scholarly journals Sensing single molecule under micromanipulation to quantify nucleic acids

2021 ◽  
Author(s):  
Qiang Zeng ◽  
Xiaoyan Zhou ◽  
Yuting Yang ◽  
Jingan Wang ◽  
Chunhui Zhai ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Single Molecule ◽  
Reaction Rate ◽  
Limit Of Detection ◽  
Rate Sensitivity ◽  
High Confidence ◽  
Single Base ◽  
Base Pair Mismatch ◽  
Synthetic Mirnas ◽  
Single Base Pair

Abstract Rapid molecular diagnosis using nucleic acid biomarkers is important for timely identification of acute pathogenic infections. We introduce an active kinetic approach called sensing single molecule under micromanipulation (SSM3) to quantify nucleic acids, which circumvents hydrodynamic limits of reaction rate, sensitivity and specificity. We demonstrate the 15-minute assay to detect synthetic miRNAs with subfemtomolar limit of detection and high-confidence discrimination of single-base-pair mismatch.

scholarly journals Hybridization of synthetic oligodeoxyribonucleotides to ΦX174 DNA: the effect of single base pair mismatch

1979 ◽  
Vol 6 (11) ◽  
pp. 3543-3558 ◽  
Author(s):  
R. Bruce Wallace ◽  
J. Shaffer ◽  
R.F. Murphy ◽  
J. Bonner ◽  
T. Hirose ◽  
...  
Keyword(s):  
Base Pair ◽  
Single Base ◽  
Base Pair Mismatch ◽  
Single Base Pair

Atomic force microscopy-based single-molecule force spectroscopy detects DNA base mismatches

Nanoscale ◽  
2019 ◽  
Vol 11 (37) ◽  
pp. 17206-17210 ◽  
Author(s):  
Wenjing Liu ◽  
Yourong Guo ◽  
Kaizhe Wang ◽  
Xingfei Zhou ◽  
Ying Wang ◽  
...  
Keyword(s):  
Single Molecule ◽  
Force Spectroscopy ◽  
Dna Origami ◽  
Single Molecule Force Spectroscopy ◽  
Force Microscopy ◽  
Atomic Force ◽  
Base Pair Mismatch ◽  
Dna Base ◽  
Single Base Pair ◽  
Target Molecules

AFM-based single-molecule-force spectroscopy is limited by low throughput. We introduce addressable DNA origami to study multiple target molecules at once. Target DNAs differing by only a single-base pair mismatch are clearly differentiated.

scholarly journals Amplified Single Base-Pair Mismatch Detection via Aggregation of Exonuclease-Sheared Gold Nanoparticles

2014 ◽  
Vol 86 (7) ◽  
pp. 3461-3467 ◽  
Author(s):  
Shuo Wu ◽  
Pingping Liang ◽  
Haixiang Yu ◽  
Xiaowen Xu ◽  
Yuan Liu ◽  
...  
Keyword(s):  
Gold Nanoparticles ◽  
Base Pair ◽  
Single Base ◽  
Mismatch Detection ◽  
Base Pair Mismatch ◽  
Single Base Pair

scholarly journals Hexameric helicase G40P unwinds DNA in single base pair steps

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Michael Schlierf ◽  
Ganggang Wang ◽  
Xiaojiang S Chen ◽  
Taekjip Ha
Keyword(s):  
Single Molecule ◽  
Base Pair ◽  
Atp Hydrolysis ◽  
Thermal Fluctuation ◽  
Dna Unwinding ◽  
Single Molecule Fluorescence ◽  
Step Size ◽  
Structural Investigations ◽  
Single Base ◽  
Single Base Pair

Most replicative helicases are hexameric, ring-shaped motor proteins that translocate on and unwind DNA. Despite extensive biochemical and structural investigations, how their translocation activity is utilized chemo-mechanically in DNA unwinding is poorly understood. We examined DNA unwinding by G40P, a DnaB-family helicase, using a single-molecule fluorescence assay with a single base pair resolution. The high-resolution assay revealed that G40P by itself is a very weak helicase that stalls at barriers as small as a single GC base pair and unwinds DNA with the step size of a single base pair. Binding of a single ATPγS could stall unwinding, demonstrating highly coordinated ATP hydrolysis between six identical subunits. We observed frequent slippage of the helicase, which is fully suppressed by the primase DnaG. We anticipate that these findings allow a better understanding on the fine balance of thermal fluctuation activation and energy derived from hydrolysis.

scholarly journals Overcoming chromatin barriers

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Babette E de Jong ◽  
John van Noort
Keyword(s):  
Single Molecule ◽  
Base Pair ◽  
Single Base ◽  
Single Base Pair

Single-molecule experiments reveal the dynamics of transcription through a nucleosome with single-base-pair accuracy.

Sequence Context and Thermodynamic Stability of a Single Base Pair Mismatch in Short Deoxyoligonucleotide Duplexes

2001 ◽  
Vol 123 (47) ◽  
pp. 11811-11812 ◽  
Author(s):  
Timothy S. Hall ◽  
Petr Pancoska ◽  
Peter V. Riccelli ◽  
Kathleen Mandell ◽  
Albert S. Benight
Keyword(s):  
Thermodynamic Stability ◽  
Base Pair ◽  
Sequence Context ◽  
Single Base ◽  
Base Pair Mismatch ◽  
Single Base Pair

scholarly journals Effects of individual base-pairs on in vivo target search and destruction kinetics of bacterial small RNA

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Anustup Poddar ◽  
Muhammad S. Azam ◽  
Tunc Kayikcioglu ◽  
Maksym Bobrovskyy ◽  
Jichuan Zhang ◽  
...  
Keyword(s):  
Small Rna ◽  
Base Pair ◽  
High Throughput Sequencing ◽  
Base Pairing ◽  
Target Search ◽  
Single Base ◽  
Base Pair Mismatch ◽  
Single Base Pair ◽  
Bacterial Small Rna

AbstractBase-pairing interactions mediate many intermolecular target recognition events. Even a single base-pair mismatch can cause a substantial difference in activity but how such changes influence the target search kinetics in vivo is unknown. Here, we use high-throughput sequencing and quantitative super-resolution imaging to probe the mutants of bacterial small RNA, SgrS, and their regulation of ptsG mRNA target. Mutations that disrupt binding of a chaperone protein, Hfq, and are distal to the mRNA annealing region still decrease the rate of target association, kon, and increase the dissociation rate, koff, showing that Hfq directly facilitates sRNA–mRNA annealing in vivo. Single base-pair mismatches in the annealing region reduce kon by 24–31% and increase koff by 14–25%, extending the time it takes to find and destroy the target by about a third. The effects of disrupting contiguous base-pairing are much more modest than that expected from thermodynamics, suggesting that Hfq buffers base-pair disruptions.

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