Planar Assemblies of Complementary and Mismatched Nucleotides on Bis(Zn 2+ -cyclen) Templates Turygin D.S. A.N. Frumkin Institute of Physical Chemistry and Electrochemistry RAS, 31-4, Leninsky Prospekt, , Moscow, Russia

From double helix to double plane (planar assemble formed under a Chargaff rule) phosphate sugar complementary bases

NN NN Zn +2 H HH H N NH OO O - P RO O - O Zn 2+ NN NN HH HH Zn 2+ -cyclens binding motives log K app = pH 7.6 log K app = pH 7.6 NN NN Zn +2 H HH H OH 2 pK a = 7.9 J. Am. Chem. Soc. 1994, 116, 3858 S. Aoki and E. Kimura J. Am. Chem. Soc. 1997, 119, 3068 E. Kikuta et al. J. Am. Chem. Soc. 1999, 121, 5426 Zn 2+ -cyclen complex Imide recognition by Zn 2+ -cyclen Phosphate monoester binding mode

4,6-Bis-(1,4,7,10-tetraazacyclododec-1-yl)- [1,3,5]-triazin-2-yl]-octadecylamine-zinc(II)- di-perchlorate (Zn 2+ -BC) Surface pressure vs area isotherms for Zn 2+ -BC on deionized water at pH 6.80 (1) and on basic subphases with pH 7.85 (2) and 8.52 (3). Au SAM CVA CVAcurves obtained for bare gold (1); thiolated gold electrode (2); and electrode covered with SAM/Zn 2+ -BC film (3). Red/Ox 0.5 M KCl/1 mM [Fe(CN) 6 ] 4- /1 mM [Fe(CN) 6 ] 3-. LB- technique Formation of SAM/LB recognition surface

Cytidine 5-triphosphate (CTP) complementarymismatched C complementary U GA purine pyrimi- dine Adenosine-5-triphosphate (ATP) Uridine-5-triphosphate (UTP) Guanosine 5-triphosphate (GTP) Watson-Crick complementary pairing Complementary and mismatched nucleotides

The SPR Analytical Applications During a binding analysis SPR changes occur as a solution is passed over the surface of a sensor chip. To perform an analysis, one interactant is captured on a sensor surface. The sensor surface forms one wall of a flow cell. Sample containing the other interactant is injected over this surface in a precisely controlled flow. Fixed wavelength light, in a fan-shaped form, is directed at the sensor surface and biomolecular binding events are detected as changes in the particular angle where SPR creates extinction of light. This change is measured continuously to form a sensorgram, which provides a complete record of the progress of association or dissociation of the interactants.

C nucleotides = 0.02 mM рН Turygin D.S., Subat M., Raitman O.A., Arslanov V.V., Konig B., Kalinina M.A. // Angewandte Chemie Int. Ed. 2006, 45, D.S. Turygin, M. Subat, O.A. Raitman, S.L. Selector, V.V. Arslanov, B. König, M.A. Kalinina // Langmuir, 2007, 23, Cooperative self-assembly of complementary nucleotides (CTP-GTP and UTP-ATP) at the bis(Zn 2+ -cyclen) template 2

H2OH2O Kinetics of the adsorption of naturally mismatched nucleotides at the pH

Kinetics of the adsorption of complementary nucleotides (except for CTP) at the pH 6.0 (pH 6.0) (pH 7.5) =2 (pH=6.0) (pH 7.5) 2 1:1

Kinetics of the adsorption of naturally mismatched nucleotides (except for CTP) at the pH 6.0 (pH 6.0) (pH 7.5) =2 (pH 6.0) (pH 7.5) 1 2:1

Kinetics of the adsorption of nucleotides, on the Zn 2+ -BC surface with an already immobilized CTP at the pH (pH 6.0) = (pH 7.5) 2(pH 6.0) = 2(pH 7.5)

Possible nucleotide binding mechanisms at pH 7.5 and pH 6.0 ? рН 7.5 рН 6.0

UTP ATP GTP UTP ATP GTP Schematics illustrating the H-bonding between nucleotides at pH 6.0 CTP

MOST IMPORTANT CONCLUSION The observed cooperativity stems from the optimal matching of ALL interacting components to each other and to the microenvironmental conditions. When the matching achieved (both evolutionary and synthetically), it results in a self-assembly of separate molecules into a single supramolecular unit and, finally, into a large planar assemble (double plane). WE CAN TUNE IT!

Acknowledgements: Dr. Kalinina M. for supervising Prof. Koenig B. for fruitful discussion and ideas Dr. Subat M. for synthesis Dr. Raitman O. for the kind help with SPR measurments Prof. Arslanov V. for advisory help Prof. Konovalov A., the Head of the RAS Program nos.7, for financial granting Department of chemistry and Material science of RAS Program 7: «Chemistry and phisicochemistry of supramolecular systems and atomic clusters», Russian Foundation for Basic Research (projects , )