Search results for: Dipankar Sen

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A Long and Reversibly Self‐Assembling 1D DNA Nanostructure Built from Triplex and Quadruplex Hybrid Tiles

Prince Kumar Lat, Clayton W. Schultz, Hua‐Zhong Yu, Dipankar Sen

Angewandte Chemie > 133 > 16 > 8804 - 8809

We report a new DNA nanostructure, an extended 1‐dimensional composite built for the first time out of structurally robust yet conveniently disassembled DNA triple helices, interspersed with short stretches of G‐quadruplexes. These “TQ Hybrid” 1‐dimensional nanostructures require potassium ions and modestly acidic pH for their formation and are easily disassembled by changes to either of these requirements...

article

A Long and Reversibly Self‐Assembling 1D DNA Nanostructure Built from Triplex and Quadruplex Hybrid Tiles

Prince Kumar Lat, Clayton W. Schultz, Hua‐Zhong Yu, Dipankar Sen

Angewandte Chemie International Edition > 60 > 16 > 8722 - 8727

article

Hemin-utilizing G-quadruplex DNAzymes are strongly active in organic co-solvents

Thomas D. Canale, Dipankar Sen

Biochimica et Biophysica Acta (BBA) - General Subjects > 2017 > 1861 > 5(PB) > 1455-1462

The widespread use of organic solvents in industrial processes has focused in recent years on the utility of “green” solvents – those with less harmful environmental, health, and safety properties – such as methanol and formamide. However, protein enzymes, regarded as green catalysts, are often incompatible with organic solvents. Herein, we have explored the oxidative properties of a Fe(III)-heme,...

article

Blending Quadruplexes and Bordeaux: A Grand Cru!

Liliya A. Yatsunyk, David Monchaud, Dipankar Sen

Cell Chemical Biology > 2016 > 23 > 3 > 320-329

The Fifth International Meeting on Quadruplex Nucleic Acids took place in Bordeaux, France. Over the course of three intense days in May 2015, the quadruplex community had an opportunity to share exciting developments in the field, especially key insights into emerging biological roles that these structures, considered for decades to be nothing more but in vitro curiosity, are playing.

article

DNA mechatronic devices switched by K⁺ and by Sr²⁺ are structurally, topologically, and electronically distinct

Yu Chuan Huang, Hua‐Zhong Yu, Dipankar Sen, Jonathan Chaires

Biopolymers > 103 > 8 > 460 - 468

DNAs and RNAs that fold via the formation of guanine quartets form G‐quadruplexes that are often highly diverse in terms of architecture and topology. G‐quadruplexes are specifically stabilized by metal cations such as K⁺ and Sr²⁺, but not Li⁺. DNA duplexes that incorporate two separated clusters of G•G mismatches (“P‐duplexes”) can function as electronic switches, capable of toggling reversibly from...

article

Assessment of Vitamin D status In Patients of Chronic Low Back Pain of Unknown Etiology

Moushumi Lodh, Binita Goswami, Rajni Dawar Mahajan, Dipankar Sen, more

Indian Journal of Clinical Biochemistry > 2015 > 30 > 2 > 174-179

Low back pain is very disabling and dispiriting because of the physical impediment it causes and its psychological effects. Innumerable factors have been implicated in its etiology. In spite of improvements in diagnostic modalities, a considerable number of such cases fall in the ambiguous zone of unknown etiology or ‘idiopathic.’Early diagnosis of low back pain will allow effective prevention...

article

A Twisting Electronic Nanoswitch Made of DNA

Yu Chuan Huang, Dipankar Sen

Angewandte Chemie > 126 > 51 > 14279 - 14283

Single‐stranded DNAs and RNAs that are rich in the nucleobase guanine form four‐stranded G‐quadruplexes, which are held together by hydrogen‐bonded guanine quartets. In aqueous solution, both DNA duplexes and G‐quadruplexes are modest conductors of electrical charge. A tight, topologically constrained DNA construct called twDNA is now reported, in which a core of four guanine‐rich single strands structurally...

