NMR of Nucleic Acids. K.V.R. Chary Workshop on NMR and it s applications in Biological Systems November 26, 2009

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1 MR of ucleic Acids K.V.R. Chary Workshop on MR and it s applications in Biological Systems TIFR ovember 26, 2009

2 ucleic Acids are Polymers of ucleotides Each nucleotide consists of a nitrogenous base, a sugar and a phosphate group.

3 2 P n-1 C A nucleotide unit P n 5` 4` 4 3 1` 2` 3` n+1 P G C 3C T 2 chain reaction n+2 P 6 P 1

4 ucleic Acids are Polymers of ucleotides Each nucleotide consists of a nitrogenous base, a sugar and a phosphate group.

5 The two types of base

6 Common pyrimidine bases

7 Common purine bases

8 Pentose sugars Ribose 2-Deoxyribose

9 The omenclature in ucleic acids

10 Deoxy D-ribose 5`` C 1` 5` 4` 3` 2` 2`` Base

11 D-Ribose 5`` C 1` 5` 4` 3` 2` Base

12 Adenine (A) χ Sugar

13 Guanine (G) χ Sugar

14 Inosine (I) χ Sugar

15 Cytosine (C) χ Sugar

16 Thymine (T) 4 3 C χ Sugar

17 Uracil (U) χ Sugar

18 Watson-Crick A:T base pair 8 9 C 1` A 4 1 T C ` C

19 Watson-Crick G:C base pair 8 9 C 1` G C C1`

20 Base-pairings in ucleic Acids Watson-Crick base pairing Reverse Watson-Crick base pairing oogsteen base pairing

21 Pairing sites in A:T base-pair oogsteen base pairing sites C 1` A 4 1 T Watson-Crick base pairing sites C ` C

22 Pairing sites in G:C base pair oogsteen base pairing sites C 1` 5 6 G C C1` Watson-Crick base pairing sites

23 oogsteen A.T base-pair 3C (+) T 1 1` C A (+) 9 2 1` C

24 oogsteen G.C+ base-pair 6 1` C (+) C 1 C G ` C (+)

25 T.A:T Triad (+) C 1` 1 2 C3 6 5 T C 1` (+) A T 3 2 C3 1 1` C (-)

26 (+) C+.G:C Triad C 1` C+ 3 C 9 C 1` (+) G C 1 1` C (-)

27 Why study ucleic Acids Structures?

28 Structures of nucleic acids and their complexes represent around 10% of the PDB

29 MR Spectroscopy is an Important Method for Structural Studies of ucleic Acids X-ray/MR X-ray/MR(2001)

30 A-DA B-DA Z-DA

31 ELICAL PARAMETERS F UCLEIC ACIDS elix Type Pitch Ao Axial Rise Ao Rotation Ao Sugar Pucker A C3 endo B C2 endo C C3 endo D C3 endo Z * -60* alternating C3 endo C2 endo * ( Per dinucleotide)

33 A TETRAMERIC DA WIT PRTATED CYTSIE-CYTSIE BASE PAIR

34 otation for torsion angles about single bonds in the ucleotide A {θ }={α i, βi, γ i, δ i, ε i, ξ i, χ i, ν i} 5' βi αi P5' γi 5' C5' ν 3i C4' δ i/ν 4 i εi C3' 3' ν 0i 5" 4' C2' C1' ν 2i χi ν 1i 2' β 0 γ 0 i B 0 P3' 2" 1 ' Ri α ξi δ ε ζ χ R χ Y Statistical distribution of various torsion angles in B-DA derived from PDB files.

35 Various backbone (α, β, γ, δ, ε, ζ ) and glycosidic (χ) torsion angles for purine (R) and pyrimidine (Y) bases. Code Torsion angle α {-3 i-1-pi-5 i-c5 i-} β {-Pi-5 i-c5 i-c4 i-} γ {-5 i-c5 i-c4 i-c3 i-} δ {-C5 i-c4 i-c3 i-3 i-} ε {-C4 i-c3 i-3 i-pi+1} ζ {-C3 i-3 i-pi+1-5 i+1-} χ(py) {-4 i-c1 i-1i- C2i-} χ(pu) {-4 i-c1 i-9i- C4i-}

36 Proteins vs ucleic acids n an average protons per residue is same in nucleotides and amino acids. The average molecular weight is three times for nucleotides (~350 Da) as compared to peptides (110 Da). This results in a three-fold lower proton density in nucleic acids.

