Analisis Komposisi DNA

Menghitung komposisi GC/AT, titik leleh (melting temperature), dan berat molekul sekuens DNA menggunakan BioPython.

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Komposisi GC/AT

gc_fraction() menghitung proporsi basa G + C dalam sekuens. Nilainya berkisar antara 0 hingga 1.

gc_composition = gc_fraction(seq) print(f"GC Composition: {gc_composition*100:.2f}%") at_composition = 1 - gc_composition print(f"AT Composition: {at_composition*100:.2f}%")

gc_composition = gc_fraction(seq)

print(f"GC Composition: {gc_composition*100:.2f}%")

at_composition = 1 - gc_composition

print(f"AT Composition: {at_composition*100:.2f}%")

gc_composition = gc_fraction(seq) print(f"GC Composition: {gc_composition*100:.2f}%") at_composition = 1 - gc_composition print(f"AT Composition: {at_composition*100:.2f}%")

Komposisi GC penting karena ikatan G–C lebih kuat (3 ikatan hidrogen) dibanding A–T (2 ikatan hidrogen), sehingga mempengaruhi stabilitas termal DNA.

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Titik Leleh (Melting Temperature)

Melting Temperature (Tm) adalah suhu di mana 50% untai DNA terdenaturasi menjadi rantai tunggal. BioPython menyediakan tiga metode kalkulasi melalui modul MeltingTemp:

1. Wallace Rules

Metode paling sederhana, akurat untuk sekuens pendek (≤ 14 bp):

$$Tm = 2(A + T) + 4(G + C)$$

mt_wallace = MeltingTemp.Tm_Wallace(seq) print(f"Melting Temp Wallace: {mt_wallace}")

mt_wallace = MeltingTemp.Tm_Wallace(seq)

print(f"Melting Temp Wallace: {mt_wallace}")

mt_wallace = MeltingTemp.Tm_Wallace(seq) print(f"Melting Temp Wallace: {mt_wallace}")

2. GC Rules

Metode berbasis persentase GC, lebih akurat untuk sekuens panjang (> 14 bp):

mt_gc = MeltingTemp.Tm_GC(seq) print(f"Melting Temp GC: {mt_gc}")

mt_gc = MeltingTemp.Tm_GC(seq)

print(f"Melting Temp GC: {mt_gc}")

mt_gc = MeltingTemp.Tm_GC(seq) print(f"Melting Temp GC: {mt_gc}")

3. Nearest Neighbor (NN) Rules

Metode paling akurat secara termodinamika — mempertimbangkan interaksi antar pasangan basa tetangga:

mt_NN = MeltingTemp.Tm_NN(seq) print(f"Melting Temp NN: {mt_NN}")

mt_NN = MeltingTemp.Tm_NN(seq)

print(f"Melting Temp NN: {mt_NN}")

mt_NN = MeltingTemp.Tm_NN(seq) print(f"Melting Temp NN: {mt_NN}")

Formula Wallace Manual

Implementasi formula Wallace dari awal, mendukung dua rentang panjang sekuens:

def TM_Wallace(seq): count_G = seq.count('G') count_C = seq.count('C') count_A = seq.count('A') count_T = seq.count('T') if len(seq) <= 28: return 2 * (count_A + count_T) + 4 * (count_C + count_G) else: return 64.9 + 41 * (count_G + count_C - 16.4) / len(seq) print(f"Melting Temp Wallace (manual): {TM_Wallace(seq)}")

def TM_Wallace(seq):

count_G = seq.count('G')

count_C = seq.count('C')

count_A = seq.count('A')

count_T = seq.count('T')

if len(seq) <= 28:

return 2 * (count_A + count_T) + 4 * (count_C + count_G)

else:

return 64.9 + 41 * (count_G + count_C - 16.4) / len(seq)

print(f"Melting Temp Wallace (manual): {TM_Wallace(seq)}")

def TM_Wallace(seq): count_G = seq.count('G') count_C = seq.count('C') count_A = seq.count('A') count_T = seq.count('T') if len(seq) <= 28: return 2 * (count_A + count_T) + 4 * (count_C + count_G) else: return 64.9 + 41 * (count_G + count_C - 16.4) / len(seq) print(f"Melting Temp Wallace (manual): {TM_Wallace(seq)}")

