MR of ucleic Acids K.V.R. Chary chary@tifr.res.in Workshop on MR and it s applications in Biological Systems TIFR ovember 26, 2009
ucleic Acids are Polymers of ucleotides Each nucleotide consists of a nitrogenous base, a sugar and a phosphate group.
2 P n-1 C A 7 6 5 8 nucleotide unit P n 5` 4` 4 3 1` 2` 3` n+1 P G 2 9 1 C 3C 4 3 5 T 2 chain reaction n+2 P 6 P 1
ucleic Acids are Polymers of ucleotides Each nucleotide consists of a nitrogenous base, a sugar and a phosphate group.
The two types of base
Common pyrimidine bases
Common purine bases
Pentose sugars Ribose 2-Deoxyribose
The omenclature in ucleic acids
Deoxy D-ribose 5`` C 1` 5` 4` 3` 2` 2`` Base
D-Ribose 5`` C 1` 5` 4` 3` 2` Base
Adenine (A) 2 1 6 2 5 4 3 7 8 9 χ Sugar
Guanine (G) 1 6 2 2 3 5 4 7 8 9χ Sugar
Inosine (I) 1 6 2 3 5 4 7 8 9χ Sugar
Cytosine (C) 2 4 3 2 5 6 1 χ Sugar
Thymine (T) 4 3 C3 5 6 2 1 χ Sugar
Uracil (U) 4 5 3 6 2 1 χ Sugar
Watson-Crick A:T base pair 8 9 C 1` 7 5 3 5 4 6 A 4 1 T 3 2 2 C3 6 1 1` C
Watson-Crick G:C base pair 8 9 C 1` 7 5 6 G 4 3 5 4 1 2 C 3 2 6 1 C1`
Base-pairings in ucleic Acids Watson-Crick base pairing Reverse Watson-Crick base pairing oogsteen base pairing
Pairing sites in A:T base-pair oogsteen base pairing sites 7 8 9 C 1` 5 3 5 4 6 A 4 1 T 3 2 2 Watson-Crick base pairing sites C3 6 1 1` C
Pairing sites in G:C base pair oogsteen base pairing sites 7 8 9 C 1` 5 6 G 4 3 5 4 1 2 C 3 2 6 1 C1` Watson-Crick base pairing sites
oogsteen A.T base-pair 3C (+) T 1 1` C 6 4 5 6 1 3 A 5 7 2 4 3 (+) 9 2 1` C
oogsteen G.C+ base-pair 6 1` C (+) 5 1 6 4 + 3 C 1 C 2 5 8 2 G 3 4 7 9 1` C (+)
T.A:T Triad (+) C 1` 1 2 C3 6 5 T 3 4 8 9 C 1` (+) 7 5 6 3 5 4 A 4 1 2 6 T 3 2 C3 1 1` C (-)
(+) C+.G:C Triad C 1` 1 2 6 5 C+ 3 C 9 C 1` (+) 7 8 4 5 6 G 4 3 5 4 1 2 3 2 6 C 1 1` C (-)
Why study ucleic Acids Structures?
Structures of nucleic acids and their complexes represent around 10% of the PDB
MR Spectroscopy is an Important Method for Structural Studies of ucleic Acids X-ray/MR 6.4 9.4 1.4 7 5.7 X-ray/MR(2001) 6.1 7.9 1.5 3.5 5.4
A-DA B-DA Z-DA
ELICAL PARAMETERS F UCLEIC ACIDS elix Type Pitch Ao Axial Rise Ao Rotation Ao Sugar Pucker A 28.1 2.6 33 C3 endo B 33.7 3.4 36 C2 endo C 30.9 3.3 39 C3 endo D 27.2 3.4 45 C3 endo Z1 44.6 7.4* -60* alternating C3 endo C2 endo * ( Per dinucleotide)
A TETRAMERIC DA WIT PRTATED CYTSIE-CYTSIE BASE PAIR
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 0 270 90 ε 180 0 ζ 180 0 180 χ R 0 180 χ Y 0 270 90 180 180 180 180 Statistical distribution of various torsion angles in B-DA derived from PDB files.
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-}
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.
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.
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.
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.
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.
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
MR of ucleic acids B A ppm 14 d-ggtaciagtacc CCATGAICATGG-d 13 2/6/8 ppm 8 12-0.5-1.0-1.5 1 /C5 3 4 /5 /5 6 4 2 /2 TC3 2
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
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
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) C12 3 4 2 /2
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
ESY spectrum of a 12mer ds DA with a emimethylated GATC-tract 1 2 3 *5 4 6 7 8 9 10 11 12 5 24G23G22C 21A20G19A18T17C16C 15G 14T 13A 3 3 C C G T C T A G G C A T 5 Sugar protons Base protons
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
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% 2 + 10% D2 ------- J Correlation
Typical Es seen in DA 8 9 C 1` 7 5 6 G 4 3 5 4 1 2 C 3 2 6 1 C1`
Typical Es seen in DA 8 9 C 1` 7 5 3 5 4 6 A 4 1 T 3 2 2 C3 6 1 1` C
ESY spectrum of a 12mer ds DA with a emimethylated GATC-tract 1 2 3 *5 4 6 7 8 9 10 11 12 5 24G23G22C 21A20G19A18T17C16C 15G 14T 13A 3 3 C C G T C T A G G C A T 5 Sugar protons Base protons
7 8 9 10 11 12 * 5 G G C A G A T C C G T A 3 1 2 3 4 24 23 22 5 6 21 20 19 18 17 16 15 14 13 3 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
7 8 9 10 11 12 * 5 G G C A G A T C C G T A 3 1 2 3 24 23 22 4 5 21 20 6 19 18 17 16 15 14 13 3 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
Assignments of non-exchangeable protons: Sequential Assignments
Correlations between exchangeable and non-exchangeable protons 8 9 C 1` 7 5 6 G 4 3 5 4 1 2 C 3 2 6 1 C1`
Correlations between exchangeable and non-exchangeable protons 8 9 C 1` 7 5 3 5 4 6 A 4 1 T 3 2 2 C3 6 1 C1`
ESY I 90% 2 + 10% 22
Correlations between exchangeable and non-exchangeable protons 8 9 C 1` 7 5 6 G 4 3 5 4 1 2 C 3 2 6 1 C1`
Correlations between exchangeable and non-exchangeable protons 8 9 C 1` 7 5 3 5 4 6 A 4 1 T 3 2 2 C3 6 1 C1`
Sugar Pucker
D-Ribose 5`` C 1` 5` 4` 3` 2` Base
Sugar Pucker 1-2 2-3 2-3 3-4 3-4 2-3 1-2
DETERMIATI F J 2 1 4 endo 1
2 1 1
2D-E.CSY
Fixing χ The glycosidic torsion angle
ESY DECAMER [Tm 80 ms]
FIXIG א Simulated isodistance contours in the P, א space (for pyrimidine)
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
P 31 Active Coupling 31 3 2 Passive 2 couplings 4
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
Trans ydrogen bond Coupling constants
Trans hydrogen-bond J-correlations 2h J()
Trans hydrogen-bond J() in non-watson-crick base pairs: 2h
Trans hydrogen-bond J() via Remote on-exchangeable Protons 2h
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
ucleic Acids Polymorphism
ucleic Acids Polymorphism
The Triplex DA (-DA) Purine strand Pyrimidine strand Part of the purine strand
MR Spectroscopy is also important for Structural Studies of RA
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
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
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