ssDNA Calculators

0 calculators tagged with “ssDNA”

Single-stranded DNA (ssDNA) is DNA in which only one polynucleotide strand exists, without a complementary paired strand. Unlike double-stranded DNA (dsDNA), ssDNA is flexible and can form complex secondary structures (hairpins, G-quadruplexes) through intramolecular base pairing. ssDNA occurs naturally in some viruses (M13, phi X174, parvoviruses), in replication intermediates, and in the lagging strand template during DNA replication. In molecular biology, ssDNA probes and oligonucleotides are used in hybridization, PCR, CRISPR-Cas systems, and as templates for DNA synthesis.

All Calculators

No calculators found for this topic.

ssDNA vs. dsDNA

  • Structure: ssDNA is a single polynucleotide chain; dsDNA is two antiparallel chains held by Watson-Crick base pairs (A:T and G:C)
  • Stability: dsDNA is more stable (two strands, stacking interactions, H-bonds); ssDNA degrades more rapidly by nucleases
  • Secondary structure: ssDNA can fold into hairpins, loops, and quadruplexes via intrastrand base pairing
  • Extinction coefficient: ssDNA at A260: 1 OD₂₆₀ = 33 μg/mL (vs. 50 μg/mL for dsDNA)

NanoDrop Quantification of ssDNA

When measuring ssDNA on a NanoDrop spectrophotometer, select 'ssDNA' in the software — this uses the 33 ng/μL per A260 conversion factor instead of the 50 ng/μL used for dsDNA. Using the wrong factor will overestimate ssDNA by 52%. Also check A260/A280 ratio (pure ssDNA ≈ 0.9–1.0, lower than dsDNA's ~1.8).

Applications of ssDNA

  • Oligonucleotide primers: PCR primers, sequencing primers are ssDNA 18–25 nt
  • Probes: Fluorescent or radioactive ssDNA probes for Southern blotting, FISH, in situ hybridization
  • Aptamers: ssDNA aptamers fold into specific shapes that bind proteins or small molecules with high affinity
  • CRISPR: Single-stranded oligodeoxynucleotides (ssODNs) serve as homology-directed repair templates

ssDNA Viruses

Bacteriophage M13 is a filamentous ssDNA phage widely used for phage display and DNA library construction. Parvovirus B19 (human pathogen) and adeno-associated virus (AAV, gene therapy vector) are also ssDNA viruses.

Glossary

ssDNA (Single-Stranded DNA)
DNA consisting of a single polynucleotide chain without a complementary strand; 1 OD₂₆₀ = 33 μg/mL; more flexible and less stable than dsDNA; forms secondary structures via intrastrand base pairing.
Aptamer
A short ssDNA or RNA sequence selected by SELEX to bind specific molecular targets with high affinity through its folded 3D structure; used in diagnostics, sensors, and therapeutics.
Extinction Coefficient (ssDNA)
The conversion factor relating A260 absorbance to ssDNA concentration: 33 μg/mL per A260 unit (lower than dsDNA's 50 μg/mL due to less base stacking in single-stranded form).

Frequently Asked Questions

ssDNA (single-stranded DNA) is one polynucleotide chain with no complement; dsDNA (double-stranded DNA) is two antiparallel chains held together by Watson-Crick base pairs (A:T, G:C) and base-stacking interactions. dsDNA is more stable and rigid; ssDNA is flexible and susceptible to nuclease degradation. ssDNA can form secondary structures (hairpins, G-quadruplexes) by folding back on itself. For quantification, 1 A260 unit = 50 μg/mL dsDNA but only 33 μg/mL ssDNA — different extinction coefficients.

Select 'ssDNA' in the NanoDrop software — this applies the correct conversion factor of 33 ng/μL per A260 unit (compared to 50 ng/μL for dsDNA). Using the dsDNA setting for ssDNA will overestimate concentration by ~52%. For pure ssDNA, expect A260/A280 ≈ 0.9–1.0 (lower than dsDNA's ~1.8) and A260/A230 > 1.5–2.0. If ratios are outside these ranges, sample may contain RNA, protein, or solvent contaminants that need removal before accurate quantification.

Natural ssDNA occurs: in ssDNA viruses (bacteriophage M13, phi X174; parvovirus B19; AAV); as lagging strand template during DNA replication; in short single-stranded overhangs (3′ and 5′ tails) at replication forks; as denatured ssDNA in melting experiments; in G-quadruplex structures at telomeres and promoters; and as recombination intermediates. Most genomic DNA exists as dsDNA, with transient ssDNA appearing during replication, transcription, and repair processes.

Aptamers are short ssDNA (or RNA) sequences selected to bind specific targets with high affinity and specificity through their 3D folded structure. They are selected by SELEX (systematic evolution of ligands by exponential enrichment) — iterative rounds of binding, selection, and amplification from a large random sequence library. Applications: diagnostic sensors (similar to antibodies but nucleic acid-based), drug delivery, biomarker detection, and therapeutic agents. DNA aptamers are more stable than RNA aptamers and can be chemically modified to resist nucleases.