Hydration of Nucleotides Thomas Wyttenbach, Dengfeng Liu, and Michael T. Bowers
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1 ydration of ucleotides Thomas Wyttenbach, Dengfeng Liu, and Michael T. Bowers ASMS 2006 Why study hydration? Is a certain property of a molecule (e.g. conformation) inherent to the molecule or a consequence of solute solvent interaction? 1
2 DA solution structure: double helix Watson-Crick base pairs Water binding energies Water binding sites D.E.VLK,X.YAG,S.M.FEE WALD,D.J.KIG,S.E.BASSETT, S.VEKITACALAM,.ERZG, B.A.LUX,D.G.GRESTEI BIRG.CEM. 30, 396, 2002 MR STRUCTURE F A 14-MER DA DUPLEX DA basics and -forms Watson-Crick base pairs -form most common DA structure -form dehydrated DA (common in RA) 2
3 DA basics ucleotide ucleotide Base Phosphate Sugar Bases A: adenine C: cytosine G: guanine T: Thymine DA basics Mononucleotides 2 Phosphate Base P Sugar Bases A: adenine C: cytosine G: guanine T: Thymine 3
4 DA basics ligonucleotides 2 cytosine dcc 2 cytosine P negative Instrumentation ESI Ion Source Ion Funnel Drift Cell MS Detector 2 Liquid 2 cooling P 2 2 dcc M + ~1 torr 2 dcc ( 2 ) n M + ( 2 ) n P Electrical heaters 4
5 Data analysis dcc ln K van t off 319 K / T ln K = S 1 R R T m/z & S 251 K Data analysis ln K van t off / T m/z 6 dcc + =.1 S = 1 kcal mol cal mol K dcc 5
6 Water binding energy for n th 2 molecule 11 2 (kcal/mol) 9 P 2 P n dcc ( 2 ) n 1 + dcc ( 2 ) n Water binding energy for n th 2 molecule 2 (kcal/mol) 11 9 P n ( 2 ) n 1 + ( 2 ) n 6
7 P P P 2 2 P P Water binding energy for n th 2 molecule (kcal/mol) n dgactcc 2 ( 2 ) n 1 + dgactcc 2 ( 2 ) n Water binding energy for n th 2 molecule (kcal/mol) mononucleotides dinucleotides bservations: n 1 st water more strongly bound (11 kcal/mol) 2 nd 6 th water 9 kcal/mol water more strongly bound to smaller oligonucleotides
8 ucleotide size Mononucleotide Dinucleotide 14 ucleotide size (kcal/mol) Water binding energy for n th 2 molecule mononucleotides dinucleotides n bservations: 1 st water more strongly bound (11 kcal/mol) 2 nd 6 th water 9 kcal/mol water more strongly bound to smaller oligonucleotides
9 MD (AMBER) DFT (B3LYP/ G**) 2 Binding energy 11.6 kcal/mol (B3LYP/ G**) kcal/mol Experiment dtmp damp dgmp Calc Exp MD (AMBER) DFT (B3LYP/ G**) 9
10 ( 2 ) 4 Charge Base MD (AMBER) ( 2 ) 4 Base 4 x Charge 2 nd shell
11 Calculations: M 2 first water molecule binds to phosphate (charge!) Experiment: 1 st water more strongly bound 11 kcal/mol 2 nd 6 th water constant at 9 kcal/mol 14 water more strongly bound to smaller oligonucleotides 13 (kcal/mol) Water binding energy for n th 2 molecule Constant n Calculations: Experiment: first water molecule binds to phosphate (charge!) numerous isoenergetic isomers (within 3 kcal/mol) many equally good hydration sites at charge on base in 2 nd hydration shell 13 M ( 2 ) 4 1 st water more strongly bound 11 kcal/mol 2 nd 6 th water constant at 9 kcal/mol 14 water more strongly bound to smaller oligonucleotides (kcal/mol) Water binding energy for n th 2 molecule Constant n 11
12 ucleotide conformation ucleotide conformation does not change upon hydration 2 ( 2 ) 4 ( 2 ) 4 ( 2 ) 4 ( 2 ) 4 ucleotide conformation C3 endo sugar puckering 12
13 ucleotide conformation dc inside C3 endo sugar puckering - double helix C2 endo ucleotide conformation dc inside - double helix C2 endo (B-helix) preferred under normal (hydrated) conditions C3 endo sugar puckering -bond C3 endo intrinsically (in the absence of solvent) preferred by monomer hydration effect monomer effect 13
14 ucleotide conformation -bond C2 endo no preference in dccc C3 endo MD (AMBER) ucleotide conformation () aq MD (AMBER) C2 endo C3 endo 14
15 ucleotide conformation network of -bonds -bond -bond () aq MD (AMBER) phosphate water sugar water phosphate sugar ucleotide conformation Monomer 2 C3 endo C3 endo D E G R EE Polymer globular gas phase DA C2 endo and C3 endo ( 2 ) 4 C3 endo F Y D R A TI -DA C3 endo () aq C2 endo -DA C2 endo Int. J. Mass Spectrom. 240 (2005) Gidden, Shammel Baker, Ferzoco, Bowers 15
16 (kcal/mol) Water binding energy for n th 2 molecule Phosphate 11 kcal/mol n Base 9 kcal/mol Phosphate hydration Base hydration Phosphate Bases B-DA double helix 16
17 Base hydration G C base pair in - DA Major Groove Sugar G Minor Groove C Sugar Base 4 x 9 = 36 kcal/mol kcal/mol G C interaction = 2 kcal/mol Jurecka, P.; obza, P. J. Am. Chem. Soc. 2003, 125, G + C G ( 2 ) 2 + C ( 2 ) 2 36 kcal/mol G C G + C +2 kcal/mol G C G ( 2 ) 2 + C ( 2 ) 2 9 kcal/mol (Base pair) (ydration) G C + ( 2 ) 4 (Base pair) Base hydration 26 kcal/mol (water condensation) G ( 2 ) 2 + C ( 2 ) 2 +1 kcal/mol (ydration) Graf, S.; Leutwyler, S. J. Chem. Phys. 199, 9,
18 Conclusions Water binding energy larger for 1 st water (11 kcal/mol) 2 nd -6 th water constant (9 kcal/mol) larger for smaller oligonucleotides larger for positive ions ucleotide conformation C3 endo intrinsic monomer conformation C2 endo B-from double helix Base pairing energetically favored over hydration of single strands Entropy of hydration correlation with Water binding sites best hydration site at phosphate many equally good 2 nd best hydration sites at charge on base in 2 nd hydration shell S (cal/mol/k) S = K (kcal/mol) Conclusions Water binding energy larger for 1 st water (11 kcal/mol) 2 nd -6 th water constant (9 kcal/mol) larger for smaller oligonucleotides larger for positive ions ucleotide conformation C3 endo intrinsic monomer conformation C2 endo B-from double helix Base pairing energetically favored over hydration of single strands Entropy of hydration correlation with Water binding sites best hydration site at phosphate many equally good 2 nd best hydration sites at charge on base in 2 nd hydration shell Acknowledgements Dengfeng Liu Mike Bowers Bowers Group $SF 1
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