Structure of nucleic acids II Biochemistry 302. Bob Kelm January 21, 2005
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1 Structure of nucleic acids II Biochemistry 302 Bob Kelm January 21, 2005
2 User: student PW: nucleicacid
3 Secondary structure of RNAs antiparallel A-form Fig High Temp Denaturants In vivo conditions Base stacking w/o base pairing/h-bonds In vivo conditions Intra-strand base pairing
4 Ribose conformation (sugar pucker) differs in double-stranded RNA helices 2 3 H DNA is C2 endo 3 2 OH RNA is C3 endo 2 OH restricts C3 to endo
5 Structure of transfer RNA (trna) and the concept of self-complementarity Self-complementary regions form A-type antiparallel hairpins. Triple-base H-bonding & non-canonical bp Folding of helices produces a tertiary structure necessary for function. Fig Theoretical cloverleaf or cruciform structure Fig Yeast trna Phe 76 bases
6 Summary of secondary structures observed in DNA and RNA Sequence-independent B-form helix (DNA in vivo) A-form helix (DNA but only in vitro or in specific protein- DNA interactions) Stacked base or single-strand helix (RNA) Random coil (no secondary structure) Sequence-dependent A-form helix in dsrna and RNA-DNA hybrids RNA hairpins and cruciforms Z-DNA (5-mCG n repeats) DNA hairpins and cruciforms (rare) Triple helices and H-DNA (rare) G tetraplex
7 Sequences predicted to form hairpins and cruciforms inverted repeat w/ twofold symmetry Intrastrand bp single strand only symmetric sequence in each strand Palindrome = segments of complementary strands that are the reverse of one another Stability of extended DNA vs cruciform? Lehninger Principles of Biochemistry, 4th ed., Ch 24 Intrastrand bp both stands involved
8 Triple helical or H-DNA (regions of high Pur/Pyr asymmetry) N7, O 6, N 6 of purines known as Hoogsteen positions 1 6 C + = protonated C H-DNA formation produces a sharp bend (mutagenic, hotspot for DSBs) Fig Fig RNA can also form triple helices: polyu:polya:polyu This atom should be a purple nitrogen.
9 Concept of DNA stability DNA does not fall apart under physiological conditions of ph and ionic strength. but some inherent instability is built in. Why? Phosphate backbones of opposing DNA strands electrostatically repulsive (an effect reduced by dissolved counterions Na +, K +, Mg 2+ ). Random coil has a entropy. helix random coil G = H T S So, S > 0 & H elrep < 0 favors transition to random coil but H total > 0 because of H- bonding and van der Waals interactions between bps Lehninger Principles of Biochemistry, 4th ed., Ch 8
10 Concept of DNA thermal stability (practical perspective, DNA melting ) Note the sharp T m transition point which is indicative of a highly cooperative transition. Fig Hypochromism: Pur and Pyr rings of stacked bases absorb light less efficiently than unstacked bases or free nucleotides.
