Biophysical Chemistry 1, Fall 2010 Web Assignment: Http .

Principles of nucleic acid structureBiophysical Chemistry 1, Fall 2010Reading assignment: Chap. 3Web assignment: http://w3dna.rutgers.edu

Nucleic acids:phosphates,sugars,3 -oxygenof nucleotidei is joinedto basesthe 5 -oxygen of nucleo(i)(I 1)

The sugar-phosphate backboneζ O3’Oβ P—O5’—C5’—C4’O5’βnucleotide unitα �3’O3’εBase Chaindirectionχ1’2’O3’OP1OP2PResidue i-1Residue iO5’C5’γ O5’—C5’—C4’-C3’δ C5’—C4’—C3’—C2’ε C4’—C3’—O3’—Pi 1ζ C3’—O3’—Pi 1-O3’i 1PC3’Basics of Nucleic Acid Structure

Sugar puckeringBasics of Nucleic Acid Structure 6323’2’C5’2’C5’C5’BT33’3’ O4’C5’ O4’ 2’3EO4’ 2’3’ O4’2BC5’BEB3T22’BC5’ 3’ O4’BE3E22’3’C5’S conformationsBBC5’N conformationsFIGURE 3.5 Various sugar ring puckering conformations. Those on the left are denoted S (forsouth); those on the right, N (for north). The C3′-endo conformation is seen at the top right, andthe C2′-endo conformation at the top left. The notation of E and T conformations is also given.Superscript numbers preceding E or T refer to carbon atoms on the same side of the referenceplane (horizontal line) as C5′. Subscripts following E or T denote atoms on the opposite side of

Sugar puckering4 A Textbook of Structural BiologyNC2’-exo324 C1’-endo11 2E2T0 C3’-endo36 332TE34TE288 4E04T10TO4’-exoC4’-endoE01T4EC4’-endo72 00E40T252 C4’-exo43T223E 3T E216 C3’-exo180 S21T108 1EC1’-exo144 C2’-endo

ation. Conformational angles of P are divided into two categories, north (N) and sopurines and ne36ON21NHOCytosineE 3.8 The most common bases found in nucleic acids: the top row is purinm row pyrimidines. The atom-numbering scheme of purines and pyrimidines is giv

The glycosidic torsion parameterBasics of Nucleic Acid Structure 65

Watson-Crick base pairingA Textbook of Structural Biologymajor grooveONRNmajor grooveHHNHHOHNNNNNHNNNRRNHONHNNORminor grooveminor grooveGuanineCytosineAdenineThymineFIGURE 3.13 The Watson–Crick base pairs. The sugar moieties are represented by R. Noticethat the GC base pair on the left interacts via three hydrogen bonds, whereas the AT base pairon the right has only two. This makes the GC base pair and thus GC-rich DNA morestable than the AT base pair and AT-rich DNA.phosphodiester linkages between adjacent nucleotides. In the sugar-phosphatepart the phosphate groups connect to the 3′ carbon of one deoxyribose moietyand the 5′ carbon of the next moiety, thereby linking successive deoxyribosestogether. The two ends of a chain differ; the end where the 5′ carbon is not con-

A and B-form helicesThe A.B transition: first known change of DNA double-helical state. H2O.- salt and/or alcohol11 bp/turnA-DNA10 bp/turnB-DNAA-DNA base pairs inclined with respect to helical axis and untwisted cf. B DNA.A-DNA minor groovewider and moreshallow, major groovenarrower and moredeep cf. B!DNABase pairs displaced from A-DNA helical axis.

10 bases per turn. One full turn measures 3.4 nm in the axial direction. TA and B-form helices

Base stackingThe overlap of successive base pairs depends on duplex form.

Concentrate on the basepair structuresBasics of Nucleic Acid Structure yxyShearyzzzTwist5'xIICoordinate frame

Getting DNA to bendCombined B.A and B.C deformations tighten the bending of DNA: ACGlobal bend:360 /75 bpleft-handed superhelixCombined B.A and B.C deformations tighten the bending of DNA:

The nucleosome core particleA Textbook of Structural BiologyFIGURE 3.21 Left: A dimer of histone proteins H3 (blue) and H4 (light blue). Right: Nucleosomestructure. The octameric complex of histone proteins forms the center and the DNA is woundaround. The color scheme of the histone subunits in the core particle is the same as in Fig. 3.20(PDB: 1KX3).

