This Shiny application calculates the required amount of peptide for a given N/P ratio when forming peptide-DNA complexes. It takes inputs such as peptide sequence, plasmid size, desired N/P ratio, DNA amount, and peptide stock concentration. The app provides detailed calculation results, including the mass and volume of peptide needed and the amino acid composition of the peptide.

• Calculate the required peptide mass and volume for a given N/P ratio.
• Provide detailed information on the DNA and peptide used in the calculations.
• Display the amino acid composition of the provided peptide sequence.
• Include detailed protocols for preparing peptide-DNA complexes and conducting Electrophoretic Mobility Shift Assay (EMSA).

• R version 3.5.0 or higher
• Shiny package
• stringr package

To install the required R packages, run the following commands in your R console:

install.packages("shiny")
install.packages("stringr")

1. Open the R console or RStudio.
2. Load the Shiny package:

library(shiny)

3. Source the Shiny application script or run the app directly:

runApp('path/to/your/script.R')

Replace 'path/to/your/script.R' with the actual path to the script file.

4. The Shiny app will open in your default web browser. Enter the peptide sequence, plasmid size, desired N/P ratio, DNA amount, and peptide stock concentration to perform the calculations.

• Peptide sequence: The amino acid sequence of the peptide.
• Plasmid size (kb): The size of the plasmid in kilobases.
• Desired N/P ratio: The desired ratio of nitrogen atoms to phosphate groups.
• DNA amount (μg): The amount of DNA in micrograms.
• Peptide stock concentration (mg/mL): The concentration of the peptide stock solution in milligrams per milliliter.
• Final complex volume (μL): The final volume of the peptide-DNA complex in microliters.

• Peptide mass needed (μg)
• Peptide solution volume (µL)
• DNA solution volume (µL)
• Buffer volume (µL)
• Total volume (µL)
• Detailed information on the DNA and peptide used in the calculations
• Amino acid composition of the provided peptide sequence

The application includes detailed protocols for:

1. Peptide-DNA Complex Formation
2. Electrophoretic Mobility Shift Assay (EMSA) Protocol

These protocols provide step-by-step instructions for preparing and analyzing peptide-DNA complexes.

• Ensure that the peptide sequence uses only standard amino acid one-letter codes.
• Always verify calculations and adjust protocols as needed for your specific experimental conditions.