A concise review article on DNA structure, replication and RNA synthesis (Transcription)
The discovery of the structure of deoxyribonucleic acid (DNA) by Watson and Crick was a major step forward event in the medical science. This finding enabled many researchers and scientists to propose new methods of genetic therapies for human diseases. Before Watson-Crick proposal of the DNA molecule, many experimenters studied the field of DNA and described that DNA molecule is the hereditary material. However, it was the collaborative effort of scientists such as Rosalind Franklin, Maurice Wilkins and finally until the publication of the DNA structure in 1953 by Watson and Crick who elucidated that DNA is a ‘double helix' that stores genetic information. The famous Watson-Crick tin and wire model of the DNA illustrated that this double helical molecule also consists of a hydrogen-bond with complementary base pairs and the chains run opposite or antiparallel to each other. This report will briefly explain this fundamental discovery, the DNA structure, and replication; and will also understand how DNA is an important factor in the making of new strands in the process of ribonucleic acid (RNA) synthesis or transcription.
Over a half-century ago, a collaborative effort by various groups of scientists from different academic backgrounds was underway to unveil the mystery of life. Early experiments were focused mostly on proteins and nucleic acids, and that cells contained several different types of these molecules (Cox 2009). However, scientists could not conclude which molecule had the capacity to carry hereditary information and have the ability to be copied into new cells (Lewis 2005). The answer to this mysterious question was not known until this century's profound discovery of all time; D.N.A (short for deoxyribonucleic acid) (Lewis 2005). DNA is one of the most famous and an ongoing studied molecule in the world today. However, DNA became an interesting subject of discovery by scientists rather late in the history of biology (Sinden 1994, Raven et al., 2008). To be fair, others such as Gregor Mendel had had inklings of the underlying regularities of heredity information almost a century before DNA was discovered (Hartl and Jones 2008). Mendel's work enabled scientists to realise that life was somehow encoded in genes (Strachan and Read 2004, Hartl and Jones 2008). Furthermore, what those genes were made of was not known and yet to be discovered. Therefore, geneticists around the world searched furiously for the molecules that carried genetic information.
Experiments on the discovery of DNA interested researchers around the world, scientists realised that in order to determine whether DNA really carries genes was to understand its structure. It was Francis Crick and James Watson from Cambridge University, England, who finally put together a coherent and tenable account into the discovery of the structure of DNA (Watson and Crick 1953, Weaver 2008). It would be an impartial judgement to give all the deserved credits to Watson and Crick. Another group of the researches was also interested in DNA structure, included Maurice Wilkins, Rosalind Franklin at King's College London as well as other researchers whose contributions should not go unnoticed (Watson and Crick 1953). In 1962 a Nobel Prize in physiology and medicine was awarded to F.H. Crick, J.D. Watson and M.F. Wilkins for the discoveries concerning the molecular structure of nucleic acids and its significance for information transfer in living materials (Raven et al., 2008).
The knowledge of DNA structure made it possible that the elucidation of the DNA molecule as a double helix (Watson and Crick 1953), comprising polynucleotide chains bound by complementary pairing between the nitrogen-containing bases, helped underscore speculation that DNA was the carrier of hereditary information (Weaver 2008). DNA's structure revealed a mechanism by which the molecule could essentially unwind and replicate, to create a new life (Kornberg and Baker 2005).
Furthermore, the focus of this report will not be on the history of DNA discovery, but elaboration of the more recent refinements in the understanding and the findings of Watson and Crick 1953 on the DNA structure, replication and ribonucleic acid (RNA) synthesis i.e. transcription.
