1D Gel Electrophoresis Calculators

1 calculator tagged with “1D Gel Electrophoresis”

One-dimensional (1D) gel electrophoresis separates biological molecules — DNA, RNA, or proteins — by size as they migrate through a porous gel matrix under an electric field. Smaller molecules migrate faster through the gel pores; larger molecules are more retarded. For DNA and RNA, agarose gels are standard; for proteins, polyacrylamide gels in denaturing conditions (SDS-PAGE) are most common. A molecular weight ladder (size marker) run alongside samples enables size estimation by comparing migration distances on a standard curve.

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DNA Agarose Gel Electrophoresis

DNA fragments are separated by size on 0.5–3% agarose gels in TAE or TBE buffer. Ethidium bromide (EtBr) or safer alternatives (SYBR Safe, GelGreen) intercalate into the DNA and fluoresce under UV light. A 1% gel resolves DNA from ~200–8000 bp well; lower percentages (0.7%) separate larger fragments; higher percentages (2–3%) resolve small fragments under 500 bp. DNA migration distance is proportional to log(molecular weight) on a standard linear gel.

SDS-PAGE for Protein Separation

Proteins are denatured with SDS (sodium dodecyl sulfate) and heat, giving all proteins a uniform negative charge proportional to length. Separated on polyacrylamide gels (8–15% for most proteins; gradient gels for wide range), migration is proportional to log(molecular weight). Coomassie brilliant blue or silver stain visualizes bands after separation. Western blotting transfers proteins to membrane for antibody detection.

Reading a Gel

Lane 1 typically contains a molecular weight ladder with bands of known size. Unknown band sizes are estimated by comparing their migration distance to the ladder on a log-linear standard curve. Band intensity reflects quantity — more nucleic acid or protein produces a brighter/darker band. Faint bands may indicate low abundance; smeared bands suggest degradation.

Calculating Fragment Size

Plot log(known ladder sizes) vs. migration distance (mm) to create a standard curve. For unknowns: read the migration distance, find the corresponding log(size) on the curve, and antilog to get size in bp or kDa.

Glossary

Agarose Gel
A porous polysaccharide gel used to separate DNA and RNA fragments by size under an electric field; standard matrix for nucleic acid electrophoresis.
SDS-PAGE
Sodium dodecyl sulfate polyacrylamide gel electrophoresis; a technique that denatures proteins and separates them by molecular weight using a polyacrylamide gel matrix.
Molecular Weight Ladder
A standard mixture of DNA fragments or proteins of known sizes run alongside experimental samples to enable size estimation from migration distance.

Frequently Asked Questions

DNA samples are loaded into wells cast in an agarose gel submerged in buffer. An electric current is applied — DNA is negatively charged (due to phosphate groups) and migrates toward the positive electrode. The agarose matrix acts like a molecular sieve: smaller fragments pass through gel pores more easily and travel farther. After running, DNA is visualized with a fluorescent dye under UV light. Band position relative to a size ladder indicates fragment size.

Agarose percentage determines the size range resolved. General guidelines: 0.7–0.8% for large DNA (2–20 kb); 1.0% for the common 200 bp–10 kb range (most PCR products and plasmids); 1.5–2.0% for 100–2000 bp fragments; 2.5–3.0% for very small fragments (50–500 bp). Higher percentage gels run more slowly but give better resolution for small fragments. For RNA, formaldehyde agarose or TBE-based gels under denaturing conditions are used to prevent secondary structure formation.

Run a DNA ladder with bands of known sizes alongside your samples. After electrophoresis, measure the migration distance (mm from well) of each ladder band and your unknowns. Plot log10(ladder band sizes in bp) vs. migration distance on graph paper or in a spreadsheet. Draw a best-fit line. For each unknown band, read its migration distance, find the corresponding log(size) on the line, and calculate size = 10^(log size). Most visualization software does this automatically.

SDS-PAGE (sodium dodecyl sulfate polyacrylamide gel electrophoresis) denatures proteins with SDS detergent and heat before separation. SDS coats proteins uniformly with negative charge, so migration depends only on molecular weight — allowing size estimation. Native PAGE separates proteins without denaturing, preserving natural charge, shape, and activity. Native gels are used to study protein complexes, enzyme activity (zymograms), and conformational isoforms, but cannot be used to estimate molecular weight directly.