Much of the information presented here is available within the program by accessing the Info page.


Technical Information

Oligonucleotide Calculations

The melting temperature (Tm) is estimated by the nearest-neighbor method using the parameters of Allawi & SantaLucia (1997) Biochemistry 36, 10581 for DNA and Xia et al. (1998) Biochemistry 37, 14719 for RNA. Concentrations of 250 nM oligonucleotide, 100 mM monovalent salt, pH near neutral and a non-self-complementary sequence are assumed. The reported Tm is only an estimate and does not consider factors such as the presence of divalent metal ions, which will raise the melting temperature.

The predicted molar extinction coefficient (L/mol-cm) at 260 nm is calculated using the nearest-neighbor method [Cantor et al. (1970) Biopolymers 9, 1059]. The hypochromicity correction of Tataurov et al. (2008) Biophys. Chem. 133, 66 is included for double-stranded oligonucleotides.

Peptide Calculations

The predicted pI is calculated using pKa values from Thurkill et al. (2006) Protein Sci. 15, 1214-1218.

The predicted molar extinction coefficient (L/mol-cm) at 280 nm is calculated using the method of Gill & von Hippel (1989) Anal. Biochem. 182, 319-326 with values from Pace et al. (1995) Protein Sci. 4, 2411-23. Cysteine residues are assumed to be in non-disulfide form and therefore do not contribute to the result. The predicted extinction coefficient might not be accurate for a peptide with no tryptophan residues.

Formula Weight Calculations

The atomic weights used are the IUPAC values from Weiser (2006) Pure Appl. Chem. 78, 2051-2066.