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Biochemistry of Medicinals I – Nucleic Acids. Instructor : Natalia Tretyakova, Ph.D. 760E CCRB (Cancer Center) Tel. 6-3432 e-mail [email protected] Lecture : MWF 2:30-3:20 7-135 WDH Web page : see “Web enhanced courses”. Chapter 1. DNA Structure.

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Biochemistry of Medicinals I – Nucleic Acids

Instructor: Natalia Tretyakova, Ph.D.

760E CCRB (Cancer Center)

Tel. 6-3432

e-mail [email protected]

Lecture: MWF 2:30-3:20 7-135 WDH

Web page: see “Web enhanced courses”


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Chapter 1. DNA Structure.

Required reading: Stryer 5th Edition p. 117-125, 144-146, 152, 745-750,

754-762, 875-877)

(or Stryer’s Biochemistry 4th edition p. 75-77,80-88, 119-122, 126-128,

787-799, 975-980)


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DNA Structure: Chapter outline

  • Biological roles of DNA. Flow of genetic information.

  • Primary and secondary structure of DNA.

  • Types of DNA double helix. Sequence-specific DNA recognition by proteins.

  • Biophysical properties of DNA.

  • DNA topology. Topoisomerases.

  • Restriction Endonucleases. Molecular Cloning


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(ribonucleic acids)

(deoxyribonucleic acids)

replication

transcription

translation

DNA


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Why ?

  • Questions?

    • How is genetic information transmitted to progeny cells?

    • How is DNA synthesis initiated?

    • What causes DNA defects and what are their biological an physiological consequences?

    • What causes the differences between cells containing the same genetic information?

  • Relevance:

    • •Cancer: ex. Xeroderma pigmentosum

    • •Genetic diseases: ex., cystic fibrosis, sickle cell anemia, inborn errors of metabolism

    • •Genetic typing: ex., drug metabolism

    • •Rational drug design: ex., antitumor and antimicrobial drugs

    • •Biotechnology: ex., growth hormones


  • The building blocks of dna l.jpg
    The Building Blocks of DNA

    -N-glycosidic bond


    Dna and rna nucleobases l.jpg
    DNA and RNA nucleobases

    (DNA only)

    (RNA only)




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    nucleobase

    (Deoxy)

    nucleoside

    5’-mononucleotide

    Adenine (A)

    Guanine (G)

    Thymine (T)

    Cytosine (C)

    Uracil (U)

    2’-Deoxyadenosine (dA)

    2’- Deoxyguanosine (dG)

    2’- Deoxythymidine

    (dT)

    2’- Deoxycytidine

    (dC)

    Uridine (U)

    Deoxyadenosine 5’-monophosphate

    (5’-dAMP)

    Deoxyguanosine 5’-monophosphate

    (5’-dGMP)

    Deoxythymidine 5’-monophosphate

    (5’-dTMP)

    Deoxycytidine 5’-monophosphate

    (5’-dCMP)

    Uridine 5’-monophosphate (5’-UMP)

    Nomenclature of nucleobases, nucleosides, and mononucleotides




    Nucleosides must be converted to 5 triphosphates to be part of dna and rna l.jpg
    Nucleosides Must Be Converted to RNA5’-Triphosphates to be Part of DNA and RNA


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    DNA is RNAArranged5’ to 3’Connected byPhosphates

    Linking inDNA biopolymer: DNA primary structure


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    DNA secondary structure – double helix RNA

    • James Watson and Francis Crick, 1953- proposed a model for DNA structure

      • DNA is the molecule of heredity (O.Avery, 1944)

      • X-ray diffraction (R.Franklin and M. Wilkins)

      • E. Chargaff (1940s) G = C and A = T in DNA

    Francis Crick Jim Watson


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    Watson-Crick model of DNA was based on X-ray RNA

    diffraction picture of DNA fibres

    (Rosalind Franklin and Maurice Wilkins)

    Rosalind Franklin


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    Watson-Crick model of DNA was consistent with Chargaff’s base composition rules

    Erwin Chargaff (Columbia University)

    G = C and A = T in DNA



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    Base Pairing is Determined by Hydrogen Bonding base composition rules

    same size



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    Forces stabilizing DNA double helix base composition rules

    • Hydrogen bonding (2-3 kcal/mol per base pair)

    • Stacking (hydrophobic) interactions

    • (4-15 kcal/mol per base pair)

    • 3. Electrostatic forces.


