Molecular Recognition of Nucleotides - Designing Receptors for the Next Generation of Biosensors - page 53

phosphate hinge:
salt-bidge,H-bonding

NH 2 O

nucleobase:
pi-stacking,H-bonding

N N

N NH

O

N N

N N NH 2

NH R R

O O O

A ( 2 ) G ( 3 )

O P O P O P O

5´

N O

O

O O

UTP ( 1 )

NH 2

O O

1´

NH N

OH X

N O N O

R R

hydroxy groups:
H-bonding

hydrocarbon backbone:
hydrophobic interactions

X = OH for DNA
X = OH for RNA T ( 4 ) C ( 5 )

Fig. 1 Uridine triphosphate (1), adenine (2), guanine (3), thymine (4), and cytosine (5)

1 Nucleotide Recognition in Water

Due to their structural features, nucleotides are quite interesting targets from a
chemist's point of view. As depicted in Fig. 1 they consist of three main parts—
nucleobase, phosphate hinge, and sugar backbone. The sugar scaffold is a five-
membered ribose for RNA and a 2 0 -deoxyribose ring for DNA building blocks. It
connects the phosphate, which is attached to the 5 0 -hydroxyl group with the
nucleobase at position 1 0 , this way clearly defining the nucleotide's geometry.
The ribose ring itself is rather difficult to target. The hydroxyl groups offer potential
for hydrogen bonding. However, they are hard to differentiate from the surrounding
water molecules. The hydrocarbon chain can be targeted by means of hydrophobic
interactions. These are, however, rather weak and nonspecific. The best artificial
carbohydrate receptors known today complex their targets with binding constants
of merely 5 10 3 M 1 (pH 7.4, buffered water) [ 1 ]. The phosphate hinge,

consisting of one to three phosphates, is an easier target. Due to its multiple
negative charges and the presence of several hydrogen bond acceptors, it may be
addressed via hydrogen bonds and salt bridges. In comparison with the aforemen-
tioned carboxylates, phosphate anions are of tetrahedral shape and therefore require
a different kind of binding motif. The nucleobases are either purine- (A, G) or
pyrimidine based (C, U, T). Their aromatic nature allows for p -stacking, while their
heterocyclic nature and the exocyclic carbonyl and amine functions offer potential
hydrogen bonding acceptor and donor sites.
Due to the huge number of nucleotide receptors reported in the literature, this
chapter will only focus on systems which have been used in aqueous media.

1.1 Polyamine-Based Receptors

Nakai has shown that the naturally occurring polyamines shown in Fig. 2 (top),
putrescine (6), spermidine (7), and spermine (8), are able to bind to nucleotides [ 2 ].
Binding constants were determined by means of an anion-exchange resin method in
buffered water at pH 7.5. While putrescine only forms a weak 1:1 complex with
AMP ( K 82 M 1 ), spermidine is already able to form somewhat stronger 1:1

¼