An algorithm allowing the prediction of sub-optimal structures was then developed by Zuker and constitutes the current version of the mfold program, available online, which is currently one of the standard tools for RNA secondary structure prediction.In addition to their secondary structure, consisting of standard base pairings, RNAs can adopt a compact, well-defined three-dimensional structure, which results from additional interactions between the classical elements of secondary structure (helices, loops).These covariations can be systematically identified by statistical analyzes on a set of homologous RNA sequences and used to construct models of secondary structure.We then have a structure locally associating three RNA strands.The cl...
3066 words (7.7 pages)
The bone structure of P. falciparum Fd, is similar with resembles those of plants Fds.As figure 20 shows, nine different stages during the development of P. falciparum 3D7 were assayed by oligonucleotide microarray analysis.PF3D7_0220100 has a strong relationship with the protein funtions due to the fact that the correct three-dimensional structure is essential to function, and some parts of functional proteins even remain unfolded.Ian AL , Mark W , Kellen LO , Simon AC , Katelynn SB , Asako T , Michael TF , Manuel L : Metabolic QTL Analysis Links Chloroquine Resistance inPlasmodium falciparumto Impaired Hemoglobin Catabolism, 2014; (1).According to the related research, ATP-binding contains biological processes includin...
1902 words (4.8 pages)
Results of statistical analysis on transcript expression level will be visualized in volcano plots with CLC Genomics Workbench 7.5 (Qiagen, Denmark).Furthermore, there are several applications used in NGS technology such as transcriptome sequencing or RNA-Sequencing (RNA-Seq), genomic sequencing and epigenetic applications which use CHIP-Seq and methylation profiling to work out analysis on interaction in between proteins and DNA and analysis on regulating chromatin structure respectively (Perdacher, 2011).The preparation before analysis such as sample collection, RNA isolation, cDNA library construction, sequencing and mapping are done.Expression analysis of samples will be observed and recorded.On proportions analysis, especially Z tes...
1912 words (4.8 pages)
Fig1.4: RNA structure.RNA: ribonucleic acid has the same structure as that of DNA but not identical, RNA has ribose sugar instead of deoxyribose.1.4: STRUCTURE OF RNA: .DNA and RNA have three different conformations each, with distinct structure which are variously suited for their functions.2009) Double helix formed between DNA & RNA or RNA & RNA has the conformation same to that of A-form DNA.
2360 words (5.9 pages)
Dandjinou, At, Levesque, N, Larose, S, Lucier, JF, Abou-Elela, S, Wellinger RJ 2004, ‘A phylogenetically based secondary structure for the yeast telomerase RNA’ Current Biology, 14: 1148-1158.Lin, J, Ly, H, Hussain, A, Abraham, M, Pearl, S, Tzfati, Y, Parslow, TG, Blackburn, EH 2004, A universal telomerase RNA core structure includes structured motifs required for binding the telomerase reverse transcriptase protein’ Proceedings of the National Academy of Sciences of the United States of America, vol.For example, the RNA of ciliates has a conserved sequence motif found in helix I (Lai 2002), where as the RNA of yeasts seeks several helical regions as the binding sites for the telomerase’s Est1 protein (Peterson et al 2001).The structure ...
1811 words (4.5 pages)
There are several main elements on the promoter of eukaryotic mRNAs (core elements): .Moreover, DNA is not free in the nucleus but coiled into a particular structure called nucleosomes and associated with non-histone proteins.The promoter is the area of DNA to which RNA polymerase initially binds, before starting RNA synthesis.The binding and activation of RNA polymerase is controlled by transcription factors (trans-regulatory elements) which bind to the cis sequences.From the analysis of the sequence of different promoter regions, consensus sequences have been established, of which there are several kinds.
424 words (1.1 pages)
When all the introns are excised, the pre-mRNA becomes an mRNA (mature messenger RNA) ready for translation, after export into the cytoplasm.The introns therefore play no role in the function of mature RNA (translation into protein for the 'MRNA, incorporation into the ribosome for rRNAs, etc.Excision of the intron by a spliceosome is quite specific: the complex will cleave the intron by a transesterification of the phosphodiester bond to its 5 ', to reattach it at the branch box by forming an unusual 5'-2' phosphodiester bond and forming an RNA loop in the shape of a lasso.An intron is a portion of a gene which is transcribed into RNA, within a precursor RNA, and which is then eliminated by a programmed excision process and which is the...
