Probing the competition between duplex and G-quadruplex/i-motif structures using a conformation-sensitive fluorescent nucleoside probe

Organic & Biomolecular Chemistry
Pramod M SabaleSeergazhi G Srivatsan

Abstract

Double-stranded segments of a genome that can potentially form G-quadruplex (GQ) and/or i-motif (iM) structures are considered to be important regulatory elements. Hence, the development of a common probe that can detect GQ and iM structures and also distinguish them from a duplex structure will be highly useful in understanding the propensity of such segments to adopt duplex or non-canonical four-stranded structures. Here, we describe the utility of a conformation-sensitive fluorescent nucleoside analog, which was originally developed as a GQ sensor, in detecting the iM structures of C-rich DNA oligonucleotides (ONs). The analog is based on a 5-(benzofuran-2-yl)uracil scaffold, which when incorporated into C-rich ONs (e.g., telomeric repeats) fluorescently distinguishes an iM from random coil and duplex structures. Steady-state and time-resolved fluorescence techniques enabled the determination of transition pH for the transformation of a random coil to an iM structure. Furthermore, a qualitative understanding on the relative population of duplex and GQ/iM forms under physiological conditions could be gained by correlating the fluorescence, CD and thermal melting data. Taken together, this sensor could provide a general platfo...Continue Reading

References

Nov 5, 1997·Nature Genetics·D BroccoliT de Lange
Jun 14, 2000·Current Opinion in Structural Biology·M Guéron, J L Leroy
Aug 31, 2002·Angewandte Chemie·Nicole AmannHans-Achim Wagenknecht
Feb 24, 2006·Chemical Communications : Chem Comm·Takumi KimuraTetsuro Majima
Mar 25, 2008·Biochimie·Saikat Chakraborty, Yamuna Krishnan
Jan 14, 2009·Nucleic Acids Research·Ilene M PedrosoTerace M Fletcher
Sep 3, 2009·Chemical Communications : Chem Comm·Il Joon LeeByeang Hyean Kim
Nov 17, 2009·Journal of the American Chemical Society·Samantha KendrickLaurence H Hurley
May 8, 2010·Chemical Communications : Chem Comm·Arivazhagan RajendranNaoki Sugimoto
Jul 31, 2010·The FEBS Journal·Tracy A BrooksLaurence Hurley
Aug 4, 2010·Proceedings of the National Academy of Sciences of the United States of America·Yan XuMakoto Komiyama
Mar 25, 2011·Angewandte Chemie·Yamuna Krishnan, Friedrich C Simmel
Apr 2, 2011·Nature Reviews. Drug Discovery·Shankar BalasubramanianStephen Neidle
May 10, 2011·Nucleic Acids Research·Anaëlle Dumas, Nathan W Luedtke
Jul 27, 2011·Chemical Society Reviews·Gavin W Collie, Gary N Parkinson
Nov 19, 2011·Angewandte Chemie·Anna Lena LiebleinHarald Schwalbe
Nov 26, 2011·Chemical Communications : Chem Comm·Il Joon Lee, Byeang Hyean Kim
Mar 28, 2012·Methods : a Companion to Methods in Enzymology·Michaela VorlíčkováJaroslav Kypr
May 29, 2012·Methods : a Companion to Methods in Enzymology·Michael AdrianAnh Tuân Phan
Jul 12, 2012·Journal of the American Chemical Society·Giulia BiffiShankar Balasubramanian
Aug 14, 2012·Topics in Current Chemistry·Eric LargyMarie-Paule Teulade-Fichou
Sep 27, 2012·Chemical Communications : Chem Comm·John A BrazierGeoffrey D Brown
Oct 17, 2012·Chembiochem : a European Journal of Chemical Biology·Arun A Tanpure, Seergazhi G Srivatsan
Jan 15, 2013·Journal of the American Chemical Society·Tao Li, Michael Famulok
Feb 27, 2013·Chembiochem : a European Journal of Chemical Biology·Balayeshwanth R VummidiNathan W Luedtke
May 9, 2013·Nature Communications·Enid Yi Ni LamShankar Balasubramanian
May 28, 2013·Nature Nanotechnology·Souvik ModiYamuna Krishnan
Oct 29, 2013·The Journal of Physical Chemistry. B·Maroti G Pawar, Seergazhi G Srivatsan
Oct 29, 2013·Nucleic Acids Research·Alexander HendersonPeter M Lansdorp
Nov 28, 2013·Angewandte Chemie·Jungkweon ChoiTetsuro Majima

❮ Previous
Next ❯

Citations

Apr 22, 2020·Nucleic Acids Research·Michela ZuffoAnton Granzhan
Dec 29, 2020·Chembiochem : a European Journal of Chemical Biology·Pallabi SenguptaSubhrangsu Chatterjee

❮ Previous
Next ❯

Methods Mentioned

BETA
circular
NMR
X-ray
fluorescence assay
Fluorescence
atomic force microscopy
electrophoresis

Software Mentioned

OriginPro
IBH DAS6

Related Concepts

Related Feeds

Cajal Bodies & Gems

Cajal bodies or coiled bodies are dense foci of coilin protein. Gemini of Cajal bodies, or gems, are microscopically similar to Cajal bodies. It is believed that Cajal bodies play important roles in RNA processing while gems assist the Cajal bodies. Find the latest research on Cajal bodies and gems here.