In the early 1950s, a number of researchers were interested to understand the detailed molecular structure of DNA in hopes that the structure would provide its importance as a hereditary molecule (Nelson 2005). The evidence that DNA is a genetic material was not fully understood and left many questions unanswered. Most importantly, questions like how would the DNA in a gene control a hereditary trait, if a mutation takes place in a gene what would happen to the DNA, furthermore, how would the DNA in a gene duplicate when a cell divides (Lewis 2005, Weaver 2008, Strachan and Read 2004). The answers were finally revealed when in 1953 James Watson and Francis Crick at Cambridge University proposed the first essentially correct three-dimensional structure of the DNA molecule (figure 1) (Watson and Crick 1953, Sinden 1994). The structure of DNA molecule, the formation of ‘double helix' was an important concept in understanding how could a hereditary material be duplicated, and how could one cell pass its hereditary material to two cells in a complete form.
(Adapted from Sinden 1994, DNA Structure and Function)
The Watson-Crick structure of a DNA molecule suggests that, a DNA is a long chain of building blocks, small molecules called nucleotides, consists of two paired complementary strands, and each composed of an ordered string of nucleotides (Lewis 2005, Sinden 1994, Brown 2006). Just as protein molecules are chains of amino acids, so DNA molecules are chains of nucleotides (Weaver 2008). A DNA molecule is too small to be seen, but DNA's exact shape has been ingeniously worked out by Watson and Crick (Figure 3). DNA consists of a pair of nucleotide chains twisted together in an elegant spiral; the ‘double helix' (Alberts 1998, Watson and Crick 1953). The X-ray crystallisation by Rosalind Franklin and Maurice Wilkins denoted a helical structure of DNA (Shown in Figure 2) (Weaver 2008).
(Adapted from: http://www.scifun.ed.ac.uk/card/images/flakes/b-form.jpg)
The importance and significance of DNA being the genetic material can be appreciated from an understanding of the double-helical structure of the DNA. The nucleotide building blocks also known as bases of DNA come in only four different kinds, such as adenine, cytosine, guanine, and thymine (Nelson 2005, Sinden 1994). These base pairs names may be shortened to A, T, C, and G. The Watson and Crick base pairing between A and T and between G and C in the complementary strands hold the strands together (Lewis 2005, Nelson 2005). These collective works of the complementary strands also hold the key to the replication which will be explained in the second part of this report. In this three-dimensional structure of the DNA molecule, the molecule consists of two polynucleotide chains twisted around one another to form a double-stranded helix in which A and T, and G and C are paired in opposite strands (see Figure 3) (Kornberg and Baker 2005, Alberts 1998).
One's DNA is located inside the body in the nucleus. It is not concentrated in a particular part of the body, though DNA is distributed among the cells (Alberts 1998, Nelson 2005). There are about a thousand million million cells making up an average human body (Raven et al., 2008); every one of those cells contains a complete copy of that body's DNA. This DNA can be regarded as a set of instruction for how to make a body, and these are written in the A, T, G, C alphabet of the nucleotides (Figure 3) (Nelson 2005). The Watson-Crick discovery of the DNA structure made it possible to appreciate the importance of this molecule and the processes involved which eventually leads to the making of a whole new life.
(Adapted from: http://www.accessexcellence.org/RC/VL/GG/nucleotide.php)
This Watson and Crick structural visualisation of DNA enabled many biochemists to understand the fundamental chemical structure of DNA. When DNA was looked into its component parts, researchers elucidated and found that DNA constituents are nitrogenous bases, phosphoric acid, and the sugar deoxyribose (hence the name deoxyribonucleic acid) (Weaver 2008, Alberts 1998, Nelson 2008). The nitrogenous bases are derivatives of two parent compounds, pyrimidines such as cytosine and thymine having one interlocked heterocyclic ring, and purines such as adenine and guanine having two such rings; (Sinden 1994, Lewis 2005, Nelson 2005) (Figure 3). Each base in DNA is chemically linked to one molecule of the sugar (deoxyribose); forming a compound called a nucleoside (Strachan and Read 2004, Nelson 2005). Furthermore, a nucleoside with a phosphate group attached at carbon atom 5 prime end (written as 5') or 3 prime end (3') constitutes a nucleotide (refer to Figure 3). The diagram in (Figure 3) also illustrates the base pairing features on the strands. Each base is paired or held together to a complementary base, by hydrogen bonds (Nelson 2005). This hydrogen bond is a weak bond where two atoms share the partially positive atom and negative atom (Nelson 2005, Kornberg and Baker 2005). The complementary base paring is that A pairs with T and G pairs with C. The A-T pairing base has two hydrogen bonds, whereas G-C has three hydrogen bonds. This can be responsible for the stability of the DNA double helix structure (Sinden 1994, Nelson 2005). The two strands opposite to each other stay together by hydrogen bonds that occur between the complementary nucleotide base pairs.