DNA binding to the histone core proteins

Comparison to elastic rod modelsBending rigidity: A M (2πνn )2;LPn4Twisting rigidity: C Stretching rigidity: Y a A/(kB T )I (2Lνn )2n2ML(2νn )2n2Lord Rayleigh, The Theory of Sound, 1894

Bending rigidity for linear duplex DNABending motionsn 1n 2n 3d(GACT) 60 base pairsn123 19A 2.44 10GB frequencies0.1140.1160.2940.2950.5220.532erg.cm 2.26 10Analytical frequencies0.1000.2750.539 19erg.cm a 594 Å 550 Å

Stretching rigidity for linear duplex DNAStretching motionsn 1n 2n 3d(GACT) 60 base pairsn123GB frequencies0.6641.2891.807Y 1502 pNAnalytical frequencies0.6191.2371.846 1000 1500 pN

Salt dependence of bending and stretching are not the sameExp: Baumann, Smith, Bloomfield, Bustamante, PNAS 94, 6185 (1997)Theory: Bomble & Case, Biopolymers 89, 722 (2008)

750700500d(G AC T )d(G C )d(AT )dG .dCdA.dTd(C T G )d(C G G 20r21r22r23r24r25r26r27r28r29r30P ersi stence length (Å)Sequence dependence of bending rigidity800dA.dTdG.dC650600550450d(CGG)S equence (60 bp)

Now consider circular DNAνn f (Ω, R , Tw , n, ρ)R is the circle radius Tw is the excess twistΩ C /Aρ is the mass densityMatsumoto, Tobias, Olson,JCTC 1, 117 (2005)

In-plane and out-of-plane modes for circular DNAIn plane bending motionsn 3n 2n234Relaxed minicircle with 94 base pairsGB frequenciesAnalytical 40.697Overtwisted minicircle with 94 base pairsGB frequenciesAnalytical 80.734Out of plane bending motionsn 3n 2n234Relaxed minicircle with 94 base pairsGB frequenciesAnalytical 10.864Overtwisted minicircle with 94 base pairsGB frequenciesAnalytical 10.958

Moving on to RNA80 A Textbook of Structural �3’BaseOPC3’-endoC2’-endoFIGURE 3.23 The two types of sugar pucker most commonly found in nucleic acids. TheC3′-endo pucker is prevalent in RNA and A-form DNA, whereas the C2′-endo pucker ischaracteristic of B-form DNA. It is seen that the C3′-endo pucker produces a significantlyshorter phosphate-phosphate distance in the backbone, resulting in a more compact helicalconformation.10 nucleotides per turn, RNA prefers the A-form with 11–12 nucleotides per turn.In DNA, the base pairs are centered over the helix axis. In an RNA double helix,the base pairs slide 5 Å away from the helix center. All these factors contributeto the tighter packing of the RNA double helix.The surface of an RNA helix is also quite different from the DNA double helix.The major groove of RNA is very narrow and deep, accentuated by the fact thatRNA does not have the thymine methyl group, which resides in the major groove.In contrast, the minor groove is wide and shallow. For this reason, the major and

tions, manifested in the degeneracy of the genetic code (Chap. 8). Figure 3.27 showsRNAmorebase-pairingthehasGU wobblebasepair, which is one possibilitiesof the most common alternative base pairing patterns, and the GU reverse wobble, where the uracil group is simply flippedONRNHNHNHRHNNNORONHNNHONRNNNHNHHNHGC Watson-CrickGC reverseFIGURE 3.25 Left: Canonical Watson–Crick GC base pair (cis). Right: GC reverse Watson–Crickbase pair (trans).HNNNNHHRNNOAU HoogsteenHHORAU reverse HoogsteenHORNNNRONNHNNRRNNHNNNNONHNOAU reverse base pairFIGURE 3.26 Left: AU Hoogsteen base pair. Center: AU reverse Hoogsteen base pair.

