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The nucleic acids
The nucleic acids
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Nucleic acids

  1. 1. Nucleic acids
  2. 2. Biologically occuring polynucleotides in which the nucleotide sequences are linked in a specific sequence by phosphoester bonds.
  3. 3. • A nucleotide has three characteristic components: a nitrogenous base, a pentose, and one or more phosphates. The molecule without a phosphate group is called a nucleoside. The nitrogenous bases are derivatives of two parent compounds, pyrimidine and purine. The bases and pentoses of the common nucleotides are heterocyclic compounds. • In the pentoses of nucleotides and nucleosides the carbon numbers are given a prime (′) designation to distinguish them from the numbered atoms of the nitrogenous bases
  4. 4. Nucleotide kinase
  5. 5. Phosp atase
  6. 6. • Purine is a heterocyclic aromatic organic compound, consisting of a pyrimidine ring fused to an imidazole ring. • Imidazole is a heterocyclic aromatic organic compound. It is further classified as an alkaloid. Imidazole refers to the parent compound C3H4N2, while imidazoles are a class of heterocycles with similar ring structure but varying substituents. • Pyrimidine is a heterocyclic aromatic organic compound similar to benzene and pyridine, containing two nitrogen atoms at positions 1 and 3 of the six-member ring. • Free pyrimidine and purine bases may exist in two or more tautomeric forms depending on the pH. • The functional groups of pyrimidines and purines are ring nitrogens, carbonyl groups, and exocyclic amino groups. Hydrogen bonds involving the amino and carbonyl groups are the most important mode of interaction between two (and occasionally three or four) complementary strands of nucleic acid.
  7. 7. Tautomer • Tautomers are structural isomers of chemical compounds that readily interconvert. This reaction commonly results in the relocation of a proton. Tautomerism is for example relevant to the behavior of amino acids and nucleic acids
  8. 8. • The base of a nucleotide is joined covalently (at N-1 of pyrimidines and N-9 of purines) in an N-β-glycosyl bond to the 1′ carbon of the pentose, and the phosphate is esterified to the 5′ carbon. The N-β-glycosyl bond is formed by removal of the elements of water (a hydroxyl group from the pentose and hydrogen from the base), as in O-glycosidic bond formation
  9. 9. Minor bases 2 methyl guanosine 7-methyl guanosine
  10. 10. 5 methyl cytidine 5 hydroxy methyl cytidine
  11. 11. Thiouridine
  12. 12. Phosphodiester • The successive nucleotides of both DNA and RNA are covalently linked through phosphate-group “bridges,” in which the 5′-phosphate group of one nucleotide unit is joined to the 3′-hydroxyl group of the next nucleotide, creating a phosphodiester linkage • The covalent backbone of DNA and RNA is subject to slow, nonenzymatic hydrolysis of the phosphodiester bonds. In the test tube, RNA is hydrolyzed rapidly under alkaline conditions, but DNA is not; the 2′- hydroxyl groups in RNA (absent in DNA) are directly involved in the process.
  13. 13. Nucleic acid structure • Watson and Crick 1953 • Friedrich Miescher 1868 • Hershey and Chase, 1952 • Franklin and Wilkins
  14. 14. Franklin and Wilkins experiment • The pattern revealed that DNA molecules are helical, with two periodicities along their long axis, a primary one of 3.4 Å and a secondary one of 34 Å. The problem then was to formulate a three-dimensional model of the DNA molecule that could account not only for the x-ray diffraction data but also for the specific A = T and G = C base equivalences discovered by Chargaff and for the other chemical properties of DNA.
  15. 15. Watson crick model
  16. 16. Different forms of DNA • The Watson-Crick structure is also referred to as B-form DNA, or BDNA. The B form is the most stable structure for a random-sequence DNA molecule under physiological conditions and is therefore the standard point of reference in any study of the properties of DNA. Two structural variants that have been well characterized in crystal structures are the A and Z forms. • The A form is favored in many solutions that are relatively devoid of water. The DNA is still arranged in a right-handed double helix, but the helix is wider and the number of base pairs per helical turn is 11, rather than 10.5 as in B-DNA. The plane of the base pairs in A-DNA is tilted about 20° relative to B-DNA base pairs, thus the base pairs in A-DNA are not perfectly perpendicular to the helix axis. These structural changes deepen the major groove while making the minor groove shallower. The reagents used to promote crystallization of DNA tend to dehydrate it, and thus most short DNA molecules tend to crystallize in the A form. • Z-form DNA is a more radical departure from the B structure; the most obvious distinction is the left-handed helical rotation. There are 12 base pairs per helical turn, and the structure appears more slender and elongated. The DNA backbone takes on a zigzag appearance. Certain nucleotide sequences fold into left-handed Z helices much more readily than others. Prominent examples are sequences in which pyrimidines alternate with purines, especially alternating C and G (that is, in the helix, alternating C≡G and G≡C pairs) or 5-methyl-C and G residues. To form the left-handed helix in ZDNA, the purine residues flip to the syn conformation, alternating with pyrimidines in the anti conformation. The major groove is barely apparent in Z-DNA, and the minor groove is narrow and deep. • Whether A-DNA occurs in cells is uncertain, but there is evidence for some short stretches (tracts) of Z-DNA in both bacteria and eukaryotes. These Z-DNA tracts may play a role (as yet undefined) in regulating the expression of some genes or in genetic recombination.
