The discipline of Molecular Biology investigates information processing pathways in living cells, identifying the key players that synthesize our genetic blueprint – the deoxyribonucleic acid (DNA) molecule – and subsequently ​‘express’ it into ribonucleic acid (RNA) and protein molecules – a process termed ​‘gene expression’. While it is fascinating to explore nature’s information-processing pathways, reading through molecular biology textbooks could be a daunting task for a rookie undergraduate not acquainted with the terminology used. 

Different books use synonymous nomenclature interchangeably, making it difficult to differentiate between terms like ​‘sense/​antisense’, ​‘coding/​non-coding’, ​‘template/​non-template’. The complementary base pairing of nucleotides and the anti-parallel nature of DNA strands add a further layer of complexity. This especially poses a challenge for students referring to multiple textbooks in their course of study. Those unable to make the right connections run the risk of incorrectly interpreting the fundamental processes of life. This article is the first in a two-part series that addresses some of the most common misconceptions in undergraduate molecular biology.

Misconception 1:

Only one strand of DNA is used to synthesize RNA.

This statement occurs in most textbooks leaving students with the notion that at all times, only one entire strand of DNA from the two strands in the duplex is transcribed into RNA, while the other strand is inert and has no role to play. This leads to an incorrect understanding of the process of ​‘transcription’. I first realized this when a student, having completed the assigned reading, asked me, ​“So, if only one strand of DNA is used for making RNA, what does the other strand do? Are there no genes present on this strand?” Since then, I make it a point to ask this very question in class to check whether students have thought about it at all and ensure to fill the gap in their understanding by means of a simple blackboard exercise.

Correct Concept:

Only one strand of the DNA duplex is used to synthesize RNA at a given time in a given region of the DNA.

Different regions of the DNA express at different stages in the life of a cell. Nucleic acid hybridization experiments have provided evidence for the same. When a particular region of the DNA is being transcribed, the strand of the DNA that is used to make a complementary RNA is termed the ​‘template’ strand. At the same time, the other strand in the same region is NOT transcribed, and is therefore termed the ​‘non-template’ strand. The latter strand may, however, act as the template strand in a different region of the DNA or at a different time in the same region. 

Figure 1 depicts a scenario where genes A and C partially overlap with genes B and D, respectively, on the opposite strand. Strand – 1 is the template strand for genes A and C, whereas strand – 2 is the template strand for genes B and D. When strand – 1 is being used for RNA synthesis from gene A, its complementary region on strand – 2 cannot be used to transcribe gene B. However, strand – 2 can be used at the same time to transcribe gene D (Fig.1, Possibility – 1). Alternatively, when gene A is being transcribed from strand – 1, at the same time, a different region on strand – 1 can be used to synthesise gene C (Fig. 1, Possibility – 2). Further, gene B can be transcribed at a different time when gene A is not being transcribed. The possible combinations of simultaneous gene transcriptions are listed in Table 1. 

Why is this so?

If the complementary regions on both strands of DNA were to be transcribed simultaneously, the two RNA molecules thus formed would pair with each other due to their complementary nature. They would thus not be available for protein synthesis (translation) (Figure 2a).

Further, if such regions were to be transcribed and translated, the two proteins synthesized would have completely different amino acid sequences (Figure 2b). They would be two completely different proteins with distinct functions. If nature were to optimize the function of one protein by modifying the DNA sequence encoding it, this would result in a corresponding change in the nucleotide sequence on the complementary DNA strand, thus changing the sequence and modifying the function of the protein encoded by that strand. Hence, a change in the coding region of one DNA strand would be possible only at the expense of a corresponding change in the coding region of the other strand. It would therefore not be possible to optimize the function of both proteins simultaneously – an evolutionary disadvantage to the cell. These are probably the reasons why nature favours transcription from only one strand of a region of DNA at a time and the occurrence of overlapping genes (like genes A and B in Fig. 1) is rare.

To aid visualization of these concepts, I write actual nucleic acid sequences on the blackboard and walk students through DNA –> RNA –> polypeptide synthesis (Figures 2a and 2b). Given a duplex DNA sequence, students are expected to transcribe it to the corresponding mRNA and translate the mRNA to the corresponding peptide sequence using the standard genetic code. This in-class exercise has helped greatly in clarifying doubts.

Misconception 2:

The ​‘sense’, ​‘coding’ and ​‘template’ strands of DNA are the same.

The ​‘antisense’, ​‘noncoding’ and ​‘non-template’ strands of DNA are the same.

Students incorrectly interpret that the ​‘sense’ strand of DNA is used to synthesize mRNA that finally encodes the protein, therefore it is called the ​‘template’ or ​‘coding’ strand. The other strand is the ​‘non-template’ or ​‘antisense’ or ​‘non-coding’ strand and has no role to play in the transcription process.

This is apparent from a simple exercise of presenting the sequence of a DNA duplex and the mRNA sequence corresponding to any one strand, and asking students to appropriately name the strands (Figure 3). In my experience, most students confuse the nomenclature since their understanding of the concept behind the definitions is not clear.

Correct Concept:

This is a classic example of ​‘too many cooks spoil the broth’ wherein the use of several alternative terms interferes with the correct understanding of the associated concept. Further, the terms are not all synonymous. Students mistakenly club them together – all positive-sounding terms in one group and their opposites in another. 

As defined earlier, in the region being transcribed, the ​‘template’ strand refers to that strand of DNA being used to synthesize RNA. The sequence of the newly synthesized RNA is, therefore, complementary to that of the template strand.

On the other hand, the non-template strand is also termed the ​‘sense’ strand since its nucleotide sequence is identical to that of the synthesized RNA, with the exception of U replacing T in RNA. Nature makes ​‘sense’ of the information coded in the DNA. In turn, the sequence of RNA (if it is mRNA), read as triplet codons, dictates the specific sequence of amino acids in the protein being translated from it. Extrapolating back to DNA, the ​‘sense’ strand contains the genetic code for making the RNA and the corresponding protein, and hence, is also known as the ​‘coding’ strand. It is important to note that the sense/​coding strand of the DNA is not transcribed. It is the same as the ​‘non-template’ strand discussed above. By corollary, the ​‘template’ strand is known as the ​‘antisense’ or ​‘non-coding’ strand.

The equalities in terms of nomenclature, therefore become:

• Template = Transcribed = Antisense = Non-coding strand = complementary in sequence to the synthesized RNA

• Non-template = Non-transcribed = Sense = Coding strand = same sequence as synthesized RNA (T replaced with U in RNA)

This can be understood better using actual nucleotide sequences (Figure 3).

The above are only a couple of common misconceptions that students of molecular biology have with respect to the transcription process. In the next article in the series, we will discuss some of the misconceptions about protein translation.