Methods and reagents: Is there any sense in antisense terminology? Methods and reagents is a unique monthly column that highlights current discussions in the newsgroup bionet.molbio.methds-reagnts, available on the Internet. This month's column reviews a recent debate held over the present sense and antisense terminology when referring to DNA. For details on how to partake in the newsgroup, see the accompanying box. A huge thread of discussion on bionet.molbio.methds-reagnts recently erupted when two netters adamantly opposed one another on which strand of DNA should be called the sense strand and which one should be called the antisense strand. One netter declared that the DNA strand that bears the same sequence as the mRNA, except with thymine instead of uracil, should be called the sense strand, while the other netter wrote that the accepted convention is the exact opposite - the sense strand of DNA is that which is used as template and transcribed into mRNA, therefore being the anti-parallel complement of the mRNA. The debate over who is using the correct sense terminology essentially grew into an electronic bulletin board virtual conference to decide which it should be. A recent paper stated that `a DNA segment encoding a protein usually has a "sense" strand and a complementary "antisense" strand, which acts as a template for RNA polymerase. Conventionally, the sense strand is considered to encode the protein since it has the same sequence as the mRNA.' [1] However, this so-called convention is still not the standard. From the net discussion, it became clear that many scientists often quote what they believe is convention, but are still confused by the terms `sense' and `antisense' when referring to DNA because the terminology has changed over the years. The evolution of this nomenclature appears mainly to have occurred because of historical reasons, and that during a time when less was understood about the mechanism of information transfer from DNA to RNA, the sense terminology was built on top of the then understood concepts and woven into today's central dogma (DNA -> RNA -> protein). Stephen R. Lasky (Stephen_Lasky@brown.edu) wrote that he was unable to find any textbooks that use the term `sense' for describing the strand of DNA which is the same as the mRNA before 1987, which led him to believe that before this time the convention was the opposite. He is convinced that the definitions had somehow changed in the late 1980s or early 1990s, perhaps as a result of the popularity of the newly developing technique of gene regulation by antisense RNA. Another person wrote that the terms sense and antisense should only be considered as scientific slang and not thought of as defined biochemically. Unfortunately, regardless of whether they are slang words or defined terms, they still change over time, which could leave scientists trained at different times and locations, and with different textbooks, at odds with each other. If scientists are trained differently, they cannot describe what they mean in terms that everyone will understand completely, and the scientific meaning of these terms is lost. This seems to be precisly what has happened. To add to the confusion, discrepancies are found throughout both scientific journals and molecular biology textbooks [2-6]. While some newer textbooks seem to avoid the use of sense and antisense, writers of many biochemistry and molecular biology textbooks apparently have taken on the task of defining these terms for their own purpose. Having devised their own intuitive or logical rules for remembering them, authors of textbooks have littered the reference material with contradictions. The newest version of the molecular biology textbook Genes V by Lewin [7] describes the transcribed (template) strand of DNA as antisense, while two other textbooks published within the last few years [8,9] still refer to the transcribed (template) strand as sense, which might suggest that some authors are not willing to follow suit, or that one or a few are trying to change direction without discussion or having to deal with a formal proposal. Some netters feel that the confusion over sense and antisense is a result of the propagation of wrong terminology by a few biology instructors for whom the original definitions were not intuitive enough. By interpreting the terms for themselves, some think that these teachers probably passed the wrong information on to a whole generation of molecular biology students who took the spoken word over that in the textbooks. The students might not be confused in class and can answer the exam questions as they are taught, but are then trained as the generation who are now believers in the