article

A Twisting Electronic Nanoswitch Made of DNA

Yu Chuan Huang, Dipankar Sen

Angewandte Chemie International Edition > 53 > 51 > 14055 - 14059

article

Mechatronic DNA devices driven by a G-quadruplex-binding platinum ligand

Yu Chuan Huang, Katherine J. Castor, Hanadi F. Sleiman, Dipankar Sen

Bioorganic & Medicinal Chemistry > 2014 > 22 > 16 > 4376-4383

Contractile duplexes are DNA double helices that incorporate two strategically placed patches of guanine–guanine (G·G) base mismatches. Such duplexes are cation-driven mechatronic devices, able to toggle between states with distinct mechanical and charge conduction properties. In aqueous lithium chloride solution contractile duplexes have an extended (E) and poorly conductive conformation; however,...

article

Guanine-Rich RNAs and DNAs That Bind Heme Robustly Catalyze Oxygen Transfer Reactions

Lester C.-H. Poon, Stephen P. Methot, William Morabi-Pazooki, Frédéric Pio, more

Journal of the American Chemical Society > 2011 > 133 > 6 > 1877 - 1884

article

Evaluation of biological nutrient removal from wastewater by Twin Circulating Fluidized Bed Bioreactor (TCFBBR) using a predictive fluidization model and AQUIFAS APP

Mehran Andalib, George Nakhla, Dipankar Sen, Jesse Zhu

Bioresource Technology > 2011 > 102 > 3 > 2400-2410

A two-phase and three-phase predictive fluidization model based on the characteristics of a system such as media type and size, flow rates, and reactor cross sectional area was proposed to calculate bed expansion, solid, liquid and gas hold up and specific surface area (SSA) of the biofilm particles. The model was subsequently linked to 1d AQUIFAS APP software (Aquaregen) to model biological nutrient...

article

A Robust Electronic Switch Made of Immobilized Duplex/Quadruplex DNA

Bixia Ge, Yu Chuan Huang, Dipankar Sen, Hua‐Zhong Yu

Angewandte Chemie > 122 > 51 > 10161 - 10163

Ein robuster Nanoschalter beruht auf einem zusammenziehbaren DNA‐Konstrukt (G‐Quadruplex) als Schalter und Ferrocen (Fc) als redoxaktivem Initiator (siehe Bild). Der Schalter wurde elektrochemisch getestet und wiederholt durch Hinzufügen oder Entfernen des Effektors (K⁺‐Ionen) an‐ und ausgeschaltet. Reversibilität und Reproduzierbarkeit des DNA‐Schalters können direkt durch elektrochemische Messungen...

article

A Robust Electronic Switch Made of Immobilized Duplex/Quadruplex DNA

Bixia Ge, Yu Chuan Huang, Dipankar Sen, Hua‐Zhong Yu

Angewandte Chemie International Edition > 49 > 51 > 9965 - 9967

Flicking a switch: A robust DNA nanoswitch has been designed by using a contractile DNA construct (G‐quadruplex) as the switch medium and ferrocene (Fc) as a redox‐active indicator (see picture). The switch was electrochemically tested and can be turned “on” or “off” repeatedly by the addition or removal, respectively, of the effector (K⁺ ions). The reversibility and repeatability of the DNA switch...

article

Photothermal Release of Single-Stranded DNA from the Surface of Gold Nanoparticles Through Controlled Denaturating and Au−S Bond Breaking

Lester Poon, Wesley Zandberg, Dennis Hsiao, Zach Erno, more

ACS Nano > 2010 > 4 > 11 > 6395 - 6403

article

A Stereochemical Glimpse of the Active Site of the 8−17 Deoxyribozyme from Iodine-Mediated Cross-Links Formed with the Substrate’s Scissile Site

Gurpreet S. Sekhon, Dipankar Sen

Biochemistry > 2010 > 49 > 42 > 9072 - 9077

article

The use of charge flow and quenching (CFQ) to probe nucleic acid folds and folding

Edward K.Y. Leung, Dipankar Sen

Methods > 2010 > 52 > 2 > 141-149

Charge flow and quenching (“CFQ”) is a relatively new, versatile, and easily carried out methodology for probing a number of unique features of DNA and RNA folded structures, and of their folding pathways. An electrical charge (an electron hole, or radical cation) is injected site-specifically into the end of a pre-determined reference helix within the larger DNA or RNA structure. The fate of the...

