Definition and General Characteristics of Nucleic Acids
Nucleic acids are high-molecular-weight compounds whose monomers are nucleotides. Based on the type of carbohydrate component, two classes are distinguished:
- RNA (ribonucleic acids) contain D-ribose;
- DNA (deoxyribonucleic acids) contain 2-deoxy-D-ribose.
Each nucleotide includes three components: a phosphoric acid residue, a pentose, and a nitrogenous base.
Nitrogenous Bases and Nucleosides
Nitrogenous bases are divided into two groups:
- Purines — adenine (A) and guanine (G); mnemonic "purGA";
- Pyrimidines — cytosine (C), thymine (T, found only in DNA), and uracil (U, found only in RNA).
The pyrimidine ring consists of 6 atoms, while the purine ring consists of condensed 5- and 6-membered rings. Bases with a hydroxyl group on the carbon atom adjacent to a ring nitrogen are characterized by keto-enol (lactim-lactam) tautomerism. In the lactam form, the bases retain aromaticity, a planar structure, and high thermodynamic stability.
Minor bases are modified forms of canonical bases: inosine (an intermediate in purine metabolism), dihydrouridine, 5-methylcytosine, 7-methylguanosine, etc.
Nucleoside — an N-glycoside of a nitrogenous base and a pentose (linkage — N-glycosidic). Natural nucleosides are β-anomers and exist in syn and anti conformations. The pentose ring adopts C2-endo/exo or C3-endo/exo conformations. Nucleotide — a phosphoric ester of a nucleoside (esterification at the 5′- or 3′-carbon atom, ester bond).
Cyclic nucleotides (3′,5′-cAMP, cGMP) act as secondary messengers in cellular signal transduction.
Nucleotide-Based Coenzymes: NAD and FAD
NAD (nicotinamide adenine dinucleotide) exists in oxidized (NAD⁺) and reduced (NADH) forms. Main functions:
- participation in oxidation-reduction reactions of glycolysis, the Krebs cycle, and the electron transport chain;
- energy metabolism — NADH transfers electrons to the ETC, ensuring ATP synthesis;
- signaling function — substrate for sirtuins, synthesis of cyclic ADP-ribose;
- DNA repair — substrate for the enzyme PARP (poly(ADP-ribose) polymerase), which is involved in repairing single-strand breaks.
FAD (flavin adenine dinucleotide) and its reduced form FADH₂ act as electron and proton acceptors/donors in the Krebs cycle, oxidative phosphorylation, and a number of dehydrogenase reactions.
Primary Structure and Chargaff's Rules
Primary structure — the sequence of nucleotides connected by phosphodiester bonds. Three types of DNA sequences are distinguished in the eukaryotic genome:
- unique sequences (~60%) — encode specific proteins;
- moderately repetitive sequences (10–25%, tens to hundreds of copies) — tRNA, rRNA, and histone genes;
- highly repetitive sequences (>100 copies) — centromeric satellite DNA, involved in chromosome distribution during mitosis and meiosis.
Chargaff's rules:
- the sum of purines equals the sum of pyrimidines: A+G = T+C;
- molar ratios: A = T, G = C (for double-stranded DNA);
- specificity coefficient (G+C)/(A+T): for DNA, it is usually <1 (AT-type predominates); for RNA, it is usually >1 (GC-type).
Secondary Structure of DNA and RNA
The secondary structure is stabilized by hydrogen bonds between complementary base pairs (Watson-Crick pairs A=T and G≡C of antiparallel strands), stacking interactions, and electrostatic forces. Stacking strength decreases in the order: purine–purine > purine–pyrimidine > pyrimidine–pyrimidine.
Main forms of the DNA double helix:
- B-form — right-handed, diameter ~20 Å, 10 base pairs per turn, pitch 3.4 Å;
- A-form — right-handed, wider (26 Å), 11 base pairs per turn;
- Z-form — left-handed, 18 Å, 12 base pairs per turn, pitch 3.7 Å.
