Random Notes 5

Xaar 128





chinese inkjet info: http://m.6lon.com/sdm/132165/2/cp-1003311/0.html

RNA Bioanalyzer

PaperQuantification pg/ul RNARunPlots
Urine RNA Processing in a Clinical Setting: Comparison of Three Protocols397.5 ng/60 mL (Qubit RNA HS)Agilent 4200 TapeStationRIN: 5.9An external file that holds a picture, illustration, etc. Object name is nihms918280f3b.jpg
Urine RNA Processing in a Clinical Setting: Comparison of Three Protocols397.5 ng/60 mL(Qubit RNA HS)Agilent 4200 TapeStationRIN: 3.3An external file that holds a picture, illustration, etc. Object name is nihms918280f3a.jpg
Deep Sequencing of Urinary RNAs for Bladder Cancer Molecular Diagnostics0.98 ng/mL0.08 ng/mLProcessed within two hours of collectionAgilent 2100 Bioanalyzer, RNA Pico chipsRIN ranged from 2.5 to 9.5Mean: 6.03No plots
Identification of microRNAs in blood and urine as tumour markers for the detection of urinary bladder cancer~2 ng/uL (fig. 1)Several urine RNA isolates showed low RIN values <3No plots
Urinary MicroRNA-Based Diagnostic Model for Central Nervous System Tumors Using Nanowire ScaffoldsQubit microRNA AssayAgilent 2100 BioanalyzerRIN: 81638356162683-129.png

RNA Papers

SingleMol Imaging

Solid state Nanopore

Hitachi, making pores with dialectric breakdown, slowing, notes on viscosity to slow etc: https://www.nature.com/articles/srep31324.pdf

Keio University group, optical observation of translocation: https://iopscience.iop.org/article/10.7567/APEX.9.017001/pdf


ASIC Design, to go to 1MHz: https://www.nature.com/articles/nmeth.1932

Noise measurements from above:

Instrumentation for Low-Noise High-Bandwidth Nanopore Recording. Engineered Nanopores for Bioanalytical Applications: https://www.sciencedirect.com/science/article/pii/B9781437734737000030

Above has lots of nice protocol information.

Ionic Speed/Current

“If we recall that an Ampere corresponds to a charge flow of 1 Coulomb each second and further, use the fact that the charge on a monovalent ion is approximately 1.6 x 10-19 Coulombs (that is 1 electron or 1 proton charge), then we see that a current of about one pA corresponds to roughly 107 ions passing through the channel each second. This value is in agreement with measurements” http://book.bionumbers.org/how-many-ions-pass-through-an-ion-channel-per-second/

Molecular Dynamics of Ionic Current: https://www.ks.uiuc.edu/Research/silica/IonRect.html

DNA Speed:
From, measures time to translocate two adjacent pores. distance is ~1.5um: https://pubs.acs.org/doi/full/10.1021/nl2030079

Folded/Knotted DNA:

Detection of knotted DNA





Double stranded Lambda DNA (16um long, 48kb). Translocates in 3 different confirmations. Grabbed at the end. Grabbed in the middle (completely folded), Grabbed near an edge (partly folded). Difference in current levels is ~1nS between each confirmation (200pA). 22nm pore is used. Translocation time ~3ms.


Hairpins, P2000 pulled quartz nano-pipette. Using hairpins to encode DNA 8bp and 16bp hairpins.

DNA Folds for data storage by Ulrich: https://www.ncbi.nlm.nih.gov/pubmed/30585490