opposite sense-orientation terminology. Whatever the case, without being agreed upon, the contradictions eventually end up back in the textbooks. Because there are good logical threads that allow one to rationalize how each strand could be designated as the sense strand of DNA, the terms become intrinsically confusing. For example, if one begins with the transcribed DNA strand and calls this the sense DNA strand, working forwards through the central dogma leads to the naming of the mRNA as antisense. However, if one begins with the mRNA as sense strand, working backwards to DNA, the transcribed strand becomes the antisense DNA strand. Netters agree that, with respect to messenger RNA, the term antisense in use today to mean a DNA or RNA oligonucleotide complementary to the mRNA expressed from a given gene is perfectly understood as it stands. However, it is the use of sense and antisense with respect to DNA that has its misgivings. To make matters worse, the sense and antisense terminology has been seeping into the protein literature. For example, anti-complementary peptide antibodies those made by transcription of the opposite strand of DNA from that which makes a sense antibody. This is creating a sense versus antisense nightmare for molecular biologists who have already adopted the sense terms for RNA and DNA [10]. Netters were quick to agree that this problem has to be fixed, and that it is of tremendous importance that one system of terms is chosen so that we know exactly which strand is which when describing them, independent of the history of how they were discovered and named. An example of how these terms cause confusion is when authors describe which strand is labeled for an in vitro footprinting experiment. If reference is made to the sense strand, it is completely ambiguous and the data is that much more difficult to interpret. When the huge debate ended and the dust settled, it became apparent that Richard Moldwin's (rmoldwin@midway.uchicago.edu) proposal is probably the best solution to the problem. It was apparent that changing the definition of existing terms would probably be more difficult than adopting a new term. His proposal was that the terminology for the strands of DNA with respect to transcription should therefore be formalized and the use of sense strand for DNA be avoided in future literature. In the simplest terms, one strand of DNA acts as the template for transcription and the other does not. When referring to DNA, the terms should be `transcribed strand' (the anti-parallel complementary strand to the mRNA) of a specific gene and `non-transcribed strand' (the strand with the same sequence as the mRNA) of a specific gene. These can be shortened to the T-strand of gene X and the N-strand of gene X. The T-strand of gene X could also be the N-strand of gene Y if X and Y are read from the same region of the DNA. As the gene is defined, these terms can be used without confusion. The term antisense would be best reserved for RNA so that there is no such conflict. When referring to RNA, messenger RNA read from the T-strand should be designated as sense RNA, and the anti-parallel complement to that message designated as antisense RNA. A vote was then called to see how many netters in methds-reagnts were willing to do away with the old and adopt the new terminology. There was an overwhelming yes vote - 92 people voted by Email, with 87 voting `yes' to adopt this terminology and five voting `no'. In short, netters feel it is time to begin inventing a new terminology and to define the new terms precisely, rather than to continue manipulating the old terminology to fit a new era of genetics. The virtual in promptu committee therefore voted for the removal of the words sense and antisense from any description of the two strands of DNA. Whether this unconventional electronic meeting and the members' decision to adopt this terminology will be taken seriously and whether it will now become the future standard remains to be seen (see the following article). One problem that still exists, however, is what should be done with all the existing textbooks so that they are now in agreement. If this proposal is adopted by the scientific population as a whole, then unfortunately many of the books currently in the library will become officially outdated. However, in such a rapidly changing field this is inevitable. It is my sincere hope that all the effort put into the net discussion and the vote tally will prompt a ripple effect and perhaps result in ousting the `S'-word with respect to DNA from the scientific literature. If it does, it could mark the beginning of an electronic conferencing era in which many soft and distant voices can combine to transform new ideas proposed on the net from virtual to reality. References ********** [1] Forsdyke, D. R. (1995) J. Mol. Evol. 41, 582-586 [2] Tanaka, Y. and Macer, D. (1994) Trends Genet. 