  17. 17. Gene • A segment of a DNA molecule that contains the information required for the synthesis of a functional biological product, whether protein or RNA, is called a gene
  18. 18. Palindrome sequences • A palindrome is a word, phrase, or sentence that is spelled identically when read either forward or backward; two examples are ROTATOR and NURSES RUN. In DNA, the term is applied to regions of DNA with inverted repeats, such that an inverted, self- complementary sequence in one strand is repeated in the opposite orientation in the paired strand.
  19. 19. Hoogsten pairing • The N-7, O6, and N6 of purines, the atoms that participate in the hydrogen bonding with a third DNA strand, are often referred to as Hoogsteen positions, and the non-Watson-Crick pairing is called Hoogsteen pairing, after Karst Hoogsteen, who in 1963 first recognized the potential for these unusual pairings. Hoogsteen pairing allows the formation of triplex DNAs.
  20. 20. G tetraplex • Four DNA strands can also pair to form a tetraplex (quadruplex), but this occurs readily only for DNA sequences with a very high proportion of guanosine residues. The guanosine tetraplex, or G tetraplex, is quite stable over a broad range of conditions.
  21. 21. • Solutions of carefully isolated, native DNA are highly viscous at pH 7.0 and room temperature (25 °C). When such a solution is subjected to extremes of pH or to temperatures above 80 °C, its viscosity decreases sharply • anneal, • The close interaction between stacked bases in a nucleic acid has the effect of decreasing its absorption of UV light relative to that of a solution with the same concentration of free nucleotides, and the absorption is decreased further when two complementary nucleic acid strands are paired. This is called the hypochromic effect. • Denaturation of a double-stranded nucleic acid produces the opposite result: an increase in absorption called the hyperchromic effect. The transition from double-stranded DNA to the denatured, single-stranded form can thus be detected by monitoring UV absorption at 260 nm. • tm; formally, the temperature at which half the DNA is present as separated single strands • cytosine deamination UV light induces the condensation of two ethylene groups to form a cyclobutane ring. In the cell, the same reaction between adjacent pyrimidine bases in nucleic acids forms cyclobutane pyrimidine dimers. This happens most frequently between adjacent thymidine residues on the same DNA strand. A second type of pyrimidine dimer, called a 6-4 photoproduct, is also formed during UV irradiation. • Nitrous acid, Sodium bisulphite • Alkylating agents
  22. 22. PCR
  23. 23. RT-PCR
  24. 24. Sanger’s sequencing
  25. 25. Chromatogram
  26. 26. Next Generation sequencing • Next generation sequencing (NGS), massively parallel or deep sequencing are related terms that describe a DNA sequencing technology which has revolutionised genomic research. Using NGS an entire human genome can be sequenced within a single day. In contrast, the previous Sanger sequencing technology, used to decipher the human genome, required over a decade to deliver the final draft. Although in genome research NGS has mostly superseded conventional Sanger sequencing, it has not yet translated into routine clinical practice. • Pyrosequencing is a method of DNA sequencing (determining the order of nucleotides in DNA) based on the "sequencing by synthesis" principle, in which the sequencing is performed by detecting the nucleotide incorporated by a DNA polymerase. Pyrosequencing relies on light detection based on a chain reaction when pyrophosphate is released. • Illumina dye sequencing is a molecular technique used to determine the series of base pairs in DNA, also known as DNA sequencing. It was developed by Shankar Balasubramanian and David Klenerman of Cambridge University, who subsequently founded Solexa, a company later acquired by Illumina. This sequencing method is based on reversible dye-terminators that enable the identification of single bases as they are introduced into DNA strands.
  27. 27. • mRNA: Messenger RNA are those are transcribed from a DNA template • Cistrons: In bacteria and archaea, a single mRNA molecule may code for one or several polypeptide chains. If it carries the code for only one polypeptide, the mRNA is monocistronic; if it codes for two or more different polypeptides, the mRNA is polycistronic. In eukaryotes, most mRNAs are monocistronic.
  28. 28. tRNA
  29. 29. rRNA, snoRNA, snRNA • rRNA: Ribosomal ribonucleic acid is a type of non-coding RNA which is the primary component of ribosomes, essential to all cells • snoRNA: Small nucleolar RNAs are a class of small RNA molecules that primarily guide chemical modifications of other RNAs, mainly ribosomal RNAs, transfer RNAs and small nuclear RNAs. • snRNA: Small nuclear RNA is a class of small RNA molecules that are found within the splicing speckles and Cajal bodies of the cell nucleus in eukaryotic cells. The length of an average snRNA is approximately 150 nucleotides. • miRNA: microRNA is a small non-coding RNA molecule found in plants, animals and some viruses, that functions in RNA silencing and post-transcriptional regulation of gene expression.
  30. 30. Energy molecules • Hydrolysis of the ester linkage yields about 14 kJ/mol under standard conditions, whereas hydrolysis of each anhydride bond yields about 30 kJ/mol. • coenzyme A • second messengers • diverse physiological • processes, including taste, inflammation, and smooth muscle contraction • ppGpp

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