What controls the hybridization thermodynamics of spherical nucleic acids?

Journal of the American Chemical Society
Pratik S RanderiaChad A Mirkin

Abstract

The hybridization of free oligonucleotides to densely packed, oriented arrays of DNA modifying the surfaces of spherical nucleic acid (SNA)-gold nanoparticle conjugates occurs with negative cooperativity; i.e., each binding event destabilizes subsequent binding events. DNA hybridization is thus an ever-changing function of the number of strands already hybridized to the particle. Thermodynamic quantification of this behavior reveals a 3 orders of magnitude decrease in the binding constant for the capture of a free oligonucleotide by an SNA conjugate as the fraction of pre-hybridized strands increases from 0 to ∼30%. Increasing the number of pre-hybridized strands imparts an increasing enthalpic penalty to hybridization that makes binding more difficult, while simultaneously decreasing the entropic penalty to hybridization, which makes binding more favorable. Hybridization of free DNA to an SNA is thus governed by both an electrostatic barrier as the SNA accumulates charge with additional binding events and an effect consistent with allostery, where hybridization at certain sites on an SNA modify the binding affinity at a distal site through conformational changes to the remaining single strands. Leveraging these insights allows...Continue Reading

References

May 1, 1989·Quarterly Reviews of Biophysics·M F Perutz
Sep 8, 2000·Science·T A TatonR L Letsinger
Jan 29, 2002·Nucleic Acids Research·A W PetersonR M Georgiadis
Nov 8, 2003·The Journal of Biological Chemistry·Irving M Klotz
May 24, 2005·Biophysical Journal·A HalperinE B Zhulina
Sep 15, 2005·Journal of the American Chemical Society·Abigail K R Lytton-Jean, Chad A Mirkin
Sep 22, 2005·Journal of the American Chemical Society·Jun Xu, Stephen L Craig
May 20, 2006·Science·Nathaniel L RosiChad A Mirkin
Nov 24, 2007·Journal of the American Chemical Society·Dwight S SeferosChad A Mirkin
Feb 1, 2008·Nature·Dmytro NykypanchukOleg Gang
Apr 3, 2008·Proceedings of the National Academy of Sciences of the United States of America·Ping Gong, Rastislav Levicky
Jul 19, 2008·The Journal of Physical Chemistry. B·Martin McCullaghGeorge C Schatz
Mar 5, 2009·Physical Review Letters·O A SalehN Ribeck
Aug 26, 2009·ACS Nano·Andrew E PrigodichChad A Mirkin
Jun 17, 2010·Biophysical Journal·Ian Y Wong, Nicholas A Melosh
Oct 5, 2010·Nature Materials·Matthew R JonesChad A Mirkin
Jun 28, 2011·Physical Review Letters·C KnorowskiA Travesset
Oct 15, 2011·Science·Robert J MacfarlaneChad A Mirkin
Feb 1, 2012·Analytical Chemistry·Andrew E PrigodichChad A Mirkin
Nov 1, 2013·Science Translational Medicine·Samuel A JensenAlexander H Stegh
Nov 19, 2014·Proceedings of the National Academy of Sciences of the United States of America·Tiffany L HaloC Shad Thaxton
Jan 3, 2013·The Journal of Physical Chemistry Letters·Kevin L KohlstedtGeorge C Schatz

❮ Previous
Next ❯

Citations

Jan 13, 2016·Langmuir : the ACS Journal of Surfaces and Colloids·Emma L C J BlundellMark Platt
Mar 5, 2016·Journal of the American Chemical Society·Leo Yt ChouWarren C W Chan
Apr 30, 2016·ACS Applied Materials & Interfaces·Jing SunHao Liang
Oct 23, 2015·Journal of the American Chemical Society·Yuliia VybornaRobert Häner
Oct 27, 2016·Analytical Chemistry·Brandi L Baldock, James E Hutchison
Jan 25, 2017·ACS Applied Materials & Interfaces·Pinliang JiangYong Wang
Feb 22, 2017·ACS Applied Materials & Interfaces·Lizhen ChenHao Pei
Apr 26, 2017·Chemical Communications : Chem Comm·Yuliia VybornaRobert Häner
Feb 11, 2016·Physical Chemistry Chemical Physics : PCCP·Stefano Angioletti-UbertiDaan Frenkel
Jan 5, 2020·Proceedings of the National Academy of Sciences of the United States of America·Gokay YamankurtChad A Mirkin
Sep 15, 2020·Science Advances·Sungi KimJwa-Min Nam
Jan 23, 2020·Physical Review. E·Pritam Kumar Jana, Bortolo Matteo Mognetti
Feb 19, 2021·Journal of the American Chemical Society·Yan HaoZhaoxiang Deng
Oct 12, 2019·Nano Letters·Leonardo Z ZornbergRobert J Macfarlane
Jun 10, 2015·Langmuir : the ACS Journal of Surfaces and Colloids·Dongbao YaoHaojun Liang
Aug 16, 2016·Bioconjugate Chemistry·Stacey N BarnabyChad A Mirkin
Mar 7, 2020·Journal of the American Chemical Society·Junxiang ZhaoJiashu Sun
Dec 21, 2016·Langmuir : the ACS Journal of Surfaces and Colloids·Abootaleb Sedighi, Ulrich J Krull
Oct 15, 2020·Accounts of Chemical Research·Shine K AlbertReji Varghese
May 16, 2018·Journal of the American Chemical Society·Lam-Kiu FongChad A Mirkin
Sep 4, 2019·Bioconjugate Chemistry·Hao WangLaura Fabris

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.