DNA Library Design for

Molecular Computation
R. Penchovsky and J. Ackermann
Journal of Computational Biology
v.10, n.2, 2003

Summarized by In-Hee Lee

 1. Introduction (1/2)
• Accuracy of the computation depends on
the ability to discriminate between
matching hybrids and those with
mismatches.
• Sequence design methods so far based on
Hamming and related distances.
– Ignoring physical property of DNA
 1. Introduction (2/2)
• DNA library design
– Based on thermodynamic stability of DNA
hybrids.
– To deal with prob. dist. of alternative
DNA/DNA duplex, a partition function is
computed.
– Used the Vienna RNA folding package.
– Also used NN parameters.
– Random search algorithm.
 2. Materials and Methods (1/2)
• Library constraints
– 12-bit library, different sequence for different positions and
bits.
– No G’s.
 Reduce the stability of possible secondary structures and hybridizat
ion among the library.
– Length – 16-mer.
– No occurrences of four or more consecutive identical nucle
otides.
– No runs of three consecutive C’s at either the 5’ or 3’ end.
– Maximize the free energy gap btw. the weakest specific hy
bridization and strongest non-specific hyb.
– Restricted range of Tm (1.5ºC).
 2. Materials and Methods (2/2)
• DNA library design algorithm
– Consists of two steps.
– Step A.
Random search algorithm
– Step B.
Construct the 12-bit DNA library.

• Tested four library sequences

– 111111111111, 000000000000, 010101010101, 101010101010
Word Sequences
 Library Generation
• Mix-and-split
 3. Experimental Results (1/4)
• The Goodness of generated sequences
Set of words

Words and the 4

library sequences
 3. Experimental Results (2/4)
• Integrity and accuracy of the library

4 library sequences with ‘zero’ capture probes

 3. Experimental Results (3/4)
• Integrity and accuracy of the library

4 library sequences with ‘one’ capture probes

 3. Experimental Results (4/4)
• Localizing the unexpected amplified
product.

Separated PCR for

4 library sequences
with primer

2: 111111111111
3: 101010101010
4: 000000000000
5: 010101010101
 4. Discussion
• Library design based on thermodynamics.
• Increasing the set size is not necessarily
connected with a reduction of the word
quality.
• More accurate than using the Hamming
distances.