TY - JOUR

T1 - The Importance of Phosphates for DNA G-Quadruplex Formation

T2 - Evaluation of Zwitterionic G-Rich Oligodeoxynucleotides

AU - Su, Yongdong

AU - Edwards, Patrick J.B.

AU - Stetsenko, Dmitry A.

AU - Filichev, Vyacheslav V.

N1 - © 2020 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

PY - 2020/9/1

Y1 - 2020/9/1

N2 - A quaternary ammonium butylsulfonyl phosphoramidate group (N+) was designed to replace all the phosphates in a G-rich oligodeoxynucleotide d(TG4T), resulting in a formally charge-neutral zwitterionic N+TG4T sequence. We evaluated the effects of N+phosphate modifications on the structural, thermodynamic and kinetic properties of the parallel G-quadruplexes (G4) formed by TG4T and compared them to the properties of the recently published phosphoryl guanidine d(TG4T) (PG-TG4T). Using size-exclusion chromatography, we established that, unlike PG-TG4T, which exists as a mixture of complexes of different molecularity in solution, N+TG4T forms an individual tetramolecular complex. In contrast to PG modifications that destabilized G4s, the presence of N+ modifications increased thermal stability relative to unmodified [d(TG4T)]4. The initial stage of assembly of N+TG4T proceeded faster in the presence of Na+ than K+ions and, similarly to PG-TG4T, was independent of the salt concentration. However, after complex formation exceeded 75 %, N+TG4T in solution with Na+showed slower association than with K+. N+TG4T could also form G4s in solution with Li+ions at a very low strand concentration (10 μM); something that has never been reported for the native d(TG4T). Charge-neutral PG-G4s can invade preformed native G4s, whereas no invasion was observed between N+and native G4s, possibly due to the increased thermal stability of [N+TG4T]4. The N+ modification makes d(TG4T) fully resistant to enzymatic digestion, which could be useful for intracellular application of N+-modified DNA or RNA.

AB - A quaternary ammonium butylsulfonyl phosphoramidate group (N+) was designed to replace all the phosphates in a G-rich oligodeoxynucleotide d(TG4T), resulting in a formally charge-neutral zwitterionic N+TG4T sequence. We evaluated the effects of N+phosphate modifications on the structural, thermodynamic and kinetic properties of the parallel G-quadruplexes (G4) formed by TG4T and compared them to the properties of the recently published phosphoryl guanidine d(TG4T) (PG-TG4T). Using size-exclusion chromatography, we established that, unlike PG-TG4T, which exists as a mixture of complexes of different molecularity in solution, N+TG4T forms an individual tetramolecular complex. In contrast to PG modifications that destabilized G4s, the presence of N+ modifications increased thermal stability relative to unmodified [d(TG4T)]4. The initial stage of assembly of N+TG4T proceeded faster in the presence of Na+ than K+ions and, similarly to PG-TG4T, was independent of the salt concentration. However, after complex formation exceeded 75 %, N+TG4T in solution with Na+showed slower association than with K+. N+TG4T could also form G4s in solution with Li+ions at a very low strand concentration (10 μM); something that has never been reported for the native d(TG4T). Charge-neutral PG-G4s can invade preformed native G4s, whereas no invasion was observed between N+and native G4s, possibly due to the increased thermal stability of [N+TG4T]4. The N+ modification makes d(TG4T) fully resistant to enzymatic digestion, which could be useful for intracellular application of N+-modified DNA or RNA.

KW - DNA

KW - enzymatic stability

KW - G-quadruplexes

KW - kinetics

KW - modified phosphate

KW - thermal stability

KW - MOTIFS

KW - PNA

KW - STABILITY

KW - CD SPECTRA

KW - COMPLEMENTARY

KW - GUANOSINE-QUARTET STRUCTURE

KW - KINETICS

KW - SEQUENCE

KW - LOCKED NUCLEIC-ACIDS

KW - BINDING

UR - http://www.scopus.com/inward/record.url?scp=85084428131&partnerID=8YFLogxK

U2 - 10.1002/cbic.202000110

DO - 10.1002/cbic.202000110

M3 - Article

C2 - 32281223

AN - SCOPUS:85084428131

VL - 21

SP - 2455

EP - 2466

JO - ChemBioChem

JF - ChemBioChem

SN - 1439-4227

IS - 17

ER -