Evaluation Of Nucleosome Forming Potentials Biology Essay

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Introduction

Although the human has many protein-DNA complexes, but nucleosome is the most complicated one among them all. As far as its preparation is concerned, a nucleosome is formed when a double-stranded DNA is wrapped around eight histone proteins in a complicated configuration. This structural composition can be found in all the eukaryotes.1 It is very essential to understand this structure and its formation because this structural configuration is involved in almost all the DNA related processes in the human body. For instance, in all the procedures like replication, recombination, transcription and repairing, naked DNA is not attacked and modified by the proteins at all. Rather it is this DNA linked with histone proteins that is the target during all these processes. This proves the significance of nucleosome complex in all these bodily processes. Not only the structure of these nucleosomes is important, but their effects on the modification of human DNA are also worth noticing in the subject of biology.[2], [3] and [4]

Nucleosome is a macromolecule and its functions are highly diverse in the human body, i.e. it is involved in the construction and gene regulation of all the eukaryotic genomes (REF).

Structure of nucleosome

A look on the structure of nucleosome reveals that it is made up of 8 highly conversed histones that are surrounded by DNA having 147 base pair. This configuration provides a cylindrical shape to the nucleosome. At the particle level, it has been experimentally demonstrated that the 147 base pairs alter in accordance with preferable particle formation. However, on atomic level, such preference based alterations are not completely known.

As far as the histone proteins present in the nucleosome are concerned, there are fout main types of these proteins i.e. H2A, H2B, H3, and H4. all these types are present in two copies and these copies are surrounded by 147 base pairs of DNA. Hence the core is octamer in shape and around it, there is a super coil with 1.7 turns at the maximum. This whole structure is formed after an assembly process is completed (Figure 1). In genomic DNA, after every 200 base pairs, you can easily locate a nucleosome. This combination of DNA and nucleosome is a first order formation, on the basis of which, many super structures can be formed like 30-nm chromatin fibre. In this structure 30-40 proteins are compacted by linear DNA coiling (Richmond and Davey, 2003).

Role of histone acetylases (HAT) and histone deacetylases (HDAC) inhibitiors

The main factor in gene expression is the process of coiling and uncoiling of DNA. Two inhibitors are involved in this process i.e. histone acetylases (HAT) and histone deacetylases (HDAC). The former inhibitor acetylates the lysine residues in core histones to form an active chromatin that is best for transcription and is also less compact. On the other hand, the latter inhibitor is involved in the removal of acetyl from those lysine residues. The chromatin thus created in inactive in terms of transcription and is also condensed. In gene expression, tails of basic histones are modified and this modification plays an important role in remodeling the high order chromatin molecules. However, these above mentioned inhibitors cause hyper acetylation in the histone protiens, thus harming gene expression.[1][2]

Forensic STR Analysis & Problems associated with analysing degraded DNA

National DNA Database® (AMPFISTR® SGM plus™) has formed a new methodology for using the DNA profiling. In this case, the polymorphic aspects of the short tandem repeats are utilized in order to differentiate among people who are related to each other and who are not related [1]. According to Author (2001), the human genome is composed of about 3 percent of STR markers and they are distributed in every 10,000 nucleotides in this particular genome (Hammond et al. 1994). STR markers are also DNA sequences having 2-7 bases in them. Depending on the human being, these repeats can vary significantly. The allele fragments of these markers are small and using smallest amounts of DNA i.e. 0.1-1 ng, these fragments can be easily improved through PCR. These augmentations are useful in the procedures like human identification and the decomposed DNA examination.

This method of modifying the DNA fragments is a highly sophisticated one and is also highly dependent on the size of DNA being used. The DNA utilized for this purpose can range between 100 to 360 bases in its length. When the DNA is decomposed, the STR alleles can no longer be amplified by the use of PCR [2]. As a result, a partial DNA molecule is created, that is highly unstable. Moreover, that DNA profile also possesses less differentiating ability among individuals. When a cell death occurs, either by necrosis or by apoptosis, the endo nucleases are activated. They attack on the linker DNA that is not protected by any mechanism. As a result, the monomeric nucleosome molecules are left behind along with 146 base pairs of DNA [3].

All this observation can be utilized for improving the DNA profiling system so as to ensure that small fragments of DNA are attacked during this process. This is very necessary for enhancing the rate of success when decomposed samples are available.

Protective nature of the nucleosome

Restriction enzymes hold very critical place in the studies of DNA and it has been experimentally demonstrated that the DNA which is linked with histone proteins is less reactive as compared to the naked DNA. The location of DNA in the nucleosome molecule determines the action of restriction enzymes. This means that the central DNA that is protected by 106 levels will not be harmed by these enzymes. But the terminal DNA having protection level of 100.5-9 can be victimized.

Review of Introduction Part of Paper

Richmond and colleagues used 1.9 A structure of Xenopus laevis (African clawed frog) to crystallize nucleosome particles present in it. Using human alpha satellite DNA, modelling of recombinant histones attached to a palindrome was also done by researchers (T.J. Richmond and C.A. Davey, 2003). Histones are the most conserved proteins of all throughout the eukaryotic kingdom. This is the reason Xenopus laevis histone proteins have been extensively used in different sorts of researches. In 1KX5 crystal of this frog species, there was a difference of only 9 amino acids from the human sample. Bishop performed and documented an in depth analysis of the histone proteins of Xenopus laevis and human beings.

3The crystallographers utilized palindromic DNA chain was selected for its positive properties in constructing nucleosome crystals (T.C. Bishop, 2005).

Hypothesis

Even though the biological scientists are trying their best and bringing forth advanced levels of techniques associated with DNA profiling, but they are still entirely ignorant of the properties that can create problems in context of decomposed DNA samples. Theoretically, as nucleosomes protect their attached DNA from exposure to restriction enzymes therefore these DNA sequences are less prone for being decomposed.

Materials and methods

Fifty eight markers along with amelogenin X and Y have been chosen by the authors for investigation. This selection relied on the use and recommendation of forensic experts regarding these markers. NXSensor and NuScore were the two internet based instruments utiliaed by the experts. The algorithm of Nucleosome eXclusion Sensor (NXSensor version 1.3.1) reads an enter chain for three identified nucleosome-free sequences:10 bases of poly-A,10 bases of poly-T, and a grouping of Gs and Cs (A_10, T_10, or[(G/C)3N2]_3). Output is given in FASTA format upon the recognition of any sequence. All these markers were investigated for their ability to bind with the DNA-binding proteins. NuScore used dinucleotide stacking properties like rise, tilt, twist, roll and slide to determine the DNA deformation energy.

Arbitrary chains were produced 100 times with the similar dinucleotide substance as the enter string. Template 2cv5 (human); best of two orientations; and 164 bp window size were the points that were chosen in the program. Two output values - DNA twist power and nucleosome positioning score (NPScore) - were utilized in this revision (Anderson and Widom, 2001).

All 60 markers were contrasted with haphazard strings of the identical dinucleotide substance to conclude if the placement of the nucleosome dyadis was reliant upon the precise activities of dinucleotides and their connections. The number of locations with an NPScore more negative than two thresholds (_2 and _3) were calculated and contrasted statistically. A marker was believed to have a lofty NFP when the positions of NPScore crossing the threshold (NPScore__2) were elevated and vice versa.

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