🧬 InSilico PCR Pro

Professional Molecular Biology Analysis & Primer Design Suite

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🔬 Professional Primer Design

How it works:

Input your DNA template sequence and specify primer binding regions. The tool calculates optimal Tm, GC content, and secondary structures for highly specific PCR.

Quick Tips:

  • Optimal primer length: 18-25 bp
  • Tm should be 60-65°C
  • GC content: 40-60%
  • Avoid homopolymeric runs
  • Tm difference < 5°C

⚙️ In Silico PCR Analysis

Virtual PCR Simulation:

Predict PCR products, detect potential mispriming sites, and validate primer specificity before wet lab synthesis.

Primer Specifications:

  • Format: 5' → 3' direction
  • IUPAC codes supported (W, R, Y, etc.)
  • Mismatches at 3' critical
  • Expected product: 200-5000 bp

📊 Gel Electrophoresis Simulator

Realistic Gel Visualization:

Visualize DNA fragment migration patterns with standard molecular weight ladders and realistic band representation.

Agarose % Fragment Range Best Use Resolution
0.5% 1-30 kb Genomic DNA, large fragments Very low
0.7% 0.8-12 kb Standard genomic work Low
1.0% 0.5-10 kb General PCR products (recommended) Medium
1.5% 0.2-5 kb Small PCR products, SNP detection High
2.0% 0.1-3 kb Sequencing, small fragments Very high
3.0% 50-500 bp Microsatellites, AFLP Excellent

1 kb Plus Ladder:

10, 15, 20, 30, 40, 50, 65, 80, 100, 130, 160, 200, 250, 330, 500, 650, 1000, 1650, 2000, 2600, 3000, 3500, 4000, 5000, 6000, 7000, 8000, 9000, 10000 bp

🧪 SDS-PAGE Protein Gel Simulation

Protein Electrophoresis:

Simulate protein separation by denaturing polyacrylamide gel electrophoresis. Estimate molecular weights from relative mobility.

Acrylamide % Protein Range Best Use Pore Size
4% 30-250 kDa Large proteins, initial screening Large
6% 20-200 kDa Medium to large proteins Medium
8% 15-150 kDa General protein analysis (recommended) Medium
10% 10-100 kDa Small to medium proteins Small
12% 5-80 kDa High resolution for small proteins Very small
15-20% 2-60 kDa Very small peptides, highest resolution Very small

⚗️ Molecular Biology Dilution Calculator

Precise Concentration Calculations:

Calculate DNA, RNA, and protein dilutions using the dilution formula: C₁V₁ = C₂V₂

Formula: C₁V₁ = C₂V₂

  • C₁ = Initial concentration
  • V₁ = Volume of stock solution needed
  • C₂ = Final desired concentration
  • V₂ = Final total volume

Example:

Stock: 100 ng/µL DNA | Desired: 10 ng/µL in 50 µL total

Calculation: (100 ng/µL × V₁) = (10 ng/µL × 50 µL)

Result: V₁ = 5 µL stock + 45 µL buffer

DNA/RNA Dilution

Protein Dilution

PCR Master Mix Scaling

Serial Dilution Series

📈 NanoDrop Analysis & Interpretation

Nucleic Acid Purity Assessment:

NanoDrop measures absorbance at 260nm (NA), 280nm (proteins), and 230nm (contaminants) to assess nucleic acid quality and purity.

Ratio/Parameter Good Range Interpretation
A260/280 1.8-2.0 (DNA)
1.9-2.2 (RNA)		 DNA purity. >2.0 = protein contamination
A260/230 2.0-2.2 Contamination with phenol, guanidine, carbohydrates. >2.2 excellent
Concentration Variable ng/µL for DNA/RNA. Use Beer-Lambert law: C = A260 × ε × l
A230 0.05-0.10 Low is good. High = salt/carbohydrate contamination

Extinction Coefficients (ε):

  • dsDNA: 50 µg/mL⁻¹cm⁻¹
  • ssDNA: 33 µg/mL⁻¹cm⁻¹
  • RNA: 40 µg/mL⁻¹cm⁻¹
  • dsDNA (molecular): 0.020 (µg/mL)⁻¹cm⁻¹

Input NanoDrop Values

🎯 CRISPR-Cas9 Guide RNA Design

sgRNA Design Tool:

Design guide RNAs for CRISPR-Cas9 gene editing. Identify PAM sites (NGG) and evaluate off-target potential.

🔍 Advanced Mutation Detection

Sequence Comparison & Analysis:

Compare sequences to identify point mutations, insertions, deletions, and generate detailed mutation reports.