Exponential Amplification of DNA Nanostructure
November 6, 2004
Abstract
1 Introduction
Previous work include the isothermal PCR [2] and the linear amplification system by [1]. Compared with these two
lines of work, the system presented here has the following advantages: 1. it is enzyme free; 2. it amplifies the
structure/configuration exponentially.
2Overview
Figure 1 illustrates the overview of the design. The overall reactions are
�������
�����������
�����������
������������
�The systems operates isothermally at room temperature.
�The lengths of the DNA segments: ���������, ���������������� ��,
����������������.
�The stem structures at the end of �(
and �)and �(��and �) are of critical
importance. The presence of such structures coupled with the looped structure in �and �can help to
�
effectively inhibit the unwanted hybridization, e.g., that between �in �and �in �[3].
�It is possible for �and �to form dimers/multimers, but these are expected not to affect the intended
reactions negatively. Furthermore, we can decrease the probability of forming dimers by decreasing the
concentration of the DNA strands.
�It is important that �and �are single strands; otherwise, we can not ensure stiochemetry (equimolar) of
reactants.
�solution and �solution are kept separate. For detecting task, mix equal
amounts of �and �, plus the unknown strand �. If we detect signal within a
predetermined time period, then we report positive result.
Figure 1: Overview
3 Experimental Implementation
3.1 Native gel electrophoresis
Run the following samples on a native gel: Lane 0, molecular marker; Lane 1, � only; Lane 2, �only; Lane 3: �+ �;Lane 4:
�+ �+ �(trace amount). We expect to see produce ���in Lane 4 but not Lane 3.
3.2 FRET
Use TAMRA and TET to lable the 5’ and 3’ ends of �respectively. We expect to see fluorescence signal in ���but not in �.
Thus we can monitor the fluorescence signal in the system �+ �+ �,using �+ �as control.
Figure 2:
4 Experimental Result
5 Conclusions
References
[1] R. M. Dirks and N. A. Pierce. Triggered amplification by hybridization chain reaction. Manuscript, 2004.
[2] J. H. Reif and colleagues. Isothermal PCR for DNA detection. In preparation, 2004.
[3] A. J. Turberfield, J. C. Mitchell, B. Yurke, Jr. A. P. Mills, M. I. Blakey, and
F. C. Simmel. DNA fuel for free-running nanomachines. Phys.Rev.Lett., 90:118102, 2003.