Chapter 12 Biochem

Biochemistry 2/e - Garrett & Grisham
Chapter 12
Structure of Nucleic Acids
to accompany Biochemistry, 2/e by Reginald Garrett and Charles Grisham
All rights reserved. Requests for permission to make copies of any part of the work should be mailed to: Permissions Department, Harcourt Brace & Company, 6277 Sea Harbor Drive, Orlando, Florida 32887-6777 Copyright 1999 by Harcourt Brace & Company
Outline
12.1 Primary Structure of Nucleic Acids 12.2 ABZs of DNA Secondary Structure 12.3 Denaturation and Renaturation of DNA 12.4 Tertiary Structure of DNA 12.5 Chromosome Structure 12.6 Chemical Synthesis of Nucleic Acids 12.7 Secondary and Tertiary Structure of RNA
Copyright 1999 by Harcourt Brace & Company
Primary Structure
Sequencing Nucleic Acids Chain termination method (dideoxy method), developed by F. Sanger Base-specific chemical cleavage, developed by Maxam and Gilbert Both use autoradiography - X-ray film develops in response to presence of radioactive isotopes in nucleic acid molecules
DNA Replication
DNA is a double-helical molecule Each strand of the helix must be copied in complementary fashion by DNA polymerase Each strand is a template for copying DNA polymerase requires template and primer Primer: an oligonucleotide that pairs with the end of the template molecule to form dsDNA DNA polymerases add nucleotides in 5'-3' direction
Chain Termination Method

Based on DNA polymerase reaction Run four separate reactions Each reaction mixture contains dATP, dGTP, dCTP and dTTP, one of which is P-32-labelled Each reaction also contains a small amount of one dideoxynucleotide: either ddATP, ddGTP, ddCTP or ddTTP

Most of the time, the polymerase uses normal nucleotides and DNA molecules grow normally Occasionally, the polymerase uses a dideoxynucleotide, which adds to the chain and then prevents further growth in that molecule Random insertion of dd-nucleotides leaves (optimally) at least a few chains terminated at every occurrence of a given nucleotide

Run each reaction mixture on electrophoresis gel Short fragments go to bottom, long fragments on top Read the "sequence" from bottom of gel to top Convert this "sequence" to the complementary sequence Now read from the other end and you have the sequence you wanted - read 5' to 3'
Chemical Cleavage Method

Not used as frequently as Sanger's Start with ssDNA labelled with P-32 at one end Strand is cleaved by chemical reagents Assumption is that strands of all possible lengths, each cleaved at just one of the occurrences of a given base, will be produced. Fragments are electrophoresed and sequence is read
Four reactions are used G-specific cleavage with dimethyl sulfate, followed by strand scission with piperidine G/A cleavage: depurination with mild acid, followed by piperidine C/T cleavage: ring hydrolysis by hydrazine, followed by piperidine C cleavage: same method (hydrazine and piperidine), but high salt protects T residues
Reading the gels... It depends on which end of the ssDNA was radioactively labelled! If the 5'-end was labelled, read the sequence from bottom of gel to top (5' to 3') If the 3'-end was labelled, read the sequence from top of gel to bottom (5' to 3') Note that the nucleotide closest to the P-32 will be missed in this procedure
The ABZs of DNA
Secondary Structure See Figure 12.10 for details of DNA secondary structure Sugar-phosphate backbone outside Bases (hydrogen-bonded) inside Right-twist closes the gaps between base pairs to 3.4 A (0.34 nm) in B-DNA
The canonical base pairs
See Figure 12.10 The canonical A:T and G:C base pairs have nearly identical overall dimensions A and T share two H-bonds G and C share three H-bonds G:C-rich regions of DNA are more stable Polar atoms in the sugar-phosphate backbone also form H-bonds
Major and minor grooves

See Figures 12.10, 12.11 The "tops" of the bases (as we draw them) line the "floor" of the major groove The major groove is large enough to accommodate an alpha helix from a protein Regulatory proteins (transcription factors) can recognize the pattern of bases and Hbonding possibilities in the major groove
Comparison of A, B, Z DNA
See Table 12.1 A: right-handed, short and broad, 2.3 A, 11 bp per turn B: right-handed, longer, thinner, 3.32 A, 10 bp per turn Z: left-handed, longest, thinnest, 3.8 A, 12 bp per turn See Figure 12.13
Z-DNA

Discovered by Alex Rich Found in G:C-rich regions of DNA G goes to syn conformation C stays anti but whole C nucleoside (base and sugar) flips 180 degrees Result is that G:C H-bonds can be preserved in the transition from B-form to Z-form!
12.3 Denaturation of DNA
See Figure 12.17 When DNA is heated to 80+ degrees Celsius, its UV absorbance increases by 30-40% This hyperchromic shift reflects the unwinding of the DNA double helix Stacked base pairs in native DNA absorb less light When T is lowered, the absorbance drops, reflecting the re-establishment of stacking
12.4 Supercoils and Cruciforms

