dsIUPAC - MetabolicEngineeringGroupCBMA/MetabolicEngineeringGroupCBMA.github.io GitHub Wiki

This document defines an extension to the IUPAC DNA alphabet for double stranded DNA. This extension is called dsIUPAC and allow unambiguous description of a double stranded DNA molecule with single stranded regions using a single sequence of characters.

IUPAC

The IUPAC DNA alphabet is a set of symbols designated by the International Union of Pure and Applied Chemistry (IUPAC) to represent nucleotide bases in DNA sequences, including ambiguity codes for cases where multiple nucleotides are possible at a particular position. Here are the symbols and their meanings:

  1. A - Adenine
  2. T - Thymine
  3. C - Cytosine
  4. G - Guanine

Ambiguity codes (representing multiple possible nucleotides):

  1. R - Purine (A or G)
  2. Y - Pyrimidine (C or T)
  3. S - Strong interaction (G or C)
  4. W - Weak interaction (A or T)
  5. K - Keto group (T or G)
  6. M - Amino group (A or C)
  7. B - Not A (C, G, or T)
  8. D - Not C (A, G, or T)
  9. H - Not G (A, C, or T)
  10. V - Not T (A, C, or G)
  11. N - Any nucleotide (A, T, C, or G)

These symbols allow for flexibility in representing DNA sequences, especially when there is uncertainty in base composition at specific positions.

dsIUPAC

Alphabet Symbol Complement Bases
IUPAC G C G
" A T A
" T A T
" C G C
" R Y G or A
" Y R T or C
" M K A or C
" K M G or T
" S S G or C
" W W A or T
" H D A or C or T
" B V G or T or C
" V B G or C or A
" D H G or A or T
" N N G or A or T or C
dsIUPAC U O U in top strand, A in complementary strand
" O U A in top strand, U in complementary strand
"" E F A in top strand, complementary strand empty
" I J C "
" P Q G "
" X Z T "
" Z X A in complementary strand, top strand empty
" Q P C "
" J I G "
" F E T "

The choice of symbols for the dsIUPAC extension facilitate intuitive recognition of compatible single stranded regions, i.e. sticky-ends.

Example

Two double stranded DNA molecules with compatible terminal 5'- single strand overhangs:

GATCaUaAa                   ad-hoc representation
    tAtUtCTAG         
    

PEXIaUaOaQFZJ               representation using dsIUPAC

We can easily recognize that alphabetically, P is followed by Q, E by F and I by J. This symmetry is only broken by the X, Z pair of necessity since Y is already used in the IUPAC alphabet.

DNA molecules with compatible terminal 3'- single strand overhangs:

    aaaGATC        aaaGATC           ad-hoc representation
CTAGttt        CTAGttt              

QFZJaaaPEXI    QFZJaaaPEXI           representation using dsIUPAC

alphabets

ASCII CAPS  = ABCDEFGHIJKLMNOPQRSTUVWXYZ
IUPAC       = ABCD  GH  K MN   RST VW Y                
dsIUPAC     =     EF  IJ L  OPQ   U  X Z   +  IUPAC

punctuation = @ # $ % + > < * (still free)

Representations of double stranded DNA



PEXIGULAOCQFZJ

>format1 two strings & space
GATCGUAAAC
    CAUTUGCTAG         

>format2 two strings & pipe
GATCGUAAAC||||
||||CAUTUGCTAG

>format3 two strings & hyphen
GATCGUAAAC----
----CAUTUGCTAG

>format4 three strings, pipe & hyphen
GATCGUAAAC----
||||||||||||||
----CAUTUGCTAG