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    B-DNA base composition rules

    • •Sugars are in the 2’ endo conformation.

    • •Bases are the anti conformation.

    • •Bases have a helical twist of 36º

    • (10.4 bases per helix turn)

    • Helical pitch = 34 A

    23.7 A

    right handed helix

    • helical axis passes through

    • base pairs

    7.0 A

    • planes of bases are nearly

    • perpendicular to the helix axis.

    • 3.4 A rise between base pairs

    Wide and deep

    Narrow and deep


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    DNA can deviate from the ideal Watson-Crick structure base composition rules

    • Helical twist ranges from 28 to 42°

    • Propeller twisting 10 to 20°

    • Base pair roll


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    Major groove and Minor groove of DNA base composition rules

    N

    NH

    O

    2

    N

    H

    N

    O

    2

    N

    NH

    N

    N

    N

    HN

    C-1’

    N

    N

    N

    N

    C-1’

    NH

    O

    O

    2

    C-1’

    Hypothetical situation: the two grooves would have similar size if dR residues

    were attached at 180° to each other

    To deoxyribose-C1’

    C1’ -To deoxyribose

    C-1’


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    N base composition rules

    NH

    2

    H

    N

    O

    2

    N

    N

    HN

    C-1’

    N

    N

    NH

    O

    2

    C-1’

    Major and minor groove of the double helix

    O

    N

    NH

    N

    N

    N

    N

    C-1’

    O

    C-1’

    Wide and deep

    Narrow and deep


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    B-type duplex is not possible for RNA base composition rules

    steric “clash”


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    A-form helix: base composition rulesdehydrated DNA; RNA-DNA hybrids

    • •Sugars are in the 3’ endo conformation.

    • •Bases are the anti conformation.

    • •11 bases per helix turn

    • Helical pitch = 25.3 A

    Right handed helix

    • planes of bases are tilted

    • 20 ° relative the helix axis.

    • 2.3 A rise between base pairs

    25.5 A

    Top View


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    The sugar puckering in A-DNA is 3’-endo base composition rules

    5.9 A

    7.0 A


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    A-DNA has a shallow minor groove and a deep major groove base composition rules

    Helix axis

    A-DNA

    B-DNA


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    Z-form double helix: base composition rulespolynucleotides of alternating purines and pyrimidines (GCGCGCGC) at high salt

    • • Backbone zig-zags because sugar puckers alternate between 2’ endo pyrimidines and 3’ endo (purines)

    • • Bases alternate between anti (pyrimidines) and syn conformation (purines).

    • •12 bases per helix turn

    • Helical pitch = 45.6 A

    Left handed helix

    • planes of the bases are

    • tilted 9° relative the helix

    • axis.

    • 3.8 A rise between base pairs

    18.4 A

    • Flat major groove

    • Narrow and deep minor groove


    Sugar and base conformations in z dna alternate l.jpg
    Sugar and base conformations in Z-DNA alternate base composition rules:

    5’-GCGCGCGCGCGCG

    3’-CGCGCGCGCGCGC

    C:sugar is 2’-endo, base is anti

    G: sugar is 3’-endo, base is syn


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    Biological relevance of the minor types of DNA secondary structure

    • Although the majority of chromosomal DNA is in B-form,

    • some regions assume A- or Z-like structure

    • Runs of multiple Gs are A-like

    • The upstream sequences of some genes contain

    • 5-methylcytosine = Z-like duplex

    • Structural variations play a role in DNA-protein interactions

    • RNA-DNA hybrids and ds RNA have an A-type structure


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