Stability and kinetics of G-quadruplex structures.

Nucleic Acids Research
Andrew N LaneJohn O Trent

Abstract

In this review, we give an overview of recent literature on the structure and stability of unimolecular G-rich quadruplex structures that are relevant to drug design and for in vivo function. The unifying theme in this review is energetics. The thermodynamic stability of quadruplexes has not been studied in the same detail as DNA and RNA duplexes, and there are important differences in the balance of forces between these classes of folded oligonucleotides. We provide an overview of the principles of stability and where available the experimental data that report on these principles. Significant gaps in the literature have been identified, that should be filled by a systematic study of well-defined quadruplexes not only to provide the basic understanding of stability both for design purposes, but also as it relates to in vivo occurrence of quadruplexes. Techniques that are commonly applied to the determination of the structure, stability and folding are discussed in terms of information content and limitations. Quadruplex structures fold and unfold comparatively slowly, and DNA unwinding events associated with transcription and replication may be operating far from equilibrium. The kinetics of formation and resolution of quadrup...Continue Reading

References

Apr 1, 1979·Biopolymers·C A SprecherW C Johnson
Jan 1, 1992·Methods in Enzymology·D M CrothersS D Levene
Nov 21, 1991·Nucleic Acids Research·V P AntaoI Tinoco
Oct 1, 1987·Genes & Development·C M Price, T R Cech
Jan 1, 1995·Annual Review of Physical Chemistry·C F Anderson, M T Record
Jan 1, 1995·Methods in Enzymology·R W Woody
Sep 12, 1995·Proceedings of the National Academy of Sciences of the United States of America·M OlivebergA R Fersht
Feb 1, 1994·Nature Structural Biology·S AhmedE Henderson
Feb 4, 1994·Journal of Molecular Biology·P SchultzeJ Feigon
Jan 1, 1994·Journal of Biochemical and Biophysical Methods·R W Hendler, R I Shrager
Jan 1, 1993·Annual Review of Biophysics and Biomolecular Structure·S N Timasheff
Jan 1, 1995·Methods in Enzymology·J FeigonF W Smith
Jan 1, 1995·Methods in Enzymology·M Guéron, J L Leroy
Jun 18, 1996·Biochemistry·J R WyattS M Freier
Jun 1, 1996·Current Opinion in Structural Biology·D H Turner
Feb 28, 1997·Biophysical Chemistry·G Xie, S N Timasheff
Nov 21, 1997·Journal of Molecular Biology·K PhillipsB Luisi
Jan 1, 1997·European Biophysics Journal : EBJ·I HaqJ B Chaires
Mar 21, 1998·Proceedings of the National Academy of Sciences of the United States of America·J SantaLucia
Mar 21, 1998·Journal of Molecular Biology·J L AsensioT Brown
May 23, 1998·Biochemistry·K E PrehodaJ L Markley
Jan 1, 1997·Biopolymers·J SantaLucia, D H Turner
May 30, 1998·Protein Science : a Publication of the Protein Society·D L Allen, G J Pielak
Jun 4, 1998·Current Opinion in Genetics & Development·J Lingner, T R Cech
Jul 3, 1998·Nucleic Acids Research·R D Blake, S G Delcourt
Oct 2, 1998·FEBS Letters·J L MergnyL Lacroix
Dec 24, 1998·Nucleic Acids Research·H HanM Salazar
Jan 8, 1999·Journal of Molecular Biology·N V HudJ Feigon
Apr 13, 1999·Nucleic Acids Research·H SunN Maizels

❮ Previous
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Citations

Feb 25, 2009·European Biophysics Journal : EBJ·Lance M HellmanMichael Gregory Fried
Sep 10, 2010·European Biophysics Journal : EBJ·Viktor VíglaskýLuboš Bauer
Nov 8, 2012·Journal of the American Society for Mass Spectrometry·Françoise BalthasartValérie Gabelica
Dec 17, 2008·Biochemical and Biophysical Research Communications·Hui LiThomas Gisler
Apr 8, 2009·Biochemistry·Jason S HudsonDavid E Graves
Jun 23, 2010·Journal of the American Chemical Society·Gavin W CollieValérie Gabelica
Aug 14, 2010·Journal of the American Chemical Society·Kah Wai LimAnh Tuân Phan
Aug 12, 2010·Journal of the American Chemical Society·Masaki HagiharaKazuhiko Nakatani
Dec 4, 2010·Journal of the American Chemical Society·Anaëlle Dumas, Nathan W Luedtke
Nov 16, 2011·Journal of the American Chemical Society·Luigi PetracconeJonathan B Chaires
Jan 14, 2012·Journal of the American Chemical Society·Melissa A MullenPhilip C Bevilacqua
Jun 2, 2012·Journal of the American Chemical Society·Ford M LannanNicholas V Hud
Sep 20, 2012·Journal of the American Chemical Society·Robert D GrayJonathan B Chaires
Jan 22, 2009·Journal of the American Chemical Society·Zhongbo YuHanbin Mao
Dec 4, 2008·Journal of the American Chemical Society·Luigi PetracconeJonathan B Chaires
Aug 27, 2009·Journal of the American Chemical Society·Shang-Te Danny HsuShankar Balasubramanian
Aug 27, 2009·The Journal of Physical Chemistry. B·Robert D GrayJonathan B Chaires
Sep 3, 2010·Nature Reviews. Drug Discovery·Marcin Drag, Guy S Salvesen
Apr 2, 2011·Nature Reviews. Drug Discovery·Shankar BalasubramanianStephen Neidle
Mar 15, 2011·Nature Structural & Molecular Biology·Jasmine S SmithF Brad Johnson
Aug 11, 2010·Chemical Communications : Chem Comm·Guangtao Song, Jinsong Ren
Jan 12, 2012·Chemical Communications : Chem Comm·Deepak KoiralaHiroshi Sugiyama
Nov 19, 2008·Proceedings of the National Academy of Sciences of the United States of America·Jens VölkerKenneth J Breslauer
Jul 25, 2009·Proceedings of the National Academy of Sciences of the United States of America·Dian G T SuJohn-Stephen A Taylor
Nov 28, 2012·Proceedings of the National Academy of Sciences of the United States of America·Feng WangZheng Tan
Apr 15, 2010·Nucleosides, Nucleotides & Nucleic Acids·Hanumantharao Paritala, Steven M Firestine
Jul 14, 2011·Nucleic Acid Therapeutics·Xiaohui JiChangqi Zhao

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Methods Mentioned

BETA
NMR
X-ray
circular dichroism
fluorescence resonance
FRET
electron spin resonance
dynamic light scattering
static light scattering
footprinting
gel filtration

Software Mentioned

APBS
SPR
Huppert

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