1273 words (3.2 pages)
About 2.5 µl of ethidium bromide is added to the solution to visualise the RNA bands.Store the purified RNA or proceeded for DNase treatment after RNA treatment.The RNA samples are RUN with the potential difference of 80V with DNA Hyper ladder II as a standard.The sample is assayed for gene expression by adding 2 ml of RNA later solution for RNA stability.Then about 5 µl RNA sample is mixed with 1 µl of DNA loading dye.
4949 words (12.4 pages)
This paper is an analysis conducted on Nucleic Acids through a variety of tests specifically, Dische, Murexide, Wheeler-Johnson and Phosphate Tests in order to exemplify structural features of nucleic acids as well as identify the principle involved in each chemical test.DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) are aldehydes, which reacts with the compound, diphenylamine, to produce a blue-colored compound.That DNA differs from RNA in the sense that only Uracil is found in RNA and Thymine is exclusively located in the DNA though Adenine, Guanine, and Cytosine are both found on DNA & RNA.. .: A biology adventure / written by Transnational College of LEX translated by Alan Gleason.New York: Wiley, 2004. .
930 words (2.3 pages)
These are RNA viruses.It is found in adults and children hospitalized for pulmonary infection with a frequency equivalent to that of the respiratory syncytial virus or that of the influenza virus.However, hMPV lacks gene structures, ns1 and NS2, and RNA contains eight slight differences.The identification of hMPV is mainly based on reverse transcriptase polymerase chain reaction (RT-PCR) to amplify it directly from RNA extracted from respiratory specimens.The disease is usually mild but it can be more serious in some people, such as the elderly or patients with a lung transplant where the infection could favor rejection.
508 words (1.3 pages)
The pairing of the regulatory RNA with its target messenger RNA can act on the capacity of the latter to be translated by the ribosome or on its stability, which results in regulation of the translation of the or genes carried by messenger RNA.The RNAs thus produced can have three main types of functions: they can be carriers of the genetic information of one or more genes encoding proteins (this is called messenger RNA), they can adopt a stable secondary and tertiary structure and perform catalytic functions (for example ribosomal RNA), they can finally serve as a guide or a template for catalytic functions performed by protein factors (which is the case for microRNAs, for example).The three-dimensional structure of a tRNA was resolved ...
5033 words (12.6 pages)
D. RNA as an Information Containing Molecule .E. RNA Can Function as a Catalytic Molecule .Secondary through quaternary structure is more limited as a result, meaning RNA cannot form the wide array of active sites observed among proteins.There are only 4 types of nitrogenous bases in RNA versus the 20 types of amino acids found in proteins ii.Because RNA has a degree of structural and chemical complexity, it is capable of stabilizing a few transition states and catalyzing at few chemical reactions.
1122 words (2.8 pages)
One motif identified in the crystal structure of cobalt(II) formate consists of a carboxyl group in which one oxygen atom is bound to the metal ion and the other is bound to metal-bound water, to give a cyclic structure.One can imagine several advantages to using hydrated ions within the ionic core of a large RNA.On the basis of that structure, it was proposed that an ionic core may substitute in RNA folding for the hydrophobic core of proteins such that the 3° structure assembles around a fixed number of discrete metal-binding sites (Cate et al.Furthermore, in these examples, the RNA structures themselves are likely to be quite flexible and can accommodate a variety of metal ions with only minor distortions to the overall RNA fold.Prote...
5090 words (12.7 pages)
The information from RNA determines the protein synthesis through the series of translation which involves three types of RNA molecules to perform different functions: .. Messenger RNA(mRNA) is a linear sequence of amino acid in polypeptide chain and has longer chain than the reading frame that has to be translated.To begin and end translation , specific start and stop codons are required.Phosphate groups are attached at the end of the sugar at 5′-carbon and at the 3’end ,the hydroxyl group is added.Most probably all natural DNA or RNA polymer extend in a direction of 5’to 3’end direction.The structures that join the nulceotides together in DNA and RNA are called phosphodiester bonds due the presence of phosphoric acid linkage between t...
2089 words (5.2 pages)
RNA folding is typically mediated by the same type of base-base interactions that are found in DNA, with the difference being that bonds are formed within a single strand in the case of RNA, rather than between two strands, in the case of DNA.There is no scientific evidence to suggest that RNA is spontaneously being created and capable of forming pre-cellular life today.The structure of RNA nucleotides is very similar to that of DNA nucleotides, with the main difference being that the ribose sugar backbone in RNA has a hydroxyl group that DNA does not.Another major difference between DNA and RNA is that DNA is usually found in a double-stranded form in cells, while RNA is typically found in a single-stranded form.Although the ribosome is...
