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. Author manuscript; available in PMC: 2014 Mar 9.
Published in final edited form as: Methods Mol Biol. 2013;1068:71–92. doi: 10.1007/978-1-62703-619-1_6

Table 1.

Summary of ascarosides found in wild-type (N2) C. elegans culture medium that have had their structures confirmed through chemical synthesisa

Structure-based name Other name(s) Orig. ref. Mol. formula [M+Na]+ [M−H]− n R Structure
Ascarosides with a saturated fatty acid side chain that is attached to the sugar at the penultimate (ω–1) carbon graphic file with name nihms-556974-t0004.jpg
asc-C4 ascr#11 [7] C10H18O6 257.1001 233.1025 1 H
asc-C5 ascr#9 [7,8] C11H20O6 271.1158 247.1182 2 H
IC-asc-C5 indolecarboxyl-
 ascaroside C5;
 ascaroside C5; icas#S		 [6] C20H25NO7 414.1529 390.1553 2 IC
OS-asc-C5 osas#9 [9] C23H33NO10 506.2002 482.2026 2 OS
asc-C7 daumone 1; ascr#l;
 ascaroside C7		 [1] C13H24O6 299.1471 275.1495 4 H
IC-asc-C7 icas#l [7,8] C22H29NO7 442.1842 418.1866 4 IC
asc-C9 ascr#10 [7,8] C15H28O6 327.1784 303.1808 6 H
Ascarosides with an α,β-unsaturated (Δ) fatty acid side chain that is attached to the sugar at the penultimate (ω–1) carbon
asc-ΔC7 ascr#7 [5] C13H22O6 297.1314 273.1339 2 H graphic file with name nihms-556974-t0005.jpg
IC-asc-ΔC7 icas #7 [7,8] C24H33NO7 440.1685 416.1709 2 IC
asc-ΔC9 ascaroside C9;
 ascr#3; daumone 3		 [2] C15H26O6 325.1627 301.1651 4 H
IC-asc-ΔC9 icas#3 [7,8] C24H31NO7 468.1998 444.2022 4 IC
HB-asc-ΔC9 hbas#3 [7] C22H30O8 445.1838 421.1862 4 HB
MB-asc-ΔC9 mbas#3 [7] C20H32O7 407.2046 383.2070 4 MB
Ascarosides with a side chain that is attached to the sugar at the penultimate (ω–1) carbon and terminates in a methyl ketone (MK)b
asc-C6-MK ascaroside C6;
 ascr#2; daumone 2		 [2] C12H22O5 269.1365 n.a. 2 H graphic file with name nihms-556974-t0006.jpg
Glu-asc-C6-MK ascr#4; daumone 4 [4] C18H32O10 431.1893 n.a. 2 Glu
Ascarosides with a saturated fatty acid side chain that is attached to the sugar at the terminal (ω) carbon
asc-ωC3 ascaroside C3; ascr#5;
 daumone 5		 [3] C9H16O6 243.0845 219.0869 1 – graphic file with name nihms-556974-t0007.jpg
asc-ωC5 oscr#9 [7] C11H20O6 271.1158 247.1182 3 –
asc-ωC9 oscr#10 [7] C15H28O6 327.1784 303.1808 7 –
Ascarosides with an α,β-unsaturated (Δ) side chain attached at the penultimate (ω–1) carbon and linked to p-aminobenzoic acid (PABA)
asc-ΔC7-PABA ascr#8 [5] C20H27NO7 n.a. 392.1709 2 - graphic file with name nihms-556974-t0008.jpg
R group definitions:
graphic file with name nihms-556974-t0009.jpg graphic file with name nihms-556974-t0010.jpg graphic file with name nihms-556974-t0011.jpg graphic file with name nihms-556974-t0012.jpg graphic file with name nihms-556974-t0013.jpg

The structure-based name given in the first column assumes that the canonical ascaroside structure is an ascaroside with a saturated fatty acid side chain that is attached to the sugar at the penultimate (ω–1) carbon. Deviations from the canonical structure are indicated such that each name conforms to the following: (modifications to the sugar)-asc-(deviations in the fatty acid)C#-(modifications at the end of the fatty acid)

Modifications to the sugar and their abbreviations are listed at the bottom of the table. Deviations in the fatty acid include attachment of the fatty acid to the sugar at the terminal (to) carbon, instead of penultimate (ω-1) carbon, as well as α-β (Δ) unsaturation of the fatty acid. Modifications at the end of the fatty acid include the methyl ketone (MK) moiety and addition of p-aminobenzoic acid (PABA)

a

Many other ascarosides, such as asc-C6 (ascr#12), asc-C8 (ascr#14), IC-asc-C9 (icas#10), asc-Cll (ascr#18), asc-ωCll (oscr#18), asc-C12 (ascr#20), OS-asc-C9 (osas#10), and OS-asc-C6-MK (osas#2), have also been detected in wild-type C. elegans culture medium, but their structures have not yet been fully confirmed through chemical synthesis [7-9]

b

Reduced versions of asc-C6-MK (ascr#6.1 and ascr#6.2) with a hydroxyl instead of a ketone have also been reported [5]