Non-canonical Hoogsteen pairs can form under alternative bonding geometries, resulting in, for example, triple helices. Features of the three-dimensional organization of DNA include bends (≥4 adenosine residues), palindromes and inverted repeats (hairpins, cruciforms), mirror repeats, and supercoiling, which is maintained by topoisomerases.
The secondary structure of RNA is formed by hairpins and loops via A–U and G–C base pairs. Key tRNA elements include the acceptor stem, anticodon loop, dihydrouridine loop, pseudouridine loop, and variable loop. Hairpins are involved in codon recognition, rho-independent transcription termination, translation initiation, and ribozyme catalytic activity. Pseudoknots are considered part of the broader definition of secondary structure.
Tertiary Structure and DNA Packaging
Tertiary structure refers to the spatial arrangement of secondary structure elements. In prokaryotes and viruses, this is achieved through supercoiling; in eukaryotes, it occurs via complexes with histone proteins rich in lysine and arginine. These include the linker histone H1 and core histones H2A, H2B, H3, and H4, which undergo methylation, acetylation, and ADP-ribosylation.
Levels of eukaryotic DNA packaging:
- Nucleosome level — 1.65 turns of DNA around the core; ~7× compaction;
- Solenoid level — condensation of nucleosomes mediated by H1; ~100× compaction;
- Loop level — 30 nm fibers form loops on a protein scaffold;
- Scaffold (folded-fiber) level — further condensation of loops; overall ~10,000× compaction.
The tertiary structure of RNA is formed through interactions between helical regions and is additionally stabilized by divalent metal ions, primarily Mg²⁺.
Physicochemical Properties of DNA
- Denaturation — rupture of hydrogen bonds and strand separation upon heating, pH changes, exposure to formamide, or mechanical stress;
- Renaturation (annealing) — restoration of the double helix upon slow cooling or removal of denaturing agents;
- Hybridization — spontaneous formation of complementary pairs between strands;
- Hyperchromic effect — increase in solution optical density upon denaturation due to the disruption of hydrogen bonds;
- UV absorption at 260 nm — the basis for spectrophotometric determination of concentration;
- High viscosity — a consequence of high molecular weight and helical structure;
- Reactivity — hydrolysis, alkylation, oxidation, methylation.
Types of RNA and Their Localization
- Messenger RNA (mRNA) — single-stranded, carries genetic information from DNA to ribosomes;
- Transfer RNA (tRNA) — a short molecule containing an anticodon, delivers amino acids to the ribosome;
- Ribosomal RNA (rRNA) — structural and functional component of ribosomes;
- MicroRNA (miRNA) — short regulators of gene expression that suppress mRNA translation;
- Long non-coding RNA (lncRNA) — involved in gene expression regulation and epigenetic processes.
RNA is predominantly single-stranded, carries a negative charge due to phosphate groups, and is capable of forming secondary and tertiary structures. Localization: nucleus (transcription, rRNA biogenesis), cytoplasm (mRNA, tRNA, rRNA on ribosomes), mitochondria, and chloroplasts, which possess their own RNA synthesis system.
Key points
- Nucleotide = nitrogenous base + pentose + phosphate; nucleoside — without phosphate.
- Purine bases (A, G) and pyrimidine bases (C, T, U); thymine is found only in DNA, uracil only in RNA.
- NAD and FAD are nucleotide coenzymes, electron and proton carriers; NAD participates in DNA repair via PARP.
- Chargaff's rules: A=T, G=C; the (G+C)/(A+T) ratio characterizes the type of nucleic acid.
- The DNA double helix exists in B-, A-, and Z-forms; it is stabilized by hydrogen bonds and base stacking.
- Levels of eukaryotic DNA packaging: nucleosome → solenoid → loops → scaffolds; compaction is ~10,000×.
- Denaturation is accompanied by a hyperchromic effect — an increase in absorbance at 260 nm.
- Main types of RNA: mRNA, tRNA, rRNA, miRNA, lncRNA — differ in function and localization.