Beyond guanine quartets: Cation-induced formation of homogenous and chimeric DNA tetraplexes incorporating iso-guanine and guanine

Christopher Roberts, John C. Chaput, Christopher Switzer

Research output: Contribution to journalArticle

41 Citations (Scopus)

Abstract

Background: iso-Guanine (iso-G) is the purine component of an isomeric Watson-Crick base pair that may have existed prebiotically. By comparing the abiotic molecular recognition properties of iso-G and its complement, iso-cytosine (iso-C), with those of genomic nucleotide bases, it may be possible to explain the exclusion of the iso-G-iso-C base pair from modem genomes. Whether a nucleobase forms quartets may have a key role in determining its functionality. Biotically, nucleic acid tetraplexes have been implicated in cellular functions; prebiotically, tetraplexes would probably interfere with replication. Recently, in vitro selection has yielded receptors and catalysts that incorporate G quartets. The versatility of these structures could be enhanced by expanding the range of bases that can form the quartet motif. Results: Native polyacrylamide gel electrophoresis of oligonucleotides bearing runs of iso-G provides strong support for tetraplex formation via cation-promoted DNA strand association. In particular, when strands of different lengths bearing the same iso-G tetrad recognition element were combined, five bands were observed after electrophoresis, corresponding to all possible heterotetraplexes with parallel strand alignment. An analogous experiment with a mixture of strands bearing iso-G or G tetrad recognition domains supports the existence of mixed iso-G/G tetraplexes with antiparallel strand alignment at chimeric junctions. iso-G tetraplex and quartet structure has also been probed by a photo-crosslinking experiment, ultra-violet spectroscopy and theoretical calculations. Conclusions: As iso-G and G both have a marked tendency to form tetraplexes, their tandem inclusion in genetic material may be problematic, leading to double-stranded DNA half composed of bases that have a tendency to auto-associate. The resulting density of 'selfish' bases could undermine Watson-Crick pair formation, especially in a prebiotic context devoid of enzymes. Nevertheless, the ability of iso-G to form mixed quartets with G may provide a basis for altering the properties of tetraplexes in the domain of artificial receptors or catalysts from in vitro selections.

Original languageEnglish (US)
Pages (from-to)899-908
Number of pages10
JournalChemistry and Biology
Volume4
Issue number12
StatePublished - Dec 1997
Externally publishedYes

Fingerprint

G-Quadruplexes
Guanine
Cations
DNA
Bearings (structural)
Cytosine
Base Pairing
Electrophoresis
Artificial Receptors
Modems
Native Polyacrylamide Gel Electrophoresis
Prebiotics
Molecular recognition
Catalysts
Oligonucleotides
Nucleic Acids
Spectrum Analysis
Ultraviolet spectroscopy
Nucleotides
Crosslinking

Keywords

  • Ab initio theoretical
  • Guanine
  • Iso-guanine
  • Quartet
  • Tetraplex

ASJC Scopus subject areas

  • Organic Chemistry

Cite this

Beyond guanine quartets : Cation-induced formation of homogenous and chimeric DNA tetraplexes incorporating iso-guanine and guanine. / Roberts, Christopher; Chaput, John C.; Switzer, Christopher.

In: Chemistry and Biology, Vol. 4, No. 12, 12.1997, p. 899-908.

Research output: Contribution to journalArticle

Roberts, Christopher ; Chaput, John C. ; Switzer, Christopher. / Beyond guanine quartets : Cation-induced formation of homogenous and chimeric DNA tetraplexes incorporating iso-guanine and guanine. In: Chemistry and Biology. 1997 ; Vol. 4, No. 12. pp. 899-908.
@article{6a3300c7bd05429a869f9164247c43a4,
title = "Beyond guanine quartets: Cation-induced formation of homogenous and chimeric DNA tetraplexes incorporating iso-guanine and guanine",
abstract = "Background: iso-Guanine (iso-G) is the purine component of an isomeric Watson-Crick base pair that may have existed prebiotically. By comparing the abiotic molecular recognition properties of iso-G and its complement, iso-cytosine (iso-C), with those of genomic nucleotide bases, it may be possible to explain the exclusion of the iso-G-iso-C base pair from modem genomes. Whether a nucleobase forms quartets may have a key role in determining its functionality. Biotically, nucleic acid tetraplexes have been implicated in cellular functions; prebiotically, tetraplexes would probably interfere with replication. Recently, in vitro selection has yielded receptors and catalysts that incorporate G quartets. The versatility of these structures could be enhanced by expanding the range of bases that can form the quartet motif. Results: Native polyacrylamide gel electrophoresis of oligonucleotides bearing runs of iso-G provides strong support for tetraplex formation via cation-promoted DNA strand association. In particular, when strands of different lengths bearing the same iso-G tetrad recognition element were combined, five bands were observed after electrophoresis, corresponding to all possible heterotetraplexes with parallel strand alignment. An analogous experiment with a mixture of strands bearing iso-G or G tetrad recognition domains supports the existence of mixed iso-G/G tetraplexes with antiparallel strand alignment at chimeric junctions. iso-G tetraplex and quartet structure has also been probed by a photo-crosslinking experiment, ultra-violet spectroscopy and theoretical calculations. Conclusions: As iso-G and G both have a marked tendency to form tetraplexes, their tandem inclusion in genetic material may be problematic, leading to double-stranded DNA half composed of bases that have a tendency to auto-associate. The resulting density of 'selfish' bases could undermine Watson-Crick pair formation, especially in a prebiotic context devoid of enzymes. Nevertheless, the ability of iso-G to form mixed quartets with G may provide a basis for altering the properties of tetraplexes in the domain of artificial receptors or catalysts from in vitro selections.",
keywords = "Ab initio theoretical, Guanine, Iso-guanine, Quartet, Tetraplex",
author = "Christopher Roberts and Chaput, {John C.} and Christopher Switzer",
year = "1997",
month = "12",
language = "English (US)",
volume = "4",
pages = "899--908",
journal = "Cell Chemical Biology",
issn = "2451-9448",
publisher = "Elsevier Inc.",
number = "12",

