Encoding text into nucleic acid sequences
Methods and apparatus are disclosed herein for encoding human readable text conveying a non-genetic message into nucleic acid sequences with a substantially reduced probability of biological impact and decoding such text from nucleic acid sequences. In one embodiment, each symbol of a symbol set of human readable symbols uniquely maps to a respective codon identifier. Mapping may ensure that each symbol will not map to a codon identifier that generates an amino acid residue which has a single-letter abbreviation that is the equivalent to the respective symbol. Synthetic nucleic acid sequences comprising such human readable text, and recombinant or synthetic cells comprising such sequences are provided, as well as methods of identifying cells, organisms, or samples containing such sequences.
1. A method of generating a sequence of codon identifiers corresponding to a sequence of human readable symbols, and assigned according to a coding scheme to convey a non-genetic message in a human reference language, the method comprising:
(i) receiving the sequence of human readable symbols at a memory module;
(ii) loading a human readable symbol map within the memory module, wherein the human readable symbol map is configured to map human readable symbols as follows:
GGA = “
GAA = ‘
TTC = #
CAG = :
TGT = ;
ACG = [
AGG = ]
AAA = {
AAG = }
CCG = ( or )
GAC = ( or )
CGG = <
AGC = >
CAC = /
CTC = \
CGA = .
GTG = ,
CCC = -
CCT = +
CCA = =
TCG = @
ATC = $
GAT = %
GAG = !
ACC = &
ATG = *
ATA =
GGG =
space
new line
TCT = 0
CTT = 1
ACT = 2
AAT = 3
AGA = 4
GCG = 5
GCC = 6
TAT = 7
CGC = 8
GTA = 9
TAG = A
AGT = B
TTT = C
ATT = D
TAA = E
GGC = F
TAC = G
TCA = H
CTG = I
GTT = J
GCA = K
AAC = L
CAA = M
TGC = N
CGT = O
ACA = P
TTA = Q
CTA = R
GCT = S
TGA = T
TCC = U
TTG = V
GTC = W
GGT = X
CAT = Y
TGG = Z
and
(iii) using a transcoder to map a sequence of codon identifiers corresponding to each human readable symbol within the sequence according to the human readable symbol map and outputting the sequence,
(iv) synthesizing a nucleic acid with the sequence of step (iii).
2. The method of claim 1 wherein said set of human readable symbols comprises a watermark that allows the authentication or identification of said recombinant or synthetic organism comprising said watermark.
3. The method of claim 2 wherein said watermark is a copyright notice, a trademark, a company identifier, a name, a phrase, a sentence, a quotation, genetic information, unique identifying information, data, or a combination of any thereof.
4. The method of claim 1 wherein the synthetic nucleic acid sequence further comprises an all-6 reading frame stop codon containing sequence 5′ to a first codon identifier in the sequence and/or an all-6 reading frame stop codon containing sequence 3′ to the last codon identifier in the sequence.
5. An apparatus for transforming a sequence of codon identifiers into a nucleic acid sequence of claim 1 , the apparatus comprising:
(i) a processor adapted to execute instructions; and
(ii) a storage module, wherein the storage module comprises a data structure for mapping codon identifiers into human readable symbols, and a set of instructions that are executed by the processor and generate a human readable symbol for each codon identifier read from a sequence of codon identifiers, wherein the human readable symbol generated is based at least in part upon the data structure; wherein the data structure is configured to map human readable symbols as follows:
GGA = “
GAA = ‘
TTC = #
CAG = :
TGT = ;
ACG = [
AGG = ]
AAA = {
AAG = }
CCG = ( or )
GAC = ( or )
CGG = <
AGC = >
CAC = /
CTC = \
CGA = .
GTG = ,
CCC = -
CCT = +
CCA = =
TCG = @
ATC = $
GAT = %
GAG = !
ACC = &
ATG = *
ATA =
GGG =
space
new line
TCT = 0
CTT = 1
ACT = 2
AAT = 3
AGA = 4
GCG = 5
GCC = 6
TAT = 7
CGC = 8
GTA = 9
TAG = A
AGT = B
TTT = C
ATT = D
TAA = E
GGC = F
TAC = G
TCA = H
CTG = I
GTT = J
GCA = K
AAC = L
CAA = M
TGC = N
CGT = O
ACA = P
TTA = Q
CTA = R
GCT = S
TGA = T
TCC = U
TTG = V
GTC = W
GGT = X
CAT = Y
TGG = Z.
6. The apparatus of claim 5 , wherein the data structure or mapping function, respectively, does not map a codon identifier to a single letter representation of an amino acid residue normally assigned to that codon identifier in the standard genetic code.
7. The apparatus of claim 5 , wherein the sequence of codon identifiers comprises an all-6 reading frame stop codon containing sequence 5′ to a first codon identifier in the sequence and/or an all-6 reading frame stop codon containing sequence 3′ to the last codon identifier in the sequence.