Oligonucleotides: RNA

Nucleic Acid Sequences

OpenMS also supports the representation of RNA oligonucleotides using the NASequence class:

import pyopenms as oms

oligo = oms.NASequence.fromString("AAUGCAAUGG")
prefix = oligo.getPrefix(4)
suffix = oligo.getSuffix(4)

print(oligo)
print(prefix)
print(suffix)
print()

print("Oligo length", oligo.size())
print("Total precursor mass", oligo.getMonoWeight())
print(
    "y1+ ion mass of",
    str(prefix),
    ":",
    prefix.getMonoWeight(oms.NASequence.NASFragmentType.YIon, 1),
)
print()

seq_formula = oligo.getFormula()
print("RNA Oligo", oligo, "has molecular formula", seq_formula)
print("=" * 35)
print()

isotopes = seq_formula.getIsotopeDistribution(oms.CoarseIsotopePatternGenerator(6))
for iso in isotopes.getContainer():
    print("Isotope", iso.getMZ(), ":", iso.getIntensity())

Which will output

AAUGCAAUGG
AAUG
AUGG

Oligo length 10
Total precursor mass 3206.4885302061
y1+ ion mass of AAUG : 1248.2298440331

RNA Oligo AAUGCAAUGG has molecular formula C97H119N42O66P9
===================================

Isotope 3206.4885302061 : 0.25567981600761414
Isotope 3207.4918850439003 : 0.31783154606819153
Isotope 3208.4952398817004 : 0.23069815337657928
Isotope 3209.4985947195 : 0.12306403368711472
Isotope 3210.5019495573 : 0.053163252770900726
Isotope 3211.5053043951 : 0.01956319250166416

The NASequence object also allows iterations directly in Python:

oligo = oms.NASequence.fromString("AAUGCAAUGG")
print(
    "The oligonucleotide", str(oligo), "consists of the following nucleotides:"
)
for ribo in oligo:
    print(ribo.getName())

Fragment Ions

Similarly to before for amino acid sequences, we can also generate internal fragment ions:

oligo = oms.NASequence.fromString("AAUGCAAUGG")
suffix = oligo.getSuffix(4)

oligo.size()
oligo.getMonoWeight()

charge = 2
mass = suffix.getMonoWeight(oms.NASequence.NASFragmentType.WIon, charge)
w4_formula = suffix.getFormula(oms.NASequence.NASFragmentType.WIon, charge)
mz = mass / charge

print("=" * 35)
print("RNA Oligo w4++ ion", suffix, "has mz", mz)
print("RNA Oligo w4++ ion", suffix, "has molecular formula", w4_formula)

Modified Oligonucleotides

Modified nucleotides can also be represented by the Ribonucleotide class and are specified using a unique string identifier present in the RibonucleotideDB in square brackets. For example, \(\ce{[m1A]}\) represents 1-methyl-adenosine. We can create a NASequence object by parsing a modified sequence as follows:

oligo_mod = oms.NASequence.fromString("A[m1A][Gm]A")
seq_formula = oligo_mod.getFormula()
print(
    "RNA Oligo",
    oligo_mod,
    "has molecular formula",
    seq_formula,
    "and length",
    oligo_mod.size(),
)
print("=" * 35)

oligo_list = [oligo_mod[i].getOrigin() for i in range(oligo_mod.size())]
print(
    "RNA Oligo",
    oligo_mod.toString(),
    "has unmodified sequence",
    "".join(oligo_list),
)

r = oligo_mod[1]
r.getName()
r.getHTMLCode()
r.getOrigin()

for i in range(oligo_mod.size()):
    print(oligo_mod[i].isModified())

DNA, RNA and Protein

We can also work with DNA and RNA sequences in combination with the BioPython library (you can install BioPython with pip install biopython):

from Bio.Seq import Seq
from Bio.Alphabet import IUPAC
bsa = oms.FASTAEntry()
bsa.sequence = 'ATGAAGTGGGTGACTTTTATTTCTCTTCTCCTTCTCTTCAGCTCTGCTTATTCCAGGGGTGTGTTTCGT'
bsa.description = "BSA Bovine Albumin (partial sequence)"
bsa.identifier = "BSA"

entries = [bsa]

f = oms.FASTAFile()
f.store("example_dna.fasta", entries)

coding_dna = Seq(bsa.sequence, IUPAC.unambiguous_dna)
coding_rna = coding_dna.transcribe()
protein_seq = coding_rna.translate()

oligo = oms.NASequence.fromString(str(coding_rna))
aaseq = oms.AASequence.fromString(str(protein_seq))

print("The RNA sequence", str(oligo), "has mass", oligo.getMonoWeight(), "and \n"
  "translates to the protein sequence", str(aaseq), "which has mass", aaseq.getMonoWeight() )