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Biochemistry

In Vitro Chemical Mapping of G-Quadruplex DNA Structures by Bis-3-Chloropiperidines

Published: May 12th, 2023

DOI:

10.3791/65373

1Department of Pharmaceutical and Pharmacological Sciences, University of Padova, 2Institute of Organic Chemistry, Justus Liebig University Giessen

Bis-3-chloropiperidines (B-CePs) are useful chemical probes to identify and characterize G-quadruplex structures in DNA templates in vitro. This protocol details the procedure to perform probing reactions with B-CePs and to resolve reaction products by high-resolution polyacrylamide gel electrophoresis.

G-quadruplexes (G4s) are biologically relevant, non-canonical DNA structures that play an important role in gene expression and diseases, representing significant therapeutic targets. Accessible methods are required for the in vitro characterization of DNA within potential G-quadruplex-forming sequences (PQSs). B-CePs are a class of alkylating agents that have proven to be useful chemical probes for investigation of the higher-order structure of nucleic acids. This paper describes a new chemical mapping assay exploiting the specific reactivity of B-CePs with the N7 of guanines, followed by direct strand cleavage at the alkylated Gs.

Namely, to distinguish G4 folds from unfolded DNA forms, we use B-CeP 1 to probe the thrombin-binding aptamer (TBA), a 15-mer DNA able to assume the G4 arrangement. Reaction of B-CeP-responding guanines with B-CeP 1 yields products that can be resolved by high-resolution polyacrylamide gel electrophoresis (PAGE) at a single-nucleotide level by locating individual alkylation adducts and DNA strand cleavage at the alkylated guanines. Mapping using B-CePs is a simple and powerful tool for the in vitro characterization of G-quadruplex-forming DNA sequences, enabling the precise location of guanines involved in the formation of G-tetrads.

In addition to the typical Watson-Crick double helix, nucleic acids can adopt various secondary structures, such as the alternative G-quadruplex (G4) form, due to their guanine-rich sequences. G4 structure is based on the formation of planar tetramers, called G-tetrads, in which four guanines interact through Hoogsteen hydrogen bonds. G-tetrads are stacked and further stabilized by monovalent cations that are coordinated in the center of the guanine core (Figure 1)1.

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1. Nucleic acid and chemical probe preparation

  1. Nucleic acids
    NOTE: The oligonucleotide named "TBA" is the 15-mer DNA sequence 5'-GGT-TGG-TGT-GGT-TGG-3' labeled at the 3'-end by the fluorophore 5-carboxyfluorescein (FAM) to enable visualization on the gel. The unlabeled oligonucleotide "cTBA" is its DNA complementary sequence 5'-CCA-ACC-ACA-CCA-ACC-3'. TBA and cTBA are employed to obtain the three different structures, as shown in Table 1

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Figure 2 shows a representative result of a chemical mapping assay performed, as described in the protocol with B-CeP 1 on the TBA oligonucleotide folded in three different structures. The G-quadruplex arrangement of TBA (G4-TBA) was obtained by folding the oligonucleotide in BPE and in the presence of the K+ cation, whereas the single-stranded form of the same TBA sequence (ssTBA) was folded in the absence of potassium. The double-stranded construct (dsTBA) was prepared by a.......

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G-quadruplexes are nucleic acid secondary structures that typically fold within guanine-rich DNA sequences, and are significant research targets because of their association with genetic control and diseases. Chemical mapping by B-CePs is a useful protocol for the characterization of DNA G4s, which can be used to identify the guanine bases involved in the formation of G-tetrads under physiological salt conditions.

The chemical probe used in this protocol is B-CeP 1 (Figure.......

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This work was supported by the Department of Pharmaceutical and Pharmacological Sciences, University of Padova (PRIDJ-BIRD2019).

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Name Company Catalog Number Comments
Acrylamide/bis-acrylamide solution 40% Applichem A3658 R45-46-20/21-25-36/38-43-48/23/
24/25-62
Ammonium per-sulfate (APS) Sigma Aldrich A7460
Analytical balance Mettler Toledo
Autoclave pbi international
Boric acid Sigma Aldrich B0252
Bromophenol blue Brilliant blue R Sigma Aldrich B0149
di-Sodium hydrogen phosphate dodecahydrate Fluka 71649
DMSO Sigma Aldrich 276855
DNA oligonucleotides Integrated DNA Technologies synthesis of custom sequences
EDTA disodium Sigma Aldrich E5134
Formamide Fluka 40248 H351-360D-373
Gel imager GE Healtcare STORM B40
Glycerol Sigma Aldrich G5516
Micro tubes 0.5 mL Sarstedt 72.704
Potassium Chloride Sigma Aldrich P9541
Sequencing apparatus Biometra Model S2
Silanization solution I Fluka 85126 H225, 314, 318, 336, 304, 400, 410
Sodium phosphate monobasic Carlo Erba 480086
Speedvac concentrator Thermo Scientific Savant DNA 120
TEMED Fluka 87689 R11-21/22-23-34
Tris-HCl MERCK 1.08387.2500
Urea Sigma Aldrich 51456
UV-Vis spectrophotometer Thermo Scientific Nanodrop 1000

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