38 MR of ucleic acids Predominantly rod like structures o long-range interactions Results in smaller chemical shift dispersion, except for non-canonical structural elements such as hairpins, bulges or internal loops.

39 MR of ucleic acids Seven of the protons in nucleotides (1, 2, 2, 3, 4, 5, and 5 ) are contributed by the sugar rings, resulting in fairly complex spincoupled system. The 100% abundant hetero-nucleus 31P shows J-coupling to 3 on one end, and 5 /5 at the other. All these factors lead to overlapping and strongly coupled spectra.

40 MR of ucleic acids Information on the backbone structure can be obtained from a limited number of nuclei, namely, 3, 4, 5, and 5 and 31P. These protons and 31P, suffers from relatively small chemical shift dispersions. This results in fewer experimental data for constraining the six backbone torsion angles. For these reasons, the structure determination of DA and RA from 1 MR has been limited to fragments containing less than 50 nucleotides.

41 MR of ucleic acids MR structure determination of nucleic acids is primarily based on: Estimation of short 1-1 distances detected by Es Dihedral angles that can be derived from the through bond couplings Characterisation of base-pairing.

42 Resonance Assignments in DA (a) Classification of individual chemical shifts in 1D MR spectrum (b) Identification of networks of coupled spin systems contained within the individual nucleotide units using CSY, E.CSY, TCSY etc., and (c) Sequential linking of the identified nucleotide units by ESY spectrum recorded in 2 or 22, where one observes inter-nucleotide E connectivities, such as (T3/G1) imino (T3/G1) (6/8)i+1 (1 /2 /2")i

43 MR of ucleic acids B A ppm 14 d-ggtaciagtacc CCATGAICATGG-d 13 2/6/8 ppm /C5 3 4 /5 / /2 TC3 2

44 Resonance Assignments in DA A) Exchangeable protons: 1D 1, 2D ESY B) on-exchangeable protons Aromatic Spin Systems: 2D DQF-CSY (5-6), 2D ESY Sugar Spin Systems: 2D DQF-CSY 2D TCSY Sequential Assignment: 2D ESY 2D (31P, 1) ELC C) Correlation of exchangeable and non-exchangeable protons : 2D ESY

45 Identification of non-exchangeable protons: C(5-6)/T(C3-6) Correlations in DQF-CSY A) a b C5 I6 G1 G1 G8 A7 A7 T3 T9 T3 G8 C11 C11 G2 G2 A10 A10 A4 A4 B) T9 C12 C5 c

46 Identification of non-exchangeable sugar protons: 1'-2'/2'' Correlations in 2D-TCSY/2D-DQF-CSY b C5 I6 G1 G1 G8 A7 A7 T3 T9 T3 C5 c T9 G8 C11 C11 G2 G2 A10 A10 C12 A4 A4 A) B) a b C5 I6 G1 G1 G8 A7 A7 T3 T9 T3 C5 a c T9 1 G8 C11 C11 G2 G2 A10 A10 A4 A4 B) C /2

47 Intranucleotide and Internucleotide connectivities in a ESY spectrum Intranucleotide peaks seen in ESY spectrum {Base(6/8)}i {Sugar(1 /2 /2 /3 )}i These distances are less than 50nm Internucleotide peaks seen in ESY spectrum {Base(6/8)}i {Base(6/8)}i {Sugar(1 /2 /2 /3 )}i-1 {Base(6/8)}i-1

48 ESY spectrum of a 12mer ds DA with a emimethylated GATC-tract * G23G22C 21A20G19A18T17C16C 15G 14T 13A 3 3 C C G T C T A G G C A T 5 Sugar protons Base protons

49 Intranucleotide and Internucleotide connectivities in a ESY spectrum Intranucleotide peaks seen in ESY spectrum {Base(6/8)}i {Sugar(1 /2 /2 /3 )}i These distances are less than 50nm Internucleotide peaks seen in ESY spectrum {Base(6/8)}i {Base(6/8)}i {Sugar(1 /2 /2 /3 )}i-1 {Base(6/8)}i-1

50 SEQUECE SPECIFIC RESACE ASSIGMETS F UCLEIC ACIDS 1. (Base) i+1 ESY (Sugar) I ESY (Base) I ESY (Base) i+1 ESY (Base) i 2. (P) i+1 ELC (3 ) i TCSY (4 )i ELC (P)I 3. (imino protein) i+1 ESY (imino protein) i AT T3 GC G1 ESY in 90% % D J Correlation

