Chapters 5 and 29

3/4/05


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Table of Contents

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

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

Some possible tautomeric conversions for bases

N-Glycoside conformation: syn and anti conformations

Furanose ring conformation: A planar ribose ring viewed down the C3_-C4_ bond showing the eclipsed substituents

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)

Nucleotide furanose conformation: C3_-endo conformation (on the same side of the sugar ring as C5_) which occurs in A-RNA and RNA-11

Nucleotide furanose conformation: C2_-endo conformation which occurs in B-DNA

Hydroxymethyl group conformation: conformational wheel showing the distribution of C4_-C5_ torsion angles of the furanose ring

Nucleotide conformation is determined by the seven indicated torsion angles.

Chemical structure of a nucleic acid

Mechanism of base-catalyzed RNA hydrolysis

Three-dimensional structure of B-DNA

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

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

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

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

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

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

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

Conversion of B-DNA to Z-DNA

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

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

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

Sizes of some DNA molecules

Watson-Crick base pairs

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

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

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

IR spectra (N-H stretch region) of guanine, cytosine, and adenine derivatives (CDCl3 solvent)

Association constants for base pair formation

Stacking of adenine rings in the crystal structure of 9-methyladenine

Variation of the osmotic coefficient _ with the molal concentrations m of adenosine derivatives in H2O

PPT Slide

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

UV absorbance spectra of native and heat-denatured E. coli DNA

Example of a DNA melting curve

Variation of the melting temperatures, Tm, of various DNAs with their G + C content

Partially renatured DNA

Melting curves for single-stranded poly(A) and ApA

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

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

Action of restriction endonucleases

Site-directed mutagenesis

Schematic diagram of translation

Ribosomal reaction: peptide bond formation

The standard “genetic” code

Action of DNA polymerases

Action of RNA polymerases

Function of DNA ligase

PPT Slide

Construction of a restriction map

Restriction map for the 5243-bp circular DNA of SV40

The pUC18 cloning vector

Construction of a recombinant DNA molecule

Splicing DNA using terminal transferase

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

Colony (in situ) hybridization

Construction of a recombinant DNA molecule by directional cloning

Bacteriophages attached to the surface of a bacterium

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

The Hershey-Chase experiment

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

The central dogma of molecular biology

Gene expression

Control of transcription of the lac operon

Nucleotide reading frames

Agarose gel electrophoretogram of restriction digests

Pneumococci

Transgenic mice

Autoradiograph of Drosophila melanogaster DNA

Electron micrograph of a T2 bacteriophage and its DNA

Function of the transcription bubble

Post-transcriptional processing of eukaryotic mRNAs

Replication of duplex DNA in E. coli

Replication of duplex DNA in E. coli

The 5˘ ® 3˘ exonuclease function of DNA polymerase I

Replacement of RNA primers by DNA in lagging strand synthesis

The 3˘ ® 5˘ exonuclease function of DNA polymerase I and DNA polymerase III

PPT Slide

Microinjection of DNA into the pronucleus of a fertilized mouse ovum

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

The polymerase chain reaction (PCR)

Restriction-fragment length polymorphisms

Inheritance of RFLPs according to the rules of Mendelian genetics

Electron micrograph of bacteriophage l

Electron micrograph of the filamentous bacteriophage M13

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

A degenerate oligonucleotide probe

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

Cloning of foreign DNA in l phages

Chromosome walking

Author: Anthony S. Serianni

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