| Criteria | Plasmid DNA | Chromosomal DNA | Remarks |
| Definition | Small, circular, double-stranded extrachromosomal DNA molecule found mainly in bacteria and some eukaryotes | Large, linear (or circular in prokaryotes) double-stranded DNA that constitutes the primary genome | Plasmids are accessory genetic elements, while chromosomes carry essential genetic information for survival. |
| Structure | Circular (mostly), double-stranded | Linear in eukaryotes; circular in prokaryotes | Structural variation contributes to function and replication strategy. |
| Size | Small (typically 1–200 kb) | Large (millions to billions of base pairs) | Chromosomal DNA is vastly larger and more complex than plasmid DNA. |
| Location in Cell | Cytoplasm (prokaryotes), sometimes in organelles (e.g., mitochondria, chloroplasts in eukaryotes) | Nucleoid (prokaryotes), nucleus (eukaryotes) | Spatial distribution reflects functional segregation in cells. |
| Replication | Independent of chromosomal DNA, via its own origin of replication (Ori) | Replicates during the cell cycle (S-phase in eukaryotes), coordinated with cell division | Plasmid replication is often autonomous and not cell-cycle dependent. |
| Genes Carried | Non-essential but advantageous genes, e.g., antibiotic resistance, virulence factors, metabolic traits | Essential genes for cell survival, metabolism, growth, and reproduction | Plasmids enhance adaptability; chromosomes carry core life-sustaining genes. |
| Copy Number | Varies; can be single-copy or multicopy (10–100+ copies per cell) | Typically one per cell (diploid cells have two homologous copies) | High-copy plasmids increase gene dosage, useful in genetic engineering. |
| Inheritance | Random or selective segregation during cell division | Strictly regulated inheritance during cell division | Plasmid inheritance may be incomplete or variable across generations. |
| Stability | Less stable; can be lost if not under selection pressure | Highly stable, retained across cell generations | Plasmid loss can occur in the absence of selective conditions, unlike chromosomes. |
| Horizontal Gene Transfer | Frequently transferred via conjugation, transformation, or transduction | Rare; usually transferred vertically from parent to offspring | Plasmids are key players in horizontal gene transfer and microbial evolution. |
| Transcription & Translation | Transcribed like chromosomal DNA, often under different regulatory control | Transcribed and translated under complex, tightly regulated systems | Plasmids may have independent or host-controlled promoters. |
| Presence in Organisms | Found in bacteria, some archaea, yeast, and rarely in higher eukaryotes | Universally present in all organisms | Chromosomal DNA is universal; plasmid DNA is more selective in distribution. |
| Role in Biotechnology | Widely used as vectors for cloning, gene expression, and recombinant protein production | Source of endogenous genes, genomic studies, and gene therapy targets | Plasmids are engineered for experimental and therapeutic use due to ease of manipulation. |
| Functional Importance | Auxiliary; provides competitive advantages under specific conditions | Essential for cell viability and fundamental cellular processes | Plasmid functions are dispensable under non-selective conditions, while chromosomal DNA is indispensable. |
| Packaging Proteins | Usually not associated with histones (in prokaryotes) | Associated with histones in eukaryotes or histone-like proteins in prokaryotes | Packaging differs significantly between chromosomal and plasmid DNA, especially in eukaryotes. |
| Mutational Consequences | Mutations may alter specific traits (e.g., antibiotic resistance), often without affecting viability | Mutations can be lethal or cause severe dysfunction | Chromosomal mutations have broader and more critical cellular implications. |
| Detection Techniques | Isolated by plasmid miniprep methods; detectable via gel electrophoresis, restriction digestion, or PCR | Requires genomic DNA extraction; analyzed via karyotyping, sequencing, or hybridization | Different methods are used based on DNA source, size, and research purpose. |
