RNA Ladder Selection Guide

Dana Bioscience RNA QC Guide

RNA Ladder Selection Guide

6K vs 9K vs 12K vs 15K — Which RNA ladder should you use?

Choosing an RNA ladder is usually straightforward — until your RNA starts getting long.

Researchers working with long IVT RNA, large mRNA constructs and self-amplifying RNA (saRNA) may need reference bands well beyond the range of conventional RNA markers.

The key is not simply choosing the largest ladder.

Choose an RNA ladder with useful reference bands close to — and ideally surrounding — the expected size of your transcript.

What does an RNA ladder do?

During agarose gel electrophoresis, RNA molecules migrate according to size. A sample band alone, however, does not provide an easy size reference.

An RNA ladder contains RNA fragments of known lengths that are run alongside the sample.

Think of it as
an RNA molecular ruler

Quick RNA Ladder Selection Guide

Expected RNA Size Suggested Ladder Typical Application
Up to ~6 kb 6K RNA Ladder IVT RNA, mRNA
6–9 kb 9K Mid Range Large mRNA, long RNA
8–12 kb 12K High Range Long RNA, saRNA
12–15 kb 15K Ultra High Range Ultra-long RNA

6K RNA Ladder

For RNA transcripts comfortably below approximately 6 kb, a 6K RNA ladder may provide all the reference range needed.

  • IVT RNA
  • Conventional mRNA constructs
  • RNA transcription studies
  • General RNA electrophoresis

9K Mid Range RNA Ladder

When your RNA extends beyond conventional marker ranges, a 9K ladder adds useful reference points for larger transcripts.

0.2 / 0.5 / 1 / 2 / 3 / 4 / 6 / 9 kb

12K High Range RNA Ladder

FEATURED FOR LONG RNA & saRNA

CR00005-50UL

The 12K High Range RNA Ladder contains nine single-stranded RNA reference fragments:

0.2 / 0.5 / 1 / 2 / 3 / 4 / 6 / 9 / 12 kb
Shop 12K High Range RNA Ladder

Why is 12K particularly useful for saRNA?

Self-amplifying RNA includes additional sequence elements required for intracellular RNA amplification. This can make saRNA constructs substantially longer than conventional mRNA.

For an RNA construct around 8–10 kb, a marker with 9 kb and 12 kb reference bands provides useful comparison points.

6K Ladder

No reference band above an 8–10 kb RNA sample.

12K Ladder

9 kb and 12 kb references help bracket long RNA constructs.

15K Ultra High Range RNA Ladder

For very large RNA constructs extending beyond 12 kb, an ultra-high-range ladder may be more appropriate.

6 / 9 / 12 / 15 kb

RNA size is only one part of RNA QC

For IVT mRNA and saRNA research, it helps to separate two different QC questions.

SIZE & INTEGRITY

Is my RNA the expected size?

RNA Ladder + Electrophoresis

  • Expected transcript size
  • Migration
  • Band pattern
  • Shorter RNA species
IMPURITY

How much dsRNA is present?

J2-based dsRNA ELISA

  • Residual dsRNA detection
  • Quantitative analysis
  • IVT mRNA research
  • Purification workflow studies

A Practical Long RNA QC Workflow

IVT RNA Production
↓
RNA Purification
↓
Size & Integrity
6K / 9K / 12K / 15K RNA Ladder
↓
dsRNA Impurity
J2-based dsRNA ELISA
↓
Downstream Research

Which RNA Ladder Should You Choose?

RNA below ~6 kb → 6K RNA Ladder
RNA around 6–9 kb → 9K Mid Range RNA Ladder
Long RNA or saRNA around 8–12 kb → 12K High Range RNA Ladder
RNA above 12 kb → 15K Ultra High Range RNA Ladder
DANA BIOSCIENCE RNA QC SOLUTIONS

Working with long RNA or saRNA?

Explore high-range RNA ladders and dsRNA detection tools for long RNA, mRNA and saRNA research.

Explore RNA QC Solutions Shop 12K RNA Ladder

For Research Use Only. RNA ladders are intended as size standards and are not quantitative RNA standards.

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