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Deoxyribose

This article is about the naturally occurring d-form of deoxyribose. If you’re looking for the l-form, that’s a different beast entirely; see L-deoxyribose for that particular, and far less relevant, detour.

d-Deoxyribose

Names

The official designation, according to the International Union of Pure and Applied Chemistry, is 2-Deoxy-d-ribose. It’s a mouthful, I know. More formally, it’s referred to as 2-Deoxy-d-erythro-pentose. Don’t let the fancy nomenclature fool you; it’s just a more precise way of saying it’s a five-carbon sugar with a specific arrangement of atoms. Other, less formal names include aldehydo-2-Deoxy-d-ribose and, rather quaintly, Thyminose. Apparently, someone thought it looked like thymine. Humans.

Identifiers

For those who track these things with obsessive precision:

  • CAS Number: 533-67-5. If you need to reference it in a lab report or, I don’t know, a black market transaction, this is your number.
  • ChEBI: CHEBI:28816. Another identifier, presumably for cataloging purposes.
  • ChemSpider: 4573703. More numbers. Fascinating.
  • EC Number: 208-573-0. For the enzymes that might interact with it, perhaps.
  • PubChem CID: 5460005. Just another way to find it in the digital ether.
  • UNII: LSW4H01241. Because clearly, we didn't have enough ways to identify this molecule.
  • CompTox Dashboard (EPA): DTXSID60190259. The government’s way of keeping tabs, I suppose.
  • InChI: InChI=1S/C5H10O4/c6-2-1-4(8)5(9)3-7/h2,4-5,7-9H,1,3H2/t4-,5+/m0/s1. This is the one that actually means something if you’re trying to draw it out or build it. It’s a string of characters that defines its structure. The mirrored version, InChI=1/C5H10O4/c6-2-1-4(8)5(9)3-7/h2,4-5,7-9H,1,3H2/t4-,5+/m0/s1, is for the less common form.
  • SMILES: C(C=O)C@@HO. A more compact way to represent the molecule’s structure, useful for computational chemistry.

Properties

  • Chemical formula: C₅H₁₀O₄. It’s a small molecule, unassuming.
  • Molar mass: 134.131 g·mol⁻¹. For stoichiometric calculations, if you’re into that sort of thing.
  • Appearance: White solid. About as exciting as a blank page.
  • Melting point: 91 °C (196 °F; 364 K). It melts at a respectable, though not particularly dramatic, temperature.
  • Solubility in water: Very soluble. It dissolves readily. Unlike some people I know.

Unless otherwise specified, all data are presented under standard conditions: 25 °C, 100 kPa. Y for verification, N for not verified. You can check this yourself if you’re truly that invested.

Chemical Compound

Deoxyribose, or more accurately, 2-deoxyribose, is a monosaccharide. Its idealized formula is H−(C=O)−(CH₂)−(CHOH)₃−H. The name itself is a clue: it’s a deoxy sugar, meaning it’s derived from the sugar ribose by the simple, yet profound, act of losing a hydroxy group. Discovered by Phoebus Levene in 1929, its true significance lies in its fundamental role within DNA. Now, the names arabinose and ribose, differing only in the stereochemistry at C2′, might seem interchangeable, leading one to believe 2-deoxyribose and 2-deoxyarabinose are the same. This is a common oversight. The latter term is seldom used because ribose, not arabinose, is the actual precursor in this biological pathway.

Structure

The formula H−(C=O)−(CH₂)−(CHOH)₃−H can, in theory, represent several isomers. Deoxyribose, however, adheres to a specific configuration: in its Fischer projection, all the hydroxyl groups are aligned on the same side. The term "2-deoxyribose" itself can be ambiguous, referring to either the biologically dominant d-2-deoxyribose or its mirror image, the rarely encountered l-2-deoxyribose. It's d-2-deoxyribose that serves as the crucial building block for DNA, the nucleic acid that carries our genetic code. Chemically, it’s classified as an aldopentose – a monosaccharide composed of five carbon atoms and featuring an aldehyde functional group.

When dissolved in water, deoxyribose doesn’t maintain a single form. It exists in a dynamic equilibrium between three structures: the linear form, H−(C=O)−(CH₂)−(CHOH)₃−H, and two distinct ring structures. One is the five-membered deoxyribofuranose ring (often described as "C3′-endo"), and the other is the six-membered deoxyribopyranose ring (termed "C2′-endo"). Interestingly, in aqueous solutions, the six-membered ring form is the more prevalent one. This contrasts with ribose, where the five-membered ring is favored.

The chemical equilibrium of deoxyribose in solution is a complex dance of molecular configurations, a subtle interplay that dictates its reactivity and function.

Biological Importance

As an integral component of DNA, derivatives of 2-deoxyribose play an undeniably vital role in the tapestry of life. The very molecule of DNA, or deoxyribonucleic acid, which acts as the primary archive for genetic information, is constructed from a linear sequence of units. These units, known as nucleotides, incorporate deoxyribose and are linked together by phosphate groups. In the standardized system of nucleic acid nomenclature, a DNA nucleotide comprises a deoxyribose molecule, to which an organic base—typically adenine, thymine, guanine, or cytosine—is attached at the 1′ carbon of the ribose sugar. The 5′ hydroxyl group of each deoxyribose unit is replaced by a phosphate group, which then connects to the 3′ carbon of the deoxyribose unit in the preceding nucleotide, forming the characteristic phosphodiester backbone.

The absence of the 2′ hydroxyl group in deoxyribose is not a mere chemical detail; it appears to be the reason for DNA’s greater mechanical flexibility compared to RNA. This flexibility is crucial, allowing DNA to adopt the stable double-helix conformation, and in eukaryotes, to be meticulously coiled and packed within the confined space of the cell nucleus. Furthermore, double-stranded DNA molecules are typically far longer than their RNA counterparts. While the backbones of RNA and DNA share structural similarities, RNA is single-stranded and utilizes ribose instead of deoxyribose.

Beyond its structural role in DNA, other biologically significant deoxyribose derivatives include its mono-, di-, and triphosphates, as well as 3′-5′ cyclic monophosphates, each with their own specific functions in cellular processes.

Biosynthesis

The generation of deoxyribose from ribose 5-phosphate is a precisely controlled enzymatic process. It is orchestrated by a class of enzymes known as ribonucleotide reductases, which expertly catalyze the deoxygenation reaction, effectively removing an oxygen atom to form the deoxy form.

Angiogenesis

Intriguingly, deoxyribose has demonstrated pro-angiogenic properties. In a study involving rats, when applied topically in a gel formulation to wounds, it was observed to promote the formation of new blood vessels. [7] Furthermore, this same gel formulation showed an increase in Vascular Endothelial Growth Factor (VEGF) levels, a factor implicated in hair growth. [8] This discovery holds potential for the development of future therapeutic products aimed at addressing hair loss in humans. It’s not just inert building material, apparently.