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

Abstract

Besides the canonical Watson-Crick (WC) linked antiparallel-stranded duplex (aps-DNA), DNA is also able to form bioactive parallel-stranded duplex (ps-DNA) with the two involving strands adopting the equal 5'-3' polarity. Discriminating ps-DNA from aps-DNA with an ideal selectivity is more challenging because of their comparable duplex topologies. Herein, we designed a unique probe of HPIN to fluorescently recognize ps-DNA but to keep an almost nonfluorescent response in binding with aps-DNA. The success of the Hoogsteen hydrogen bonding pattern in lighting up the HPIN fluorescence over the reverse Watson-Crick (rWC) one suggests the critical role of HPIN in structurally adaptive recognition to the strand polarity-determined base-pairing peculiarity. The turn-on fluorescence should result from restriction of the HPIN cis/trans isomerization upon the adaptive Hoogsteen base pair binding. Such high performance in recognizing ps-DNA against aps-DNA demonstrates the promising applications of HPIN in developing unique DNA polarity-based sensors.

Novel Tautomerisation Mechanisms of the Biologically Important Conformers of the Reverse Löwdin, Hoogsteen, and Reverse Hoogsteen G*·C* DNA Base Pairs via Proton Transfer: A Quantum-Mechanical Survey

“…However, at the studying of the nature of the mutagenic tautomerization of DNA bases, the researchers limited themselves to the A·T and G·C Watson-Crick base pairs (Löwdin, 1963, 1966; Florian et al, 1994; Gorb et al, 2004; Bertran et al, 2006; Brovarets' and Hovorun, 2014a,b). Now this problem is considered more complex with the involvement of several biologically important conformers of these pairs (Hoogsteen, 1963; Pous et al, 2008; Alvey et al, 2014; Brovarets' and Hovorun, 2014a,b; Nikolova et al, 2014; Acosta-Reyes et al, 2015; Poltev et al, 2016; Zhou, 2016; Szabat and Kierzek, 2017; Ye et al, 2017).…”

Surprising Conformers of the Biologically Important A·T DNA Base Pairs: QM/QTAIM Proofs

“…We chose as the object of the investigation of the biologically-important A·T DNA base pairs, in particular–Watson-Crick A·T(WC), reverse Watson-Crick A·T(rWC), Hoogsteen A·T(H) and reverse Hoogsteen A·T(rH) base pairs (Donohue and Trueblood, 1960 ; Haschemeyer and Sobell, 1963 ; Hoogsteen, 1963 ; Tchurikov et al, 1989 ; Liu et al, 1993 ; Parvathy et al, 2002 ; Sühnel, 2002 ; Zagryadskaya et al, 2003 ; Brovarets', 2013a , b ; Alvey et al, 2014 ; Nikolova et al, 2014 ; Yang et al, 2015 ; Poltev et al, 2016 ; Zhou, 2016 ; Sathyamoorthy et al, 2017 ; Szabat and Kierzek, 2017 ; Ye et al, 2017 ).…”

“…Thus, the reverse A·T(rWC) Watson-Crick or so-called Donohue DNA base pair (Donohue and Trueblood, 1960 ), which is formed by the rotation of one of the bases according to the other by 180° around the N1–N3 axis of the Watson-Crick A·T(WC) DNA base pair, has been registered in the bioactive parallel-stranded DNA (Tchurikov et al, 1989 ; Parvathy et al, 2002 ; Brovarets', 2013a , b ; Poltev et al, 2016 ; Szabat and Kierzek, 2017 ; Ye et al, 2017 ).…”

Unexpected A·T(WC)↔A·T(rWC)/A·T(rH) and A·T(H)↔A·T(rH)/A·T(rWC) conformational transitions between the classical A·T DNA base pairs: A QM/QTAIM comprehensive study

“…Traditional А·Т Watson–Crick DNA base pair may acquire different conformations with various organization of the H‐bonds through the rotation of one of the bases according to the other: On 180 ° around the (A)N1–N3(T) axis, leading to the formation of the reverse Watson–Crick А·Т(rWC) or so‐called Donohue DNA base pair, registered in the bioactive parallel‐stranded DNA; On 180 ° around the (A)C9′‐N9 axis from the anti‐ to syn‐ conformation, representing Hoogsteen A·T(H) base pair involved into a number of biologically important processes such as recognition, damage induction, replication; On 180 ° around the (A)N7–N3(T) axis in the Hoogsteen base pair forming the reverse Hoogsteen A·T(rH) or so‐called Haschemeyer–Sobell base pair …”