article

Modeling biological nutrient removal in a liquid–solid circulating fluidized bed bioreactor

Nabin Chowdhury, George Nakhla, Dipankar Sen, Jesse Zhu

Journal of Chemical Technology & Biotechnology > 85 > 10 > 1389 - 1401

BACKGROUND: Both laboratory‐scale and pilot‐scale liquid–solid circulating fluidized bed (LSCFB) bioreactors have demonstrated excellent biological nutrient removal (BNR) from municipal wastewater. In this study, a model for the LSCFB for biological nutrient removal has been developed, calibrated, and validated using pilot‐scale experimental results. RESULTS: An efficient reactor arrangement predicted...

article

A Contractile Electronic Switch Made of DNA

Yu Chuan Huang, Dipankar Sen

Journal of the American Chemical Society > 2010 > 132 > 8 > 2663 - 2671

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Local Rather than Global Folding Enables the Lead-dependent Activity of the 8-17 Deoxyribozyme: Evidence from Contact Photo-crosslinking

Yong Liu, Dipankar Sen

Journal of Molecular Biology > 2010 > 395 > 2 > 234-241

The 8-17 deoxyribozyme is an in vitro selected enzyme capable of sequence-specific cleavage of RNA. While selected to be a magnesium and zinc-utilizing enzyme, the 8-17 DNAzyme has been shown to utilize lead for its catalysis. Fluorescence-based experiments have indicated that the magnesium- and zinc-utilizing versions of the DNAzyme–substrate complex need to form a defined tertiary structure to be...

article

Design and testing of aptamer-based electrochemical biosensors for proteins and small molecules

Alan K.H. Cheng, Dipankar Sen, Hua-Zhong Yu

Bioelectrochemistry > 2009 > 77 > 1 > 1-12

The fabrication of aptamer-based electrochemical biosensors as an emerging technology has made the detection of small and macromolecular analytes easier, faster, and more suited for the ongoing transition from fundamental analytical science to the early detection of protein biomarkers. Aptamers are synthetic oligonucleotides that have undergone iterative rounds of in vitro selection for binding with...

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Search results for: Dipankar Sen

A Long and Reversibly Self‐Assembling 1D DNA Nanostructure Built from Triplex and Quadruplex Hybrid Tiles

A Long and Reversibly Self‐Assembling 1D DNA Nanostructure Built from Triplex and Quadruplex Hybrid Tiles

Hemin-utilizing G-quadruplex DNAzymes are strongly active in organic co-solvents

Blending Quadruplexes and Bordeaux: A Grand Cru!

DNA mechatronic devices switched by K⁺ and by Sr²⁺ are structurally, topologically, and electronically distinct

Assessment of Vitamin D status In Patients of Chronic Low Back Pain of Unknown Etiology

A Twisting Electronic Nanoswitch Made of DNA

A Twisting Electronic Nanoswitch Made of DNA

Mechatronic DNA devices driven by a G-quadruplex-binding platinum ligand

Guanine-Rich RNAs and DNAs That Bind Heme Robustly Catalyze Oxygen Transfer Reactions

Evaluation of biological nutrient removal from wastewater by Twin Circulating Fluidized Bed Bioreactor (TCFBBR) using a predictive fluidization model and AQUIFAS APP

A Robust Electronic Switch Made of Immobilized Duplex/Quadruplex DNA

A Robust Electronic Switch Made of Immobilized Duplex/Quadruplex DNA

Photothermal Release of Single-Stranded DNA from the Surface of Gold Nanoparticles Through Controlled Denaturating and Au−S Bond Breaking

A Stereochemical Glimpse of the Active Site of the 8−17 Deoxyribozyme from Iodine-Mediated Cross-Links Formed with the Substrate’s Scissile Site

The use of charge flow and quenching (CFQ) to probe nucleic acid folds and folding

Modeling biological nutrient removal in a liquid–solid circulating fluidized bed bioreactor

A Contractile Electronic Switch Made of DNA

Local Rather than Global Folding Enables the Lead-dependent Activity of the 8-17 Deoxyribozyme: Evidence from Contact Photo-crosslinking

Design and testing of aptamer-based electrochemical biosensors for proteins and small molecules

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