106 H. GOBIND KHORANA 



them with the letter "d." It may be noted that according to this method 

 the polynucleotide chain is specified in the direction C 3 '-C 5 ' . The reverse 

 procedure, in which the letter "p" at the right terminus indicates a 5'-phos- 

 phate group, has also been used. 4 The former method has recently been 

 adopted by the Editors of The Journal of Biological Chemistry 5 and is used 

 here as well. Such abbreviated names for three oligonucleotides are shown 

 along with the full names below. 



2. Diagrammatic Representations 



The above procedure for the naming of the polynucleotide chain in the 

 direction C 3 '-C 5 ' can be incorporated in diagrammatic representations of 

 polynucleotide chains. These are again very useful in illustrating many 

 chemical and enzymic reactions. 6 ' 7 In these diagrams, a nucleoside is de- 

 picted by a vertical line (the sugar residue) capped with the initial letter of 

 its purine or pyrimidine base. A diagonal line broken by the letter "p," 

 joining the midpoint (C-3' position) of one vertical line with the bottom 

 (C-5' position) of the next vertical line to the right, represents the phospho- 

 diester linkage. A letter "p" at either end of the chain indicates a terminal 

 phosphomonoester group. Furthermore, the 2'-hydroxyl groups in ribopoly- 

 nucleotides as well as any terminal hydroxyl groups in all polynucleotides 

 may be designated by horizontal lines attached to the vertical lines. This 

 designation is consistent with the diagrammatic formulations often used for 

 sugars. 



3. Nomenclature 



A system of nomenclature which is finding wide acceptance 5 has been pro- 

 posed. 8 In this system, following after the generally accepted polypeptide 

 nomenclature, a polynucleotide is considered as a chain in which each nu- 

 cleotide esterifies the hydroxyl function of the succeeding one rather than 

 as a number of nucleosides joined together by phosphodiester bonds. Fur- 

 ther elaboration is, however, necessary, because although the naturally 

 occurring polynucleotides probably all have the C3<-C 5 < internucleotide 

 linkage, synthetic compounds can be made which contain a variety of types 

 of linkage. For the mononucleotides the trivial names, e.g., thymidylic-(5') 

 acid and adenylic-(3') acid are used; the number in parentheses refers to 

 the carbon atom to which the phosphoryl group is attached. The internu- 



4 H. S. Shapiro and E. Chargaff, Biochim. el Biophys. Acta 26, 596 (1957). 



5 See "Use of Abbreviations," J. Biol. Chem. 233 (1958). 



6 L. A. Heppel and J. C. Rabinowitz, Ann. Rev. Biochem. 27, 613 (1958). 



7 L. Shuster, H. G. Khorana, and L. A. Heppel, Biochim. et Biophys. Acta 33, 452 

 (1959). 



8 P. T. Gilham and H. G. Khorana, /. Am. Chem. Soc. 80, 6212 (1958). 