10, 417-418 [3] Coddington, A. (1995) Trends Genet. 11, 124 [4] Sam, M. (1995) Trends Genet. 11, 124 [5] Cornelius, G. (1995) Trends Genet. 11, 125 [6] Macer, D. and Tanaka, Y. (1995) Trends Genet. 11, 125 [7] Lewin, B. (1994) Genes V, p. 163, Oxford [8] Mathews, C. K. and van Holde, K. E. (1990) Biochemistry, p. 920, Benjamin/Cummings [9] Gardner, E. J., Simmons, M. J. and Snustad, D. P. (1991) Principles of Genetics, p. 255, John Wiley and Sons [10] Blalock, J. E. (1995) Nat. Med. 1, 876-878 PAUL N. HENGEN National Cancer Institute, Frederick Cancer Research and Development Center, Frederick, MD 21702-1201, USA. email: pnh@ncifcrf.gov The Nomenclature Committee of the IUBMB comment: The argument over the pairs coding/non-coding, sense/nonsense and transcribing/non-transcribing already existed in the late 1980s, and was raised with the Nomenclature Committee of International Union of Biochemistry (NC-IUB) in 1988. The view of NC-IUB at that time was that `the word "coding" refers to the relationship between nucleic acids and proteins, rather than the mere transcription of DNA into RNA', and that therefore `it is logical to call the strand with the mRNA sequence the coding strand'. NC-IUB also felt that the pair coding/non-coding was the least liable to misinterpretation of the three mentioned (at that time the pair sense/antisense had not become widely enough used to be included in the argument). These points were set out (at somewhat greater length) in the Newsletter of JCBN and NC-IUB for 1989 (Refs 1-5), and have been reproduced more recently in the Compendium of Biochemical Nomenclature and Related Documents (Ref. 6). Although the 1989 recommendation is consistent with the proposal to eliminate the terms sense and antisense from use for DNA strands, as discussed in Dr Hengen's column, the proposed Transcribed Strand and Non-Transcribed Strand are sufficiently similar to transcribing and non-transcribing strands that they should not be considered as completely new terms. It would be over-optimistic to think that introducing them will eliminate all confusion. None of this means, of course, that the matter was settled once and for all in 1989, and a further discussion is on the agenda of the forthcoming meeting of NC-IUBMB in May. Any comments stimulated by Dr Hengen's column will be welcome, and may be addressed to Dr Barry Whyte, Secretary of NC-IUBMB, Editorial Office, European Journal of Biochemistry, Postfach, Kleinstrasse 6, CH-8032 Zurich, Switzerland. These should arrive before the end of April if they are to be taken into account. References ********** [1] NC-IUB (1989) Arch. Biochem. Biophys. 272, 262-266 [2] NC-IUB (1990) Biochem. Internat. 20, 209-214 [3] NC-IUB (1989) Biochem. J. 265, I-IV [4] NC-IUB (1989) Biol. Chem. Hoppe-Seyler 370, 1153-1156 [5] NC-IUB (1989) Eur. J. Biochem. 183, 1-4. [6] IUBMB (1992) Biochemical Nomenclature and Related Documents (2nd edn.), p. 334, Portland Press ATHEL CORNISH-BOWDEN Chairman, NC-IUBMB and JCBN, Laboratoire de Chimie Bacterienne, Centre National de la Recherche Scientifique, 31 chemin Joseph-Aiguier, B.P. 71, 13402 Marseille Cedex 20, France ******************************************************************************* Any statements made by the author are not meant to advocate the use of a particular commercial product or endorse any company. All opinions are those of the author and do not reflect the opinion of the National Cancer Institute or the National Institutes of Health. Copyright: This manuscript is not copyrighted by Elsevier Publishing Company. However, you may not reproduce any portion for resale or edit the text for redistribution, sale, or otherwise without written permission from the author. You found this at the World Wide Web (WWW) Uniform Resource Locator (URL) ftp://ftp.ncifcrf.gov/pub/methods/TIBS/apr96.txt Any reference to this column must be cited as the following published article: Hengen, P. N. 1996. Methods and reagents - Is there any sense in antisense terminology? Trends in Biochemical Sciences 21(4):153-154. ******************************************************************************* * Paul N. Hengen, Ph.D. /--------------------------/* * National Cancer Institute |Internet: pnh@ncifcrf.gov |* * Laboratory of Mathematical Biology | Phone: (301) 846-5581 |* * Frederick Cancer Research and Development Center| FAX: (301) 846-5598 |* * Frederick, Maryland 21702-1201 USA /--------------------------/* *******************************************************************************