In duplex DNA, ten bp per turn of helix Circular DNA sometimes has more or less than 10 bp per turn - a supercoiled state Enzymes called topoisomerases or gyrases can introduce or remove supercoils Cruciforms occur in palindromic regions of DNA Negative supercoiling may promote cruciforms
Chromosome Structure
Human DNAs total length is ~2 meters! This must be packaged into a nucleus that is about 5 micrometers in diameter This represents a compression of more than 100,000! It is made possible by wrapping the DNA around protein spools called nucleosomes and then packing these in helical filaments
Nucleosome Structure
Chromatin, the nucleoprotein complex, consists of histones and nonhistone chromosomal proteins Histone octamer structure has been solved (without DNA by Moudrianakis, and with DNA by Richmond) Nonhistone proteins are regulators of gene expression
Chemical Synthesis of Nucleic Acids

Laboratory synthesis of nucleic acids requires complex strategies Functional groups on the monomeric units are reactive and must be blocked Correct phosphodiester linkages must be made Recovery at each step must high!
Solid Phase Oligonucleotide Synthesis

Dimethoxytrityl group blocks the 5-OH of the first nucleoside while it is linked to a solid support by the 3-OH Step 1: Detritylation by trichloroacetic acid exposes the 5-OH Step 2: In coupling reaction, second base is added as a nucleoside phosphoramidate
Solid Phase Synthesis

Step 3: capping with acetic anhydride blocks unreacted 5-OHs of N-1 from further reaction Step 4: Phosphite linkage between N-1 and N-2 is reactive and is oxidized by aqueous iodine to form the desired, and more stable, phosphate group
12.7 Sec/Tert Structure of RNA
Transfer RNA Extensive H-bonding creates four double helical domains, three capped by loops, one by a stem Only one tRNA structure (alone) is known Phenylalanine tRNA is "L-shaped" Many non-canonical base pairs found in tRNA
Ribosomal RNA
Ribosomes synthesize proteins All ribosomes contain large and small subunits rRNA molecules make up about 2/3 of ribosome High intrastrand sequence complementarity leads to (assumed) extensive base-pairing
Ribosomal RNA
Secondary structure features seem to be conserved, whereas sequence is not There must be common designs and functions that must be conserved

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Biochemistry 2/e - Garrett & Grisham

Biochemistry 2/e - Garrett & Grisham

Copyright 1999 by Harcourt Brace & Company

Biochemistry 2/e - Garrett & Grisham

Copyright 1999 by Harcourt Brace & Company

Biochemistry 2/e - Garrett & Grisham

Biochemistry 2/e - Garrett & Grisham

Biochemistry 2/e - Garrett & Grisham

Copyright 1999 by Harcourt Brace & Company

Biochemistry 2/e - Garrett & Grisham

Chain Termination Method

Biochemistry 2/e - Garrett & Grisham

Copyright 1999 by Harcourt Brace & Company

Biochemistry 2/e - Garrett & Grisham

Chain Termination Method

Biochemistry 2/e - Garrett & Grisham

Chain Termination Method

Biochemistry 2/e - Garrett & Grisham

Chemical Cleavage Method

Copyright 1999 by Harcourt Brace & Company

Biochemistry 2/e - Garrett & Grisham

Chemical Cleavage Method

Copyright 1999 by Harcourt Brace & Company

Biochemistry 2/e - Garrett & Grisham

Copyright 1999 by Harcourt Brace & Company

Biochemistry 2/e - Garrett & Grisham

Chemical Cleavage Method

Copyright 1999 by Harcourt Brace & Company

Biochemistry 2/e - Garrett & Grisham

Copyright 1999 by Harcourt Brace & Company

Biochemistry 2/e - Garrett & Grisham

Copyright 1999 by Harcourt Brace & Company

Biochemistry 2/e - Garrett & Grisham

Copyright 1999 by Harcourt Brace & Company

Biochemistry 2/e - Garrett & Grisham

The ABZs of DNA

Copyright 1999 by Harcourt Brace & Company

Biochemistry 2/e - Garrett & Grisham

Copyright 1999 by Harcourt Brace & Company

Biochemistry 2/e - Garrett & Grisham

Copyright 1999 by Harcourt Brace & Company

Biochemistry 2/e - Garrett & Grisham

The canonical base pairs

Copyright 1999 by Harcourt Brace & Company

Biochemistry 2/e - Garrett & Grisham

Copyright 1999 by Harcourt Brace & Company

Biochemistry 2/e - Garrett & Grisham

Major and minor grooves

Biochemistry 2/e - Garrett & Grisham

Copyright 1999 by Harcourt Brace & Company

Biochemistry 2/e - Garrett & Grisham

Copyright 1999 by Harcourt Brace & Company

Biochemistry 2/e - Garrett & Grisham

Copyright 1999 by Harcourt Brace & Company

Biochemistry 2/e - Garrett & Grisham

Copyright 1999 by Harcourt Brace & Company

Biochemistry 2/e - Garrett & Grisham

Copyright 1999 by Harcourt Brace & Company

Biochemistry 2/e - Garrett & Grisham

Copyright 1999 by Harcourt Brace & Company

Biochemistry 2/e - Garrett & Grisham

Copyright 1999 by Harcourt Brace & Company

Biochemistry 2/e - Garrett & Grisham

Copyright 1999 by Harcourt Brace & Company