1217 words (3.0 pages)
The PRF diagnostic testing program.There are three types of genetic tests: gene tests, which look at fairly short lengths of DNA or RNA, chromosomal tests, which examine whole chromosomes, and biochemical tests, which test protein levels and/or enzyme activities (NHGRI, 2014).Learning about progeria.There are many uses for this type of testing, including, but not limited to, diagnosis of rare genetic disorders, risk analysis for hereditary diseases, and determining appropriate treatments for patients.Cracking your genetic code.
358 words (0.9 pages)
The RNA polymerase 3D unwinds to develop viral RNA synthesis (Bedard and Semler, 2004).The poly(A) tract at the 3′ end functions for virus viability, impart stability and also for the efficient RNA replication by interacting with viral RNA at the 5′ end (Bedard and Semler, 2004).When PCBP2 was depleted, there was poor RNA synthesis in poliovirus and hence it was recognised that PCBP2 play a vital role in RNA replication.IRES (Internal ribosome entry site) is a clover leaf secondary structure at the 5′ non-coding region and in the polypeptide there is a 3′ noncoding region which contains the poly(A) tract required for the synthesis of minus RNA strand for RNA replication and translation.2C binds with the minus strand of poliovirus RNA at ...
3317 words (8.3 pages)
Whereas the RNA is formed in the chromosomes and occur in nucleolus and cytoplasm.This species of RNA are usually single stranded is the smallest polymer in the RNAs making (10-15) % of the total RNA.DNA is the usual genetic material of the most organisms while RNA is the genetic material of some viruses.The core task of RNA molecule is to manufacture protein by a process so called translation, with the help of information from DNA.structure of ribosomal RNA.
1823 words (4.6 pages)
However, some species of non coding RNAs are also transcribed by RNA pol III and I.The term non-coding RNA (ncrna) is usually utilized for RNA that does not encode a protein, however this does not imply that such Rnas don’t contain data nor have capacity.Both long and short non coding RNAs are mostly transcribed by RNA polymerase II.They code for either long (>200) or short (200<) non coding RNA.The highly abundant short non coding RNA genes have been well characterized and are known to play an important role in various cellular functions such as transcriptional regulation, translation regulation, RNA editing etc.
1284 words (3.2 pages)
RNA viruses can also be classified, depending on the polarity of their RNA, into negative polarity (antisense), positive polarity (sense), or double polarity (ambisense) viruses.As such, purified RNA from a positive polarity RNA virus can directly cause infection although it may be less infectious than the whole virus.In recent years, remarkable progress has been made in determining, at the atomic and subnanometric level, the structure of a number of critical viral proteins that make up the virion capsid of several double-stranded RNA viruses, highlighting important parallels in the structure and replication processes of many of these viruses.RNA viruses generally have a high mutation rate, in the absence of DNA polymerase capable of spo...
696 words (1.7 pages)
RNA was reverse transcribed into cDNA.* Sampling & RNA extracting from patients.High-temperature performance is also very important for tackling RNA with secondary structure or when working with gene-specific primers (GSPs).Two-step qRT-PCR Two-step qRT-PCR starts with the reverse transcription of either total RNA or poly(A)+ RNA into cDNA using a reverse transcriptase (RT).SYBR Green I advantages • Low cost assay • Easy design and set up SYBR Green I disadvantages • Non specific system • Not adapted to multiplex • Non suitable for qualitative qPCR Primer-Based Detection Systems Primer-based fluorescence detection technologies can provide highly sensitive and specific detection of DNA and RNA.
4694 words (11.7 pages)
.. Ribosomes are large complex of both RNA and protein, the RNA component catalyses protein synthesis.The ribosomal RNA (rRNA) is present in all existing species and therefore use to establish the evolutionary relationships among them.Throughout RNA evolution, the structure is considerably more conserved than the sequence.RNA molecules fold into characterized structures that are basic for their biological functions.This rapid rate of evolution of mitochondrial DNA can prompt homoplasy since frequent base pair progressions might result in convergently similar sequences in two unrelated taxa (Rubinoff, 2006a).