Metode	Keunggulan	Digunakan untuk
Wallace	Sederhana, cepat	Sekuens pendek (≤ 14 bp)
GC	Mudah dihitung	Sekuens panjang, estimasi cepat
Nearest Neighbor	Paling akurat	Primer PCR, analisis presisi tinggi

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Berat Molekul (Molecular Weight)

molecular_weight() menghitung berat molekul sekuens DNA dalam g/mol berdasarkan komposisi basanya:

$$MW = n_A \cdot m_A + n_C \cdot m_C + n_G \cdot m_G + n_T \cdot m_T$$

mw = molecular_weight(seq) print(f"molecular_weight = {mw}")

mw = molecular_weight(seq)

print(f"molecular_weight = {mw}")

mw = molecular_weight(seq) print(f"molecular_weight = {mw}")

Nilai berat molekul berguna untuk preparasi larutan DNA dan perhitungan konsentrasi molar (misalnya: nmol/µg, OD₂₆₀).

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Kode Lengkap

Explorer

dna-composition

sesi2.py

dna-composition/sesi2.py

import Bio
from Bio.SeqUtils import gc_fraction
from Bio.Seq import Seq

seq = Seq('GCTAGCATTAGCTAGCCGGTTAATTA')

# ── Komposisi GC/AT ───────────────────────────────────────────────
gc_composition = gc_fraction(seq)
print(f"GC Composition: {gc_composition*100:.2f}%")

at_composition = 1 - gc_composition
print(f"AT Composition: {at_composition*100:.2f}%")

# ── Titik Leleh (Melting Temperature) ────────────────────────────
from Bio.SeqUtils import MeltingTemp

# Wallace Rules (<= 14 BP)
mt_wallace = MeltingTemp.Tm_Wallace(seq)
print(f"Melting Temp Wallace: {mt_wallace}")

# GC Rules
mt_gc = MeltingTemp.Tm_GC(seq)
print(f"Melting Temp GC: {mt_gc}")

# NN Rules (Nearest Neighbor)
mt_NN = MeltingTemp.Tm_NN(seq)
print(f"Melting Temp NN: {mt_NN}")

# Formula Wallace Manual
def TM_Wallace(seq):
    count_G = seq.count('G')
    count_C = seq.count('C')
    count_A = seq.count('A')
    count_T = seq.count('T')

    if len(seq) <= 28:
        return 2 * (count_A + count_T) + 4 * (count_C + count_G)
    else:
        # TM = 64.9 + 41 x (G + C - 16.4) / N
        return 64.9 + 41 * (count_G + count_C - 16.4) / len(seq)

print(f"Melting Temp Wallace (manual): {TM_Wallace(seq)}")

# ── Berat Molekul (Molecular Weight) ─────────────────────────────
# MW = countA * massA + countC * massC + countG * massG + countT * massT
from Bio.SeqUtils import molecular_weight

print(f"molecular_weight = {molecular_weight(seq)}")

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Ringkasan

Fungsi	Modul	Deskripsi
gc_fraction(seq)	Bio.SeqUtils	Proporsi GC (0–1)
MeltingTemp.Tm_Wallace(seq)	Bio.SeqUtils.MeltingTemp	Tm metode Wallace
MeltingTemp.Tm_GC(seq)	Bio.SeqUtils.MeltingTemp	Tm berbasis % GC
MeltingTemp.Tm_NN(seq)	Bio.SeqUtils.MeltingTemp	Tm Nearest Neighbor (paling akurat)
molecular_weight(seq)	Bio.SeqUtils	Berat molekul (g/mol)

Perbandingan Metode Melting Temperature

Metode	Hasil (contoh 26 bp)	Kompleksitas
Wallace	74.0°C	Rendah
GC	54.17°C	Sedang
Nearest Neighbor	55.12°C	Tinggi

Kapan memilih metode? Untuk desain primer PCR, gunakan Nearest Neighbor karena paling akurat secara termodinamika. Wallace cocok untuk estimasi cepat pada oligonukleotida pendek.