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Split Hybridization Probe Utilizing a DNA Fluorescent Light-up Aptamer as a Signal Reporter for Sequence-Specific Nucleic Acid Analysis

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Adaptively Recognizing Parallel-Stranded Duplex Structure for Fluorescent DNA Polarity Analysis.

Mei-Yun Ye¹, Rui-Tao Zhu², Xiang Li³

¹Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University , Jinhua 321004, Zhejiang, China.

Analytical Chemistry

|August 17, 2017

Summary

Researchers developed HPIN, a fluorescent probe that distinguishes parallel-stranded DNA (ps-DNA) from antiparallel-stranded DNA (aps-DNA). This advancement enables selective detection of ps-DNA, crucial for novel DNA sensors.

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Area of Science:

Molecular Biology
Biochemistry
Chemical Biology

Background:

DNA exists in canonical antiparallel-stranded (aps-DNA) and bioactive parallel-stranded (ps-DNA) forms.
Distinguishing ps-DNA from aps-DNA is challenging due to similar duplex structures.

Purpose of the Study:

To design a selective fluorescent probe for ps-DNA detection.
To differentiate ps-DNA from aps-DNA with high selectivity.

Main Methods:

Design and synthesis of a novel fluorescent probe (HPIN).
Fluorescence spectroscopy to assess probe binding with ps-DNA and aps-DNA.
Analysis of hydrogen bonding patterns (Hoogsteen vs. reverse Watson-Crick).

Main Results:

HPIN exhibits strong fluorescence with ps-DNA via Hoogsteen base pairing.
HPIN shows minimal fluorescence with aps-DNA via reverse Watson-Crick pairing.
The probe's turn-on fluorescence is attributed to restricted cis/trans isomerization.

Conclusions:

HPIN selectively recognizes ps-DNA over aps-DNA.
The probe's mechanism relies on adaptive structural recognition of base-pairing peculiarities.
HPIN shows potential for developing DNA polarity-based sensors.