}

TY - JOUR

T1 - Beyond guanine quartets

T2 - Cation-induced formation of homogenous and chimeric DNA tetraplexes incorporating iso-guanine and guanine

AU - Roberts, Christopher

AU - Chaput, John C.

AU - Switzer, Christopher

PY - 1997/12

Y1 - 1997/12

N2 - Background: iso-Guanine (iso-G) is the purine component of an isomeric Watson-Crick base pair that may have existed prebiotically. By comparing the abiotic molecular recognition properties of iso-G and its complement, iso-cytosine (iso-C), with those of genomic nucleotide bases, it may be possible to explain the exclusion of the iso-G-iso-C base pair from modem genomes. Whether a nucleobase forms quartets may have a key role in determining its functionality. Biotically, nucleic acid tetraplexes have been implicated in cellular functions; prebiotically, tetraplexes would probably interfere with replication. Recently, in vitro selection has yielded receptors and catalysts that incorporate G quartets. The versatility of these structures could be enhanced by expanding the range of bases that can form the quartet motif. Results: Native polyacrylamide gel electrophoresis of oligonucleotides bearing runs of iso-G provides strong support for tetraplex formation via cation-promoted DNA strand association. In particular, when strands of different lengths bearing the same iso-G tetrad recognition element were combined, five bands were observed after electrophoresis, corresponding to all possible heterotetraplexes with parallel strand alignment. An analogous experiment with a mixture of strands bearing iso-G or G tetrad recognition domains supports the existence of mixed iso-G/G tetraplexes with antiparallel strand alignment at chimeric junctions. iso-G tetraplex and quartet structure has also been probed by a photo-crosslinking experiment, ultra-violet spectroscopy and theoretical calculations. Conclusions: As iso-G and G both have a marked tendency to form tetraplexes, their tandem inclusion in genetic material may be problematic, leading to double-stranded DNA half composed of bases that have a tendency to auto-associate. The resulting density of 'selfish' bases could undermine Watson-Crick pair formation, especially in a prebiotic context devoid of enzymes. Nevertheless, the ability of iso-G to form mixed quartets with G may provide a basis for altering the properties of tetraplexes in the domain of artificial receptors or catalysts from in vitro selections.

AB - Background: iso-Guanine (iso-G) is the purine component of an isomeric Watson-Crick base pair that may have existed prebiotically. By comparing the abiotic molecular recognition properties of iso-G and its complement, iso-cytosine (iso-C), with those of genomic nucleotide bases, it may be possible to explain the exclusion of the iso-G-iso-C base pair from modem genomes. Whether a nucleobase forms quartets may have a key role in determining its functionality. Biotically, nucleic acid tetraplexes have been implicated in cellular functions; prebiotically, tetraplexes would probably interfere with replication. Recently, in vitro selection has yielded receptors and catalysts that incorporate G quartets. The versatility of these structures could be enhanced by expanding the range of bases that can form the quartet motif. Results: Native polyacrylamide gel electrophoresis of oligonucleotides bearing runs of iso-G provides strong support for tetraplex formation via cation-promoted DNA strand association. In particular, when strands of different lengths bearing the same iso-G tetrad recognition element were combined, five bands were observed after electrophoresis, corresponding to all possible heterotetraplexes with parallel strand alignment. An analogous experiment with a mixture of strands bearing iso-G or G tetrad recognition domains supports the existence of mixed iso-G/G tetraplexes with antiparallel strand alignment at chimeric junctions. iso-G tetraplex and quartet structure has also been probed by a photo-crosslinking experiment, ultra-violet spectroscopy and theoretical calculations. Conclusions: As iso-G and G both have a marked tendency to form tetraplexes, their tandem inclusion in genetic material may be problematic, leading to double-stranded DNA half composed of bases that have a tendency to auto-associate. The resulting density of 'selfish' bases could undermine Watson-Crick pair formation, especially in a prebiotic context devoid of enzymes. Nevertheless, the ability of iso-G to form mixed quartets with G may provide a basis for altering the properties of tetraplexes in the domain of artificial receptors or catalysts from in vitro selections.

KW - Ab initio theoretical

KW - Guanine

KW - Iso-guanine

KW - Quartet

KW - Tetraplex

UR - http://www.scopus.com/inward/record.url?scp=0031461121&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0031461121&partnerID=8YFLogxK

M3 - Article

C2 - 9427655

AN - SCOPUS:0031461121

VL - 4

SP - 899

EP - 908

JO - Cell Chemical Biology

JF - Cell Chemical Biology

SN - 2451-9448

IS - 12

ER -