1919 words (4.8 pages)
If the conditions of the pre-biotic site are favorable for the polymerization of RNA, it has two key advantages to then promote its own replication: strands of RNA can have a certain catalytic activity, and several RNA segments.It is, for example, its optimal capacity to duplicate rapidly in an environment populated by RNA-dependent RNA polymerase enzymes and DNA bases, including without an initial RNA primer, that characterizes the Spiegelman monster: this 218 nucleotide chain of RNA is a parasite that thrives in a medium containing RNA polymerase and RNA bases.Currently, it can be observed that the enzymes necessary for the retrotranscription of RNA to DNA are very present in retroviruses, whose genome is carried by RNA.Genetic transla...
12886 words (32.2 pages)
In order to characterize small non-coding RNA, small RNA-SEQ or miRNA microarrays are used.In this report, analysis of the differential expression between two groups of samples corresponding to two Drosophila melanogaster tissues was implemented.The most effective method in analysing RNA both qualitatively and quantitatively is next generation sequencing.Secondly, tophat was run for both tubule and wholefly samples followed by running Cuffdiff for the analysis of differential expression between these two types of tissue.More specifically, the whole RNA transcripts or parts of them are purified and then reverse transcribed into c DNAs.
2172 words (5.4 pages)
However, isolating and handling RNA ask for special precautions because naked RNA is highly susceptible to degradation by ribonucleases (RNases) (1).The principle of RT-qPCR is straight forward: following the reverse transcription of RNA in to cDNA, it needs an appropriate detection chemistry to detect the presence of PCR products, an instrument to monitor the amplification in real-time and compatible software for quantitative analysis.The quality of the isolated RNA was verified by agarose gel electrophoresis... A DNase digestion step was performed as a precaution using RQ1 RNase-free DNase kit although the TRIzol method generally results in RNA which is essentially free from genomic DNA (2).The quantity of the isolated RNA was determi...
1090 words (2.7 pages)
RNA is central to protein synthesis.First a type of RNA called messenger RNA (mRNA) carries information from DNA to structures called ribosomes.This requires the help of transfer RNA or tRNA.RNA strands are continually made, broken down and reused.RNA is formed from DNA by a process called transcription.
599 words (1.5 pages)
Transcription is carried out by a DNA-dependent RNA polymerase which copies a DNA sequence into RNA.The complementarity of the messenger RNA codon and the transfer RNA anticodon is based on Watson-Crick-type pairing rules governing the secondary structure of double-stranded DNAs.The three bases of these anticodons can pair with three consecutive bases of the messenger RNA, this triplet of bases forming a codon complementary to the anticodon of the transfer RNA.This RNA is structurally very similar to a single-stranded DNA molecule but differs in the nature of the ose of its nucleotides - RNA contains ribose where DNA contains deoxyribose - as well as one of its nucleotides.In the first case, it has its own physiological function in the c...
9663 words (24.2 pages)
At the same time, however, the study of nucleic acids has revealed remarkable properties of DNA and RNA molecules that could make them attractive therapeutic agents, independent of their well-known ability to encode biologically active proteins.It is a direct test based on DNA ribosomal RNA hybridization, with demonstrated sensitivity of 89.9% to 97.1%, and specificity of 93% to 98%.The structure of the nucleic acids in a cell determines the structure of the proteins produced in that cell.It represents nearly 80% of the total RNA in the cell.Organic Bases Structure of RNA  .. RNA differs, however, from DNA because it does not form an analogous double helical structure.
2073 words (5.2 pages)
Translation is the process by which messenger RNA is translated into proteins in eukaryotes.RNA is a much less stable molecule than DNA so it is not very good for holding the large amounts of DNA typically seen in Eukaryotic cells.Ribosomes bind to the mature mRNA at an AUG site and, for each codon (3 mRNA nucleic acids), a tRNA brings an amino acid for the translation, until the stop codon where the newly synthesized polypeptide is released in its primary structure.The role of RNA in protein synthesis is extremely important as protein synthesis could not occur without RNA.Three forms of RNA exist solely to create proteins.
282 words (0.7 pages)
These maps were very similar, often with the same loops, suggesting that the three-dimensional structure that defines a specific type of cell has not changed much in mammals during evolution.To locate genes, there are various complementary tools: statistical methods that identify coding regions on the basis of codon frequency analysis, pattern search methods and in particular signatures starting and ending characteristics, junctions between introns and exons, promoter sequences, terminators, ribosome binding sites (RBS).In viruses, the genome is contained either in one (or more) molecule (s) of DNA (DNA virus) or RNA (RNA virus or ribovirus), single or double strand, protected within a particle or capsid of protein nature.Most of the tim...
2383 words (6.0 pages)