DNA molecules do two important things. Firstly to replicate, in other words, making copies and secondly translation by indirectly supervising the manufacture of a different kind of molecule such as protein (Cox 2009, Hartl and Jones 2008). At every division the DNA plans accurate copying with scarcely any mistakes in the duplication of the DNA. This brings the second important thing DNA does.
3.0 REPLICATION of DNA
As Watson and Crick deciphered the structure of DNA, its mechanism for replication became more obvious after the release of the 1953 report. The DNA replication elegantly noted by Watson and Crick stating that ‘by understanding the fundamental structure of DNA and its base paring specificity, it is possible to copy the genetic materials' (Watson and Crick 1953).
The process of DNA synthesis or DNA replication was envisioned by Watson and Crick. The DNA replication process helped by the enzyme helicase is capable of unwinding the double helix and separating the two strands (Nelson 2005, Weaver 2008, Kornberg and Baker 2005). Then the two strands are copied. As a result two new DNA molecules are created each of which, is identical to the parent molecule (Figure 4) (Kornberg and Baker 2005, Nelson 2005). In the process the daughter DNA will contain one strand from the parental molecule and one newly synthesised DNA strand, this replication process is known as semi-conservative (Kornberg and Baker 2005, Cox 2009).
(Adapted from: http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/D/DNAReplication.html)
Once the new strands unwound, the enzyme DNA polymerase (Figure 4) catalyses the synthesis of these strands by using the four deoxynuleoside triphosphates (dATP, dCTP, dGTP and dTTP) as nucleotide precursors (Cox 2009, Nelson 2005). However, DNA replication is initiated at specific points, known as the origins or replication (Figure 5).
(Adapted from: http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/D/DNAReplication.html)
Due to the initiation of the DNA replication being synthesised at that origin the Y-shaped replication fork illustrated in (Figure 4) is formed, indicating that the parental DNA duplex splits into two daughter DNA duplexes (Cox 2009, Kornberg and Baker 2005). Therefore, the two strands of the parental DNA duplex are antiparallel, though each strands act individually as templates for the synthesis of a complementary antiparallel daughter strand (shown in Figure 4) (Kornberg and Baker 2005). Furthermore, the diagram (Figure 4) also represents that one daughter strands run in the direction of 5' to 3' which is known as the leading strand and the second daughter strand in the opposite direction as from 3' to 5' end which is described as the lagging strand (Weaver 2008, Lewis 2005, Kornberg and Baker 2005).
The 5' to 3' prime end movement in the synthesis of the lagging strand is opposite to that in which the replication fork moves (Kornberg and Baker 2005). This movements of the prime ends will produce a continuous new DNA strand from the many separate pieces typically 100-1000 nucleotides long, which is better known as Okazaki fragments, of DNA made on the lagging strand (Kornberg and Baker 2005, Nelson 2005). The leading strand i.e. 5' to 3' is always synthesised continuously to the lagging strand 3' to 5' end and these synthesised fragments are covalently joined at the end of the strands by the use of enzyme called DNA ligase (Figure 4) (Nelson 2005, Weaver 2008, Kornberg and Baker 2005). Therefore, the lagging strand grows in the direction in which the replication fork moves (Kornberg and Baker 2005). Moreover, the purpose of the DNA replication is simply to duplicate the DNA of a cell by the aid of different enzymes, repair and produce new strands as explained in the latter part of the report.
