NUCLEIC ACIDS. Basic terms and notions. Presentation by Eva Fadrná adapted by Radovan Fiala
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1 UCLEIC ACIDS Basic terms and notions Presentation by Eva Fadrná adapted by Radovan Fiala
2 RA vs DA Single strand A-RA B-DA duplex
3 Length of A Total length of DA in a human cell 1 m (1000 km) DA in typical human chromozome 1 cm (10 km) DA from bacterial chromozome 1 mm Diameter of typical human cell 0.01 mm Diameter of folded DA 0.1 µm (0.1 m) Diameter of DA fiber 1 nm (1 mm) Diameter of atom 1 Å (multiplied by 10 6 ) 1 chromozome would be 10km long with fiber diameter of 1 mm and it would fold into 10 cm diameter extraordinary DA flexibility
4 ukleotide H C3 O3 H H O5 C5 H O4 H C4 O O P 9 C1 H C2 H O2 H H 2 H C3 O3 H H O5 C5 H O4 H C4 O O P H 9 C1 H C2 H O2 H H 2 H C3 O3 chain H H O5 C5 H O4 H C4 O O P H 9 C1 H C2 H O2 H H 2 H C3 H H O5 C5 H O4 H C4 H 9 C1 H C2 H nucleotide H 2 H O3 O2 H
5 Grooves major vs. minor
6 RA vs DA deoxythymidine uridine
7 ukleotide/nukleoside base + sugar (ribose/deoxyribose) nukleoside + phosphate nukleotide
8 DA Bases RA Guanin (Gua) Adenin (Ade) PURIES PYRIMIDIES Thymin (Thy) sugar Cytosin (Cyt) Uracil (Ura)
9 Base numbering PURIES PYRIMIDIES H
10 Base tautomerism enol keto fysiolog. conditions C = C O H CH C = O enamin imin H C = C H CH C = H
11 Base tautomerism enol keto enamin imin H C = C O H CH C = O C = C CH C = H H 4 tautomers O OH OH O H H O H O H HO HO
12 Sugar - pentoses HO RA CH 2 O OH 1 2 semiacetal hydroxyl group HO CH 2 O OH 2 1 DA OH OH OH ß D - ribose 2 deoxy ß D - ribose semiacetal hydroxyl group + base -glycosidic bond nukleoside C1-1 C1-9 pyrimidines purines
13 ukleosides purines pyrimidines C1-9 H 2 C1-1 O H HO O 9 C1 -glykosidic bond HO O O 1 C1 OH OH HO OH
14 ukleosides Ribonukleosides uridine cytidine adenosine guanosine = U = C = A = G HO O base Deoxyribonukleosides deoxythymidine deoxycytidine deoxyadenosine deoxyguanosine = dt = dc = da = dg HO (OH)
15 Phosphate group H 2 H 2 OH O = P OH OH HO O 9 C1 O O = P O O - - O 9 C1 + adenosine OH OH OH OH acid orthophosphoric acid H 3 PO 4 + alcohol ester adenosine adenosine(mono)phosphate (AMP)
16 ukleotides OH O = P O OH O base Ribonucleotides uridyl acid = uridine 5 monophosphate = UMP, pu cytidyl acid = cytidin - - = CMP, pc adenyl acid = adenosin - - = AMP, pa guanyl acid = guanosin - - = GMP, pg HO (OH) Deoxyribonucleotides deoxytymidyl acid = 2 deoxythymidine-5 -monophosphate = dtmp, pdt deoxycytidyl acid = - - cytidin - - = dcmp, pdc deoxyadenyl acid = - - adenosin - - = damp, pda deoxyguanyl acid = - - guanosin - - = dgmp, pdg
17 H 2 Phosphate H 2 group HO O OH OH O = P O O - alcohol OH 9 C1 O 9 C1 H 2 OH OH + acid diester (ester) HO 5 O O O = P O O - OH 9 C1 3 OH O OH 9 C1 H 2 nukleoside-nukleotide ApA
18 H 2 H C3 O3 H H O5 C5 H O4 H C4 O 5 nucleotide O P 9 C1 H C2 H O2 H H C3 O3 H H O5 C5 H O4 H C4 O O P H 9 C1 H C2 H O2 H H 2 H C3 O3 H H O5 C5 H O4 H C4 O O 3 P H 9 C1 H C2 H O2 H H 2 H C3 O3 H H O5 C5 H O4 H C4 H 9 C1 H C2 H O2 H H 2 H ucleotide chain
19 Torsion angle A D B C <0 o, 360 o > <-180 o, 180 o >
20 Torsion angle synperiplanar (sp) -gauche (-g) +gauche (+g) synclinal (sc) anticlinal (ac) antiperiplanar (ap) trans (t)
21 Torsion angles in A Sugar-phosphate backbone
22 Torsion angles cont. α β γ δ ε ζ χ
23 Torsion angle χ SY: Pyrimidines: O2 above the sugar ring Purines: 6-member purine ring above the sugar ring
