Restricting the conformational heterogeneity of RNA by specific incorporation of 8-bromoguanosine

David J. Proctor, Elzbieta Kierzek, Ryszard Kierzek, Philip C. Bevilacqua

Research output: Contribution to journalArticle

28 Citations (Scopus)

Abstract

In an effort to reduce the conformational heterogeneity of RNA, the modified nucleobase 8-bromoguanosine (8BrG) was introduced into oligonucleotides having the hairpin tetraloop motif YNMG (Y = U or C and M = C or A). Purine nucleobases with bromine at position eight are known to preferentially adopt the syn conformation as nucleosides. The hairpin tetraloop motif YNMG was chosen as a model system because it has a syn guanosine at position four of the loop that is essential for thermodynamic stability. Thermodynamic and structural characterization of modified oligonucleotides with the hairpin sequences UUCG, CGCG, and CGAG by UV-melting and NMR spectroscopy revealed that 8BrG substitution has a small effect upon the hairpin conformation, while the duplex conformation is strongly destabilized (ΔΔG°37 ≈ +4.7 kcal mol-1), thus inhibiting dimerization. These results support a model in which 8BrG substitution shifts the hairpin-duplex equilibrium constant toward the hairpin conformation by destabilizing the duplex. This methodology should be useful for limiting conformational heterogeneity in large RNAs, with potential applications in structural biology and enzymology.

Original languageEnglish (US)
Pages (from-to)2390-2391
Number of pages2
JournalJournal of the American Chemical Society
Volume125
Issue number9
DOIs
StatePublished - Mar 5 2003

Fingerprint

RNA
Conformations
Thermodynamics
Oligonucleotides
Bromine
Substitution reactions
Guanosine
Dimerization
Nucleosides
Freezing
Equilibrium constants
Magnetic Resonance Spectroscopy
Nuclear magnetic resonance spectroscopy
Melting
Thermodynamic stability
8-bromoguanosine

All Science Journal Classification (ASJC) codes

  • Catalysis
  • Chemistry(all)
  • Biochemistry
  • Colloid and Surface Chemistry

Cite this

@article{92b3fe15d6494f0694066dcae409c965,
title = "Restricting the conformational heterogeneity of RNA by specific incorporation of 8-bromoguanosine",
abstract = "In an effort to reduce the conformational heterogeneity of RNA, the modified nucleobase 8-bromoguanosine (8BrG) was introduced into oligonucleotides having the hairpin tetraloop motif YNMG (Y = U or C and M = C or A). Purine nucleobases with bromine at position eight are known to preferentially adopt the syn conformation as nucleosides. The hairpin tetraloop motif YNMG was chosen as a model system because it has a syn guanosine at position four of the loop that is essential for thermodynamic stability. Thermodynamic and structural characterization of modified oligonucleotides with the hairpin sequences UUCG, CGCG, and CGAG by UV-melting and NMR spectroscopy revealed that 8BrG substitution has a small effect upon the hairpin conformation, while the duplex conformation is strongly destabilized (ΔΔG°37 ≈ +4.7 kcal mol-1), thus inhibiting dimerization. These results support a model in which 8BrG substitution shifts the hairpin-duplex equilibrium constant toward the hairpin conformation by destabilizing the duplex. This methodology should be useful for limiting conformational heterogeneity in large RNAs, with potential applications in structural biology and enzymology.",
author = "Proctor, {David J.} and Elzbieta Kierzek and Ryszard Kierzek and Bevilacqua, {Philip C.}",
year = "2003",
month = "3",
day = "5",
doi = "10.1021/ja029176m",
language = "English (US)",
volume = "125",
pages = "2390--2391",
journal = "Journal of the American Chemical Society",
issn = "0002-7863",
publisher = "American Chemical Society",
number = "9",

}

Restricting the conformational heterogeneity of RNA by specific incorporation of 8-bromoguanosine. / Proctor, David J.; Kierzek, Elzbieta; Kierzek, Ryszard; Bevilacqua, Philip C.

In: Journal of the American Chemical Society, Vol. 125, No. 9, 05.03.2003, p. 2390-2391.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Restricting the conformational heterogeneity of RNA by specific incorporation of 8-bromoguanosine

AU - Proctor, David J.

AU - Kierzek, Elzbieta

AU - Kierzek, Ryszard

AU - Bevilacqua, Philip C.

PY - 2003/3/5

Y1 - 2003/3/5

N2 - In an effort to reduce the conformational heterogeneity of RNA, the modified nucleobase 8-bromoguanosine (8BrG) was introduced into oligonucleotides having the hairpin tetraloop motif YNMG (Y = U or C and M = C or A). Purine nucleobases with bromine at position eight are known to preferentially adopt the syn conformation as nucleosides. The hairpin tetraloop motif YNMG was chosen as a model system because it has a syn guanosine at position four of the loop that is essential for thermodynamic stability. Thermodynamic and structural characterization of modified oligonucleotides with the hairpin sequences UUCG, CGCG, and CGAG by UV-melting and NMR spectroscopy revealed that 8BrG substitution has a small effect upon the hairpin conformation, while the duplex conformation is strongly destabilized (ΔΔG°37 ≈ +4.7 kcal mol-1), thus inhibiting dimerization. These results support a model in which 8BrG substitution shifts the hairpin-duplex equilibrium constant toward the hairpin conformation by destabilizing the duplex. This methodology should be useful for limiting conformational heterogeneity in large RNAs, with potential applications in structural biology and enzymology.

AB - In an effort to reduce the conformational heterogeneity of RNA, the modified nucleobase 8-bromoguanosine (8BrG) was introduced into oligonucleotides having the hairpin tetraloop motif YNMG (Y = U or C and M = C or A). Purine nucleobases with bromine at position eight are known to preferentially adopt the syn conformation as nucleosides. The hairpin tetraloop motif YNMG was chosen as a model system because it has a syn guanosine at position four of the loop that is essential for thermodynamic stability. Thermodynamic and structural characterization of modified oligonucleotides with the hairpin sequences UUCG, CGCG, and CGAG by UV-melting and NMR spectroscopy revealed that 8BrG substitution has a small effect upon the hairpin conformation, while the duplex conformation is strongly destabilized (ΔΔG°37 ≈ +4.7 kcal mol-1), thus inhibiting dimerization. These results support a model in which 8BrG substitution shifts the hairpin-duplex equilibrium constant toward the hairpin conformation by destabilizing the duplex. This methodology should be useful for limiting conformational heterogeneity in large RNAs, with potential applications in structural biology and enzymology.

UR - http://www.scopus.com/inward/record.url?scp=0242500942&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0242500942&partnerID=8YFLogxK

U2 - 10.1021/ja029176m

DO - 10.1021/ja029176m

M3 - Article

VL - 125

SP - 2390

EP - 2391

JO - Journal of the American Chemical Society

JF - Journal of the American Chemical Society

SN - 0002-7863

IS - 9

ER -