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 (CDCl3 solvent)

31. Association constants for base pair formation

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

33. = 0: infinite association
= 1: no association
= 0: infinite association
p = fRTm
= osmotic pressure
f measures the degree of
association
Variation of the osmotic coefficient  with the molal concentrations m of adenosine derivatives in H2O

34. Data are consistent with a successive
aggregation model:
A + A  A2 + A  A3 + A  …….An
where n = at least 5

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

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

37. Example of a DNA melting curve
The melting temperature, Tm,
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.
Example of a DNA melting curve

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

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

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

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
Ribosomal reaction: peptide bond formation

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
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. Replication of duplex DNA in E. coli

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

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 l

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 l phages

92. Chromosome walking