51 Typical Es seen in DA 8 9 C 1` G C C1`

52 Typical Es seen in DA 8 9 C 1` A 4 1 T C ` C

53 ESY spectrum of a 12mer ds DA with a emimethylated GATC-tract * G23G22C 21A20G19A18T17C16C 15G 14T 13A 3 3 C C G T C T A G G C A T 5 Sugar protons Base protons

54 * 5 G G C A G A T C C G T A C C G T C T A G G C A T 5 T11 C9 C8 C3 G1 T7 G5 G10 A4 A12 A6 G2

55 * 5 G G C A G A T C C G T A C C G T C T A G G C A T 5 T13 C15 T19 C23 C24 T21 G22 G16 G17 A14 A18 C20

56 Assignments of non-exchangeable protons: Sequential Assignments

57 Correlations between exchangeable and non-exchangeable protons 8 9 C 1` G C C1`

58 Correlations between exchangeable and non-exchangeable protons 8 9 C 1` A 4 1 T C3 6 1 C1`

61 ESY I 90% % 22

62 Correlations between exchangeable and non-exchangeable protons 8 9 C 1` G C C1`

63 Correlations between exchangeable and non-exchangeable protons 8 9 C 1` A 4 1 T C3 6 1 C1`

64 Sugar Pucker

65 D-Ribose 5`` C 1` 5` 4` 3` 2` Base

66 Sugar Pucker

67 DETERMIATI F J endo 1

68 2 1 1

69 2D-E.CSY

72 Fixing χ The glycosidic torsion angle

74 ESY DECAMER [Tm 80 ms]

75 FIXIG א Simulated isodistance contours in the P, א space (for pyrimidine)

76 31 P 1 Correlation Small molecules: Fine, o problem Large molecules: - Small chemical shift differences (3,4,5,5 and 31P) - Complex multiplet structures - Short T2 s of 5 & 5. - Frequency dependent T2 s of 31P P 31 Spin ½ 100% atural Abundance

79 P 31 Active Coupling Passive 2 couplings 4

83 ew and ovel Constraints -ydrogen-bond constraints from J couplings across hydrogen bonds -Sugar pucker and backbone angles from cross-correlated relaxation -Long-range orientation constraints from residual dipolar couplings

84 Trans ydrogen bond Coupling constants

85 Trans hydrogen-bond J-correlations 2h J()

86 Trans hydrogen-bond J() in non-watson-crick base pairs: 2h

87 Trans hydrogen-bond J() via Remote on-exchangeable Protons 2h

88 ucleic Acids Polymorphism Examples of non-duplex structures are Single stranded hair-pins Triplexes, Tetraplexes i-motif structures Such nucleic acid polymorphism is principally governed by the factors such as sequence, concentration, temperature, p, and other persistent solvent conditions

89 ucleic Acids Polymorphism

90 ucleic Acids Polymorphism

92 The Triplex DA (-DA) Purine strand Pyrimidine strand Part of the purine strand

94 MR Spectroscopy is also important for Structural Studies of RA

95 Resonance Assignment of RA Exchangeable protons: 1D 1, 2D ESY 2D ( 15, 1) SQC 3D 15-edited ESY-SQC on-exchangeable protons 2D ( 13C, 1) SQC 3D CC-CSY 3D CC-TCSY 2D ( 15, 1) C

96 Resonance Assignment of RA Sequential Assignment: 3D/4D 13C-edited ESY-SQC CP-type only for small RA Correlation of exchangeable and non-exchangeable protons: 2D G-specific (C)-TCSY-(C)- 2D A-specific ()(C)-TCSY-(C)- 2D C-specific (CCC) 2D U-specific (CCC) 3D/4D 13C-edited ESY-SQC

97 Conclusions Conformational freedom of nucleotides Structure of DA, Watson & Crick Model Base pairing and base stacking MR spectroscopy of DA Assignment Strategies Use of MR parameters to fix sugar pucker, glycosidic dihedral angle and backbone torsion angles Base-pairing and stacking information from MR Structure Simulations of ucleic acids Variations in DA structure, polymorphism, unusual DA strcutures igher order structures Strcuture of RA: Ribosomal and T-RA

NUCLEIC ACIDS. Basic terms and notions. Presentation by Eva Fadrná adapted by Radovan Fiala

NUCLEIC ACIDS. Basic terms and notions. Presentation by Eva Fadrná adapted by Radovan Fiala UCLEIC ACIDS Basic terms and notions Presentation by Eva Fadrná adapted by Radovan Fiala RA vs DA Single strand A-RA B-DA duplex Length of A Total length of DA in a human cell 1 m (1000 km) DA in typical