24 Torsion angle χ Orientation around the C1 glycosidic bond O4 C1 1 C2 pyrimidines O4 C1 9 C4 purines SY χ <0 o, 90 o > <270 o, 360 o > ATI χ <90 o, 270 o >
25 Torion χ border intervals high-syn (corresponds to +ac) 90 o + high-anti (corresponds -sc) 270 o + intrudes into anti intrudes into syn SY χ <0 o, 90 o > <270 o, 360 o > ATI χ <90 o, 270 o >
26 Torsion angles in DA Angle B-DA A-DA α β γ δ ε ζ χ
27 Sugar conformation C5 δ endocyclic O3 δ C5 C4 C3 O3 δ, ν3 relation exocyclic
28 Puckering of the sugar ring Envelope 4 atoms in a plane, the 5 th above or below Twist oposite plane 3 atoms in a plane, the 4 th and the 5 th on the sides of the
29 Definition of the puckering modes The sugar ring is not planar C1 O4 C4 plane Envelope C3 -endo With respect to C5 - endo - exo 3 E (prevalent in RA) Envelope C2 -endo 2 E (prevalent in DA) symmetric Twist C2 -exo-c3 -endo 3 2 T on-symmetric Twist C3 -endo-c2 -exo 3 T 2
30 Pseudorotation cycle Theoretically infinite number of conformations, can be characterized by maximum torsion angle (degree of pucker) and pseudorotation phase angle Torsion angles are not independent (ring closed) Pseudorotation phase angle P P = 0 o : symmetric Twist C2 -exo-c3 -endo 3 2 T P = 180 o : asymmetric Twist C2 -endo-c3 -exo 2 3 T
31 ν max amplitude Maximum out-of-plane pucker ν max = ν 2 / cos(p)
32 P, ν j relation P value defines unambiguously all endocyclic torsion angles ν 0 to ν 4 ν 2 = ν max cos(p + (j - 2) 144 ) ν 0 + ν 1 + ν 2 + ν 3 + ν 4 = 0 j = Sum of all 5 ν = 0
33 P in nucleic acids ORTH SOUTH 0 o P 36 o north (prevalent in RA) 144 o P 190 o south (prevalent in DA)
34 axis-base, axis-base pair intra-base pair inter-base or inter-base pair Helical parameters Distance/shift Angle
35 Helical D displacement from helical axis t twist = 360 o / n θ R roll θ T tilt
36 Helical parameters for A and B DA Global B-DA A-DA Shifts in Å, angles in degrees X disp Y disp Inclin Tip Shear Stretch Stagger Buckle Propeller Openning Shift Slide Rise Tilt Roll Twist Bases per turn 360/36=10 360/32.7=11
37 Base pairing Watson-Crick pairs
38 Base pairing Hoogsteen and reverse Hoogsteen pairs
39 A and B double helix A-RA Ball and stick models B-DA
40 A and B helices A-DA B-DA A-RA with bulge
41 A and B helices A-DA B-DA A-RA with bulge View tilted by 32 to show grooves
42 uclear properties of selected isotopes
43 Spin systems in ribose and deoxyribose
44 Spin systems in nucleic acid bases
45 1 H chemical shift ranges in DA and RA
46 1 H chemical shift ranges in DA and RA
47 1 H MR spectra of d(gcatgc) Single strand Duplex
48 1 H MR spectra in D 2 O and H 2 O d(gcattaatgc) 2
49 1 H COSY spectrum of DA a b c d e f g H2 -H2 H4 -H5,5 H5 -H5 H3 -H4 H2,2 -H3 H1 -H2,2 H5-H6 (Cyt) CH 3 -H6 (Thy) d(cgcgaattcgcg) 2
50 1 H OESY spectrum of DA d(cgcgaattcgcg)2
51 Water Suppression
52
53
54 WATERGATE
55 Structure Determination Procedure
56 Resonance Assignment
57 Sequential connectivities with exchangeable protons d(ggaattgtgagcgg) d(ccgctcacaattcc) imino-imino imino-amino
58 Sequential resonance assignments d(gcattaatgc) 2
59 Connectivities between H1 and H6/8 d(cgcgaattcgcg) 2 i intra-residue s sequential
60
61
62
63
64
65 Assignment of Sugar-Phosphate Backbone HP-COSY HP-TOCSY
66
67
68
69 J-couplings from COSY spectra
70 P determination from J-couplings
71 Equilibrium of and S conformations 3 -endo 2 -endo
72
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75
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