LNCS 2950 - Aspects of Molecular Computing (Frontmatter Pages)

354 M. Sakthi Balan and Kamala Krithivasan
The specificity of an epitope recognition by an antibody need not be absolute.
Sometimes the antibody may recognize a different site which is very similar to
its own binding site. This issue is called cross-reactivity. This paper does not
address the issue of cross-reactivity between antibodies and peptides.
Using DNA strands H. Hug et al [4] propose a model to solve simple binary
addition in parallel. In [1] we propose a model to do simple arithmetic (addition
and subtraction) operations using peptides and antibodies.
The organization of the paper is as follows. In the next section we define our
proposed model of performing gate operations OR, AND and NOT. We explain
with some examples how the operations are carried out. In section 4 our method
is extended to do XOR, NAND and NOR gates. Our paper concludes with
some discussion on the bio-chemical implementation of our proposed model.
2 Proposed Model
The proposed model uses a peptide sequence and a set of antibodies. The peptide
sequence consists of five epitopes; if P denotes the peptide sequence, then P can
be represented as follows:
P = yx1xx2z,
where each y, x1, x, x2 and z are epitopes. We take six antibodies denoted by
A1,A2,B1,B2,Cinit and Cf . Basically,
1. the antibodies A1,A2,B1 and B2 denote the inputs,
2. Cinit denote the initial value of the result of the operation,
3. Cinit and Cf denote the output of the operation,
4. the epitopes x and y are the binding places for the antibodies denoting the
input,
5. the epitope x1xx2 is the place where the antibody representing the initial
output binds,
6. the epitopes x1x, xx2 and x are the binding places for the antibodies denoting
the output.
The peptide sequence P is given in Fig. 1. The peptide sequence with possible
antibodies binding on it is represented in Fig. 2. Note that at a time only one
antibody can be there in the overlapping epitopes. The figure is meant only to
show the binding sites of the antibodies pictorically.
y x1 x x2
z
Fig. 1. Peptide sequence