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Chemical structures of (a) ribonucleotides and (b) deoxyribonucleotides.

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Presentation on theme: "Chemical structures of (a) ribonucleotides and (b) deoxyribonucleotides."— Presentation transcript:

1 Chemical structures of (a) ribonucleotides and (b) deoxyribonucleotides

2 Names and abbreviations of nucleic acid bases, nucleosides, and nucleotides

3 Some possible tautomeric conversions for bases

4 N-Glycoside conformation: syn and anti conformations

5 Furanose ring conformation: A planar ribose ring viewed down the C3-C4 bond showing the eclipsed substituents

6 Furanose ring pucker: Steric strain in the planar form is partially relieved by ring puckering in which C3 is the out-of-plane atom (envelope form)

7 Nucleotide furanose conformation: C3-endo conformation (on the same side of the sugar ring as C5) which occurs in A-RNA and RNA-11

8 Nucleotide furanose conformation: C2-endo conformation which occurs in B-DNA

9 Hydroxymethyl group conformation: conformational wheel showing the distribution of C4-C5 torsion angles of the furanose ring

10 Nucleotide conformation is determined by the seven indicated torsion angles.

11 Chemical structure of a nucleic acid

12 Mechanism of base-catalyzed RNA hydrolysis

13 Three-dimensional structure of B-DNA

14 X-ray diffraction photograph of a vertically oriented Na + DNA fiber in the B conformation taken by Rosalind Franklin

15 B-DNA structure: Ball-and-stick and space-filling models viewed perpendicular to the helical axis

16 B-DNA structure: Ball-and-stick and space- filling models viewed parallel to the helical axis

17 A-DNA structure: Ball-and-stick and space-filling models viewed perpendicular to the helical axis

18 A-DNA structure: Ball-and-stick and space-filling models viewed parallel to the helical axis

19 Z-DNA structure: Ball-and-stick and space-filling models viewed perpendicular to the helical axis

20 Z-DNA structure: Ball-and-stick and space-filling models viewed parallel to the helical axis

21 Conversion of B-DNA to Z-DNA

22 Structural features of ideal A-, B-, and Z-DNA

23 X-ray structure of two ADAR1 Z  domains in complex with Z-DNA

24 X-ray structure of a 10-bp RNA–DNA hybrid helix consisting of d(GGCGCCCGAA) in complex with r(UUCGGGCGCC)

25 Sizes of some DNA molecules

26 Watson-Crick base pairs

27 Non-Watson-Crick base pairs: Pairing of adenine residues in the crystal structure of 9-methyladenine

28 Non-Watson-Crick base pairs: Hypothetical pairing between cytosine and thymine residues

29 Non-Watson-Crick base pairs: Hoogsteen pairing between adenine and thymine residues in the crystal structure of 9-methyladenine·1-methylthymine

30 IR spectra (N-H stretch region) of guanine, cytosine, and adenine derivatives (CDCl 3 solvent)

31 Association constants for base pair formation

32 Stacking of adenine rings in the crystal structure of 9-methyladenine Base stacking associations in aqueous solution are largely stabilized by hydrophobic forces. H-bonding contributes little to the stability of the DNA double helix.

33 Variation of the osmotic coefficient  with the molal concentrations m of adenosine derivatives in H 2 O  = 1: no association  = 0: infinite association  =  RTm  = osmotic pressure  measures the degree of association

34 Data are consistent with a successive aggregation model: A + A  A 2 + A  A 3 + A  …….A n where n = at least 5

35 Schematic representation of strand separation in duplex DNA resulting from heat denaturation heat

36 UV absorbance spectra of native and heat- denatured E. coli DNA The hyperchromic effect

37 Example of a DNA melting curve The melting temperature, T m, is defined as the temperature at which half of the maximum absorbance increase is attained. Denaturation over a narrow T range implies a cooperative process.

38 Variation of the melting temperatures, T m, of various DNAs with their G + C content T m increases linearly with the mole fraction of G-C content (G-C base-pairs are more stable than A-T base pairs).

39 Partially renatured DNA DNA that has been heat denatured then rapidly cooled to well below its T m

40 Melting curves for single-stranded poly(A) and ApA Non-cooperative processes are involved.

41 Thermodynamic parameters for the stacking/unstacking reaction: stacking is enthalpically driven and entropically opposed (opposite to what is observed in protein stabilization)

42 Transfer RNA (tRNA) drawn in its “cloverleaf” form

43 Action of restriction endonucleases

44 Site-directed mutagenesis

45 Schematic diagram of translation

46 Ribosomal reaction: peptide bond formation The peptide is constructed from N-terminus to C-terminus

47 The standard “genetic” code

48 Action of DNA polymerases

49 Action of RNA polymerases

50 Function of DNA ligase

51 END

52 Construction of a restriction map

53 Restriction map for the 5243-bp circular DNA of SV40

54 The pUC18 cloning vector

55 Construction of a recombinant DNA molecule

56 Splicing DNA using terminal transferase

57 Construction of a recombinant DNA molecule through the use of synthetic oligonucleotide adaptors

58 Colony (in situ) hybridization

59 Construction of a recombinant DNA molecule by directional cloning

60 Bacteriophages attached to the surface of a bacterium

61 Diagram of T2 bacteriophage injecting its DNA into an E. coli cell

62 The Hershey-Chase experiment

63 Demonstration of the semi-conservative mode of DNA replication in E. coli using density gradient ultracentrifugation

64 The central dogma of molecular biology

65 Gene expression

66 Control of transcription of the lac operon

67 Nucleotide reading frames

68 Agarose gel electrophoretogram of restriction digests

69 Pneumococci

70 Transgenic mice

71 Autoradiograph of Drosophila melanogaster DNA

72 Electron micrograph of a T2 bacteriophage and its DNA

73 Function of the transcription bubble

74 Post-transcriptional processing of eukaryotic mRNAs

75 Replication of duplex DNA in E. coli

76

77 The 5  3 exonuclease function of DNA polymerase I

78 Replacement of RNA primers by DNA in lagging strand synthesis

79 The 3  5 exonuclease function of DNA polymerase I and DNA polymerase III

80

81 Microinjection of DNA into the pronucleus of a fertilized mouse ovum

82 Use of green fluorescent protein (GFP) as a reporter gene

83 The polymerase chain reaction (PCR)

84 Restriction-fragment length polymorphisms

85 Inheritance of RFLPs according to the rules of Mendelian genetics

86 Electron micrograph of bacteriophage

87 Electron micrograph of the filamentous bacteriophage M13

88 Electron micrograph of an inclusion body of the protein prochymosin in an E. coli cell.

89 A degenerate oligonucleotide probe

90 Detection of DNAs containing specific base sequences by the Southern transfer technique

91 Cloning of foreign DNA in phages

92 Chromosome walking


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