DNA Structure

DNA is a polymer of deoxyribonucleotides organized into an antiparallel double helix and packaged into chromatin. Its structural features (base composition, strand polarity, helical geometry, and higher-order chromatin organization) determine how genes are replicated, transcribed, and regulated, and they directly shape the spectrum of disease-causing variants observed in clinical genetics.

• Nucleotide composition: Each nucleotide consists of a deoxyribose sugar, a phosphate group, and one of four nitrogenous bases. Purines (adenine, guanine) are double-ringed; pyrimidines (cytosine, thymine) are single-ringed. The mnemonic "PURe As Gold" pairs purines with A and G. Uracil replaces thymine in RNA.
• Phosphodiester backbone and polarity: Nucleotides are joined by phosphodiester bonds between the 3' hydroxyl of one sugar and the 5' phosphate of the next. This gives each strand directional polarity (5' → 3'). DNA polymerase synthesizes only in the 5' → 3' direction, which is why the lagging strand requires Okazaki fragments.
• Double helix and base pairing: Watson-Crick pairing (A-T with 2 hydrogen bonds, G-C with 3 hydrogen bonds) holds the two antiparallel strands together. Higher GC content increases melting temperature (T_m), a property exploited in PCR primer design and methylation analysis. The helix has a wider major groove (where most sequence-specific transcription factor binding occurs) and a narrower minor groove.
• DNA forms: B-DNA is the canonical right-handed helix found under physiological conditions (~10.5 bp/turn, 3.4 Å rise per bp). A-DNA is right-handed and more compact (forms in dehydrated or RNA-DNA hybrid contexts). Z-DNA is left-handed and forms in GC-rich, alternating purine-pyrimidine sequences under negative supercoiling; it is implicated in regulation and genome instability.
• Chromatin organization: DNA is wrapped around histone octamers (two copies each of H2A, H2B, H3, H4) to form the nucleosome, the fundamental unit of chromatin (~147 bp wrapped in 1.65 turns). Histone H1 is the linker histone that stabilizes higher-order folding into the 30-nm fiber, which is further organized into topologically associating domains (TADs) and chromosome territories.
• Euchromatin vs heterochromatin: Euchromatin is loosely packed, gene-rich, and transcriptionally active (light G-bands). Heterochromatin is densely packed and transcriptionally silent. Constitutive heterochromatin (centromeres, telomeres, Yq) is permanently condensed; facultative heterochromatin (e.g., the inactive X / Barr body) is conditionally silenced. This distinction underlies position-effect variegation and explains why translocations into heterochromatin can silence otherwise-active genes.
• Telomeres: Repetitive (TTAGGG)_n sequences at chromosome ends form a t-loop with shelterin complex proteins (TRF1, TRF2, POT1) that prevents end-to-end fusion and recognition as DNA damage. Telomeres shorten with each replication cycle (the "end-replication problem"); critically short telomeres trigger senescence or crisis. Telomerase (TERT catalytic subunit + TERC RNA template) maintains length in germ cells, stem cells, and most cancers.
• Centromeric DNA: Built on tandem alpha-satellite (alphoid) repeats (~171 bp monomers). Centromeric identity is epigenetically defined by the histone H3 variant CENP-A, not by sequence alone. This allows neocentromere formation when canonical centromeres are deleted.
• Repetitive DNA: Roughly half the human genome is repetitive. Tandem repeats (centromeric satellites, telomeric TTAGGG, microsatellites/STRs of 1-6 bp, minisatellites/VNTRs of 10-100 bp) are clustered. Interspersed repeats are dispersed and largely transposon-derived: LINE-1 (~6 kb autonomous retroelements, ~17% of the genome), SINEs including Alu elements (~300 bp, ~10% of the genome), and endogenous retroviruses (LTR elements). Active LINE-1 and Alu insertions cause sporadic disease (e.g., hemophilia A, neurofibromatosis).
• Mitochondrial DNA: A circular, double-stranded, ~16.6 kb genome encoding 13 proteins (all OXPHOS components), 22 tRNAs, and 2 rRNAs. Maternally inherited, lacks introns and protective histones, has a higher mutation rate than nuclear DNA, and exists in many copies per cell, giving rise to heteroplasmy and threshold effects in mitochondrial disease.
• DNA modifications: 5-methylcytosine at CpG dinucleotides is the dominant mammalian DNA modification, concentrated at CpG islands and important for imprinting, X-inactivation, and silencing of repetitive elements. CpG sites are also mutational hotspots: spontaneous deamination of 5-methylcytosine yields thymine, producing C→T transitions that account for ~30% of point mutations in genetic disease.
• Genome size and content: The haploid human genome is ~3.1 Gb, contains ~20,000 protein-coding genes (only ~1.5% of sequence), and is distributed across 22 autosomes plus X/Y. The mitochondrial genome contributes an additional ~16.6 kb per organelle.

• GC-rich regions and sequencing: GC-rich first exons and CpG islands are difficult to amplify and sequence, contributing to coverage gaps in clinical NGS panels (e.g., the GC-rich GBA region complicates Gaucher disease analysis).
• CpG hotspots: CpG dinucleotides represent ~1% of the genome but harbor a disproportionate share of pathogenic point mutations, e.g., recurrent C→T transitions in achondroplasia (FGFR3 c.1138G>A is technically the reverse-strand C→T at a CpG), MEN2 (RET), and many tumor suppressor genes.
• Telomere biology disorders: Germline variants in telomerase components (TERT, TERC) and shelterin/related factors (DKC1, TINF2, RTEL1) cause dyskeratosis congenita and idiopathic pulmonary fibrosis: short telomere syndromes with bone marrow failure, pulmonary disease, and cancer predisposition.
• Repeat expansion disorders: Tandem repeat instability causes >50 disorders, including Huntington disease (CAG, exonic), fragile X syndrome (CGG, 5' UTR), myotonic dystrophy type 1 (CTG, 3' UTR), Friedreich ataxia (GAA, intronic), and C9orf72 ALS/FTD (GGGGCC, intronic). Expansion mechanisms involve replication slippage and stalling at non-B DNA structures (hairpins, G-quadruplexes).
• Structural variation driven by repeats: Segmental duplications and Alu-Alu non-allelic homologous recombination underlie recurrent microdeletion/microduplication syndromes (e.g., 22q11.2 deletion, Charcot-Marie-Tooth 1A duplication of PMP22, Smith-Magenis/Potocki-Lupski 17p11.2).
• Mitochondrial inheritance and heteroplasmy: mtDNA mutations show maternal inheritance and threshold effects: the same variant can produce MELAS, MIDD, or be clinically silent depending on heteroplasmy level. Mitochondrial bottleneck during oogenesis explains rapid shifts in heteroplasmy between mother and child.