4.0RNA SYNTHESIS (TRANSCRIPTION)
The double helical structure of DNA that was postulated by Watson and Crick 1953 clearly indicates how DNA might be copied; so that the information it contains can be transmitted from one generation to the next, as seen earlier. The final part of this concise report includes the RNA synthesis or transcription, which is basically a process by which parts of the genetic information encoded in DNA, copied faithfully into RNA (Weaver 2008, Raven et al., 2008, Gnatt et al., 2001). In simple term, making RNA from a DNA template. Before elaborating on this area it is essential to understand the differences between DNA and RNA. RNA is made of ribonucleic acid just like DNA as in deoxyribonucleic acid, consists of 5 carbons, though in ribonucleic acid there is two OH (Hydroxyl) groups, unlike DNA only one (Weaver 2008, Nelson 2005). Furthermore, the nitrogenous bases are adenine, guanine, cytosine and thymine is replaced by uracil; alphabet (U) (Figure 6). Other than that there is no major difference between RNA and DNA.
(Adapted from: http://www.odec.ca/projects/2004/mcgo4s0/public_html/t3/RNA.html)
The transcription process involves several key factors and these include the specific part of the DNA to be transcribed, transcription factors (TFIIA and TFIIB, etc), RNA polymerase, and ATP (Figure 6) (Gnatt et al., 2001, Weaver 2008). This process has three stages such as initiation, elongation and termination (Nelson 2005). Moreover, the transcription process first starts with the strand of DNA, once the DNA strand is divided into several important regions, the largest of these fragmented units will be the transcription site. This transcription unit of the DNA will then be used to make RNA. At the upstream of the transcription unit is the TATA Box and another region called the enhancer region may also be involved in the process. Furthermore, transcriptional factors i.e. TFIIA and TFIIB are needed to begin with the process and eventually start for a successful transcription (Kornberg and Baker 2005, Nelson 2005).
(Adapted from: http://www.accessexcellence.org/RC/VL/GG/ecb/RNA_transcription.php)
Once the origin of the transcription is noted from the DNA strand, the first complex or TFIID, which is the largest of the general factors; begins to join the site. A component of this factor TBP as shown in (Figure 6) then binds to the DNA using the TATA Box to position TFIID near the transcription initiation site (Alberts 1998, Raven et al., 2008). By doing so, other factors including TFIIA and TFIIB or TFIIF then attach successfully. These complexes prepare the DNA for the successful binding of the RNA polymerase. Since the transcription of DNA into RNA is a highly chemical reaction, RNA polymerase acts as an enzyme-catalyst to direct the process (Nelson 2005, Gnatt et al., 2001). Therefore, once RNA polymerase is bound other transcription factors complete the mature transcription complex. Moreover, energy is required to power the system of transcription to begin, so the sufficient energy needed is provided by the reduction of ATP (adenosine triphosphate) into ADP and Pi and these are the energy currency of the cell (Raven et al., 2008). The synthesis of RNA template from the DNA strand begins by the help of RNA polymerase. Finally, then the RNA polymerase dissociates and the newly formed strand of RNA is released.
Understanding of DNA structure as double helix, and the synthesis of RNA from a DNA strand emphasise that the major function of DNA is to code for protein in the processes of transcription and translation. DNA encodes information, since DNA has the capability to store genetic details and the cells uses to synthesis protein. Therefore, this system of process is known to be the central dogma for the molecular biology.
Without any doubt the discovery of Watson and Crick over 50 years ago is one of the iconic inventions of the 21st century. Ever Since the structure of DNA was elucidated, the area of medical science has changed dramatically. The basic knowledge imparted by the DNA molecule, laid the foundation in the understanding of gene structure, regulation and function of gene expression and how genes work. Furthermore, such knowledge about the DNA molecule enhanced the understanding of hereditary diseases to propose a better diagnosis or therapies, as in the case of gene therapies.