11 T m depends on base-pair composition AT-rich regions melt (i.e. denature) more easily than GC-rich regions. Why? At T m, G denat = 0 so 0 = H T m S and T m = H/ S S is the same for most polynucleotides on a per bp basis. H is higher for G C base pairs. Thermal stability of hybrids: RNA-RNA > RNA-DNA > DNA-DNA Fig. 4.32
12 Structural features of DNA molecules in living organisms Single or double-stranded Linear or circular Small or large 5243 bp for SV40 genome (circular, DS) 6407 b for bacteriophage M13 genome (circular, SS) 4.6 x 10 6 for E. coli genome (circular, DS) 6.5 x 10 7 bp for 1 fruit fly chromosome (linear, DS) 3.2 x 10 9 bp for 23 human chromosomes (linear, DS) B-form except where sequence dictates otherwise Relaxed or supercoiled E. coli cell (2 µm) chromosome (1.7 mm) Lehninger Principles of Biochemistry, 4th ed., Ch 24
13 Tertiary structure of DNA (supercoiling of the helix) Higher-order folding of regular secondary structural elements Supercoiling Twist of DNA strands around one another Extra twists in the helix itself Normal state of closed circular DNA molecules (to relieve strain of being underwound) Lehninger Principles of Biochemistry, 4th ed., Ch 24
14 Topological property of dsdna can be described quantitatively as L Twist (T) = # bp/10.5 bp/turn = # of helical turns in DNA of fixed length Writhe (W) = # superhelical turns required to restore original Twist Linking number (L) = # times strands of closed DNA are interlinked L = T + W Topoisomerases change L. Fig Unnatural twist or underwound by one turn to the left Right (-)
15 Utility of superhelical density (σ) G sc, free energy stored in supercoiling is proportional to superhelical density, G sc = Kσ 2 (σ = L/L 0 ) where L = # turns removed or added relative to # in relaxed DNA. When DNA is relaxed..σ = 0 so G sc = 0. Decreasing σ (local unwinding) reduces stored energy G sc. Imposing superhelical stress on DNA may thus promote Localized melting (AT-rich DNA) Formation of short stretches of Z-DNA (alternating CG n tract) Cruciform extension (palindromic sequences) H-DNA formation (asymmetric poly Pur/Pyr tract) Lehninger Principles of Biochemistry, 4th ed., Ch 24
16 Characteristics of naturally occurring circular DNA (e.g. plasmids, mito DNA) Underwound (common) Right-handed superhelical twist, negative supercoiling σ = 0.05 to 0.07 Overwound (rare) Left-handed superhelical twist, positive supercoiling Processive enzyme movement Exist as topoisomers Relaxed Supercoiled Topoisomerases Cut and reseal DNA Some (e.g. E.coli DNA gyrase) require ATP Plasmid DNA treated with type I topoisomerase for different times Lehninger Principles of Biochemistry, 4th ed., Ch 24
17 Tertiary structure of DNA in vitro and in vivo: importance of compaction Plectonemic ( twisted thread ) supercoiling pr otein Solenoidal supercoiling (greater compaction) Lehninger Principles of Biochemistry, 4th ed., Ch 24
18 Metazoans have major size and biological issues to contend with. Super-sized genome Fit 2 meters worth of DNA (~6 x 10 9 bp) into a nucleus ~8 µm in diameter Compaction solenoid Exquisite control of Gene Expression Maintain and regulate genetic programs essential to cell growth and differentiation Structure must accommodate chromosomal organization where only 5-10% of DNA is actually transcribed Lehninger Principles of Biochemistry, 4th ed., Ch 24
19 The Solution. Use special proteins to form chromatin Histones Small (~11-23 kda), basic, & highly conserved Building blocks of chromatin Subject to post-translational modification Five types core & linker Non-histone chromosomal proteins SMC (structural maintenance of chromosomes) proteins Cohesins link sister chromatids after replication Condensins mediate chromosome condensation as cells enter mitosis Polymerases and other nuclear enzymes plus gene regulatory proteins (e.g. transcription & remodeling factors, 1000 different proteins) Lehninger Principles of Biochemistry, 4th ed., Ch 24
20 Structure of the nucleosome core particle (histone octamer plus DNA) H3 H4 H2A H2B Octamer acts like a helical ramp K. Luger et al. (1997) Nature 389:251 Fig bp of DNA/octamer; 1.7 left-hand superhelical turns
21 Other features of nucleosome structure (2 nd level of organization) Histone core-dna binding is not random (positioned near clusters of A=T bp). Nucleosomes separated by 20 to 100 bp (but linker distance varies among organisms and cell types. Linker DNA is occupied by H1-type histones and other non-histone proteins. H1 plays important role in higher order organization (one H1/nucleosome core). Gene-specific nucleosomes occupy defined positions. Subject to remodeling. beads-on-a-string (3 rd level of organization) Lehninger Principles of Biochemistry, 4th ed., Ch 24
22 30 nm fiber ~100-fold DNA compaction (need 10 4 fold) Heterochromatin (condensed) Euchromatin (open) MARs (sites of topoisomerase action and gene activation) Fig Lehninger Principles of Biochemistry, 4th ed., Ch 24
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![2012 GENERAL [5 points]](/thumbs/75/72452386.jpg "2012 GENERAL [5 points]")
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