RNAhasbase-pairingpossibilities Left: CanonicalFIGURE3.25 moreWatson–Crick GCbase pair (cis). Right: GC reverse Watson–Crickbase pair (trans).HNNNNHHRNNOAU HoogsteenHHORAU reverse HoogsteenHORNNNRONNHNNRRNNHNNNNONHNOAU reverse base pairFIGURE 3.26 Left: AU Hoogsteen base pair. Center: AU reverse Hoogsteen base pair.Right: AU reverse Watson–Crick base pair. The blue dashed line shows the line of symmetryused to define the cis/trans conformation of the base pair. The AU Hoogsteen base pair is thuscis-H/WC, and the AU reverse Hoogsteen is trans H/WC.

RNA has more base-pairing possibilitiesTextbook of Structural BiologyOORNONRHNNNNHNNH2GU wobbleOONRRNNHHNONNH2GU reverse wobbleFIGURE 3.27 Left: GU wobble. Right: GU reverse wobble.around the axis of the amine hydrogen bond. The GU wobble base pairing resultsin the loss of a hydrogen bond from the guanine, but the vacant amino group oftenforms hydrogen bonds to other bases nearby, perhaps in concert with the neighboring imino group. The GU wobble base pairings can be viewed as a canonicalWatson–Crick pattern, with a shift of the pyrimidine partner.

If lysidine is absent, the tRNA will instead be recognized and mischarged by theRNAuses chemically-modifiedCAT-recognizingmethionyl tRNA ligase. Sobasesa single posttranslational modificationis responsible for both the codon and amino acid specificity of this tRNA.OSHHNOHNHHOHdihydrouracil (D)NH2ONHNH2NNORR4-thiouracil (S4U)3-methylcytosine (m3C)ONNNHNNRR5-methylcytosine (m5C)Inosine (I)H COOC3NH2NHORHNONNHpseudouridine (Ψ)FIGURE 3.32for ribose. NRN6-methyladenine (m6A)ONNN N NH3NHROlysidine (L)ONNRNHNNNNH2COOCH3Nwyosine (Y)Examples of modified bases in RNA. Modifications are marked in red. R stands

Tetraloopsare tetraloopsa particularly common motif in RNA structures. An especiallyRNAmotifs:well-known case of this hairpin loop is the GNRAa loop motif, which closes theFIGURE 3.36 Three-dimensional structures of various tetraloop folds. Left : GNRA loop from 5SrRNA (PDB: 1JJ2). The first G in the loop stabilizes the loop by hydrogen bonding to the fourthmember. Middle: ANYA loop from MS2-RNA complex (PDB: 1DZS). Bases one and two form astacking interaction, while bases of three and four of the loop are looped out and poised to interact with other species. Right: UNCG tetraloop from 16S rRNA (PDB: 1BYJ). The first U and thelast G in the tetraloop interact via hydrogen bonds, while bases of one and two in the loop forma stacking interaction. The third base in the loop is available for interaction with other species.aR stands for puRine; N stands for aNy; Y stands for pYrimidine.

the ribosomal RNAs after the normal Watson–Crick base pair.Stems, bulges, loops, internal loops3’G100A GC C U C UGGG ACGCCA120 CCGCCG110CAA C CC G GU UC G GAGGUC AU AGGGGCCUUGU807090Loop DHelix 4Loop EHelix 55’UUAG Helix 1GCGG 10CC AG30CU G20A40GC CCC UGC GGUGGGCG U A C C C A UCGCG C CA CCC GGGCACA AG CCA UAAGA AA6050Loop AHelix 2Loop BHelix 3Loop C

efficiency.Theseuntranslatedregions (UTRs) are present before the start codonEvenmRNAhasstructure(5′ UTRs) and after the stop codon (3′ UTRs). They contain areas of well-definedAAAAAAAAAAAAAAAAAAAAAAAAm7G cap5’UTR3’ UTRpoly(A) tailFIGURE 3.50 Schematic representation of eukaryotic mRNA showing the 5′ cap, the codingregion (red), and the 5′ and 3′ UTRs.