CDD Vault Update (February #2 2025): Advanced Macromolecules - Modified Bioconjugates Support in CDD Vault
Collaborative Drug
FEBRUARY 21, 2025
CDD Update February 2025 #2 New Macromolecule Mode Edit DNA, RNA & Peptides with Bioconjugate Support
Blog DNA RNA 
Build Your CRISPR Vocabulary
addgene Blog
JULY 2, 2024
We’ll cover the common terminology for the proteins, DNA, and RNA used in CRISPR. CRISPR is an elegant bacterial immune system and an efficient gene editing tool… but boy does it have a lot of parts! If you’re still a bit confused by CRISPR acronyms, this post is for you.
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PRIDICT: Predicting Efficiencies of Prime Editing Guide RNAs
addgene Blog
JUNE 25, 2024
Prime editing is a versatile genome editing technology that allows precise modifications of DNA (replacements, small insertions, and deletions) without introducing DNA double-strand breaks (Anzalone et al., 2019; Chen & Liu, 2023).
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Reinventing the small molecule toolbox: from proteins to RNA
Dark Matter Blog
APRIL 4, 2023
Prior to 2015, I had a casual relationship, at best, with targeting RNA. Targeting RNA is a Whole New World Then in 2015, I became smitten and eloped with RNA, setting out to build a company devoted to bringing to bear industrial drug discovery concepts and methods on a new problem of drugging RNA with small molecules.
Reaching cruising altitude: New discovery tools to target RNA
Dark Matter Blog
AUGUST 31, 2020
Our overall mission at Arrakis is to expand the set of “druggable” targets for small-molecule medicines to include RNA. Today, we are pleased to announce that our article describing one such platform: “ PEARL-seq, A Photoaffinity Platform for the Analysis of Small Molecule-RNA Interactions ” was published in ACS Chemical Biology.
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Next Generation Sequencing (NGS): why is quantifying nucleic acids important? | BMG LABTECH
BMG Labtech
OCTOBER 4, 2023
These numbers reflect impressive developments in DNA sequencing technologies but in most cases represent the immediate costs of consumables on the sequencing instrument. 2 DNA sequencing is also reliant on sample processing and DNA library preparation before sequencing as well as bioinformatics and data analysis after sequencing.
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A Look Back
Dark Matter Blog
JULY 16, 2021
As soon as I learned about DNA and RNA, I wanted to be a molecular biologist. Last stops at RNA My last roles in biotech were where my original passion began: DNA and RNA. My last stop at Arrakis Therapeutics is with a company targeting RNA with small molecules. Arrakis is the capstone of my career.
Breaking Down Biomarker Discovery: 5 Points
PerkinElmer
AUGUST 12, 2020
The steps taken during the analytical phase are dependent on the type of biomarker, which can range from DNA, RNA, protein, peptide, biomolecular modification(s), or biochemical pathway(s). The post Breaking Down Biomarker Discovery: 5 Points first appeared on PerkinElmer Blog.
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From hibernation to neurodegeneration: how a cold-resistance protein is paving the way to dementia treatments
The Open Targets Blog
AUGUST 15, 2023
These results were corroborated by an RNA sequencing analysis we carried out in parallel, which revealed that depending on the temperature, RBM3 had different isoforms created by differential self-splicing. RBM3 is an RNA-binding protein, and we needed an RNA biologist, which is when Deepak joined the project.
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A Molecular Biologist’s Advice For Life
LifeSciVC
JULY 1, 2024
The central dogma of molecular biology is that information generally (with few exceptions) flows from DNA to RNA to Protein. In my own career, starting to write a blog was one of my most impactful “Friday afternoon experiments” – I even called it an experiment in my very first blogpost back in March 2011.
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Top Ten Reasons to Attend the SLAS International Conference & Exhibition
PerkinElmer
JANUARY 19, 2020
We will present a fully automated end-to-end solution inclusive of automation and reagents optimized for miniaturized NGS that is guaranteed to generate high-quality libraries.
Five Promising Treatment Areas in Early-Phase Drug Development in 2024
Alta Sciences
APRIL 17, 2024
In this blog article, we review some of these areas of investigation where Altasciences has robust expertise and solution offerings. Several viral vectors are being used currently, in addition to non-viral vectors, such as oligonucleotides, naked DNA, and lipoplexes and polyplexes.
TACACICLIB, AUR-102, AURIGENE
New Drug Approvals
JANUARY 9, 2024
CDK7 also plays a role in transcription and possibly in DNA repair. The trimeric Cak complex CDK7/CyclinH/MATl is also a component of TFIIH, the general transcription/DNA repair factor IIH (Morgan, DO., As a TFIIH subunit, CDK7 phosphorylates the CTD (Carboxy-Terminal-Domain) of the largest subunit of RNA polymerase II (pol II).
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Optical density and absorbance measurements | BMG LABTECH
BMG Labtech
DECEMBER 20, 2024
Whether it is determining concentrations of molecules like proteins or DNA, looking at enzyme kinetics for crucial reactions, or measuring something as fundamental as cell growth, you will find references to absorbance or optical density measurements. But how do they relate to each other? Lets start by looking at some definitions.
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Fast Biology
Codon
FEBRUARY 20, 2024
Thanks to decades of progress in molecular sequencing technologies, it is simple to read out the order of nucleotides in a DNA sequence, for example, or to quantify messenger RNAs as they are made by a cell. Escherichia coli have about 5 million base pairs of DNA in their genome, and divide every 20 minutes.
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Cave Coronavirus in Wuhan Lab Seeded COVID – The Truth Has Always Been Out There, in the Genetics
PLOS: DNA Science
JUNE 13, 2024
Experiments at the Wuhan facility were done at the lowest two of the four standard biosafety levels, which were established at the dawn of recombinant DNA research in the 1970s. The Likely Predecessor of SARS-CoV-2 – From my Past Blog Posts I wrote 100+ DNA Science blog posts during the pandemic about the virus.
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EIDD-2173, ATI-2173, Fosclevudine alafenamide
New Drug Approvals
AUGUST 22, 2023
kb relaxed circular DNA (rcDNA) genome that is used to form covalently closed circular DNA (cccDNA) in a host cell. The cccDNA is then transcribed by RNA polymerase II, a host DNA-dependent RNA polymerase, to produce pregenomic RNA (pgRNA). HBV possesses a 3.2- The results are shown below in Tables 8 and 9.
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Codon Digest: Injected Gene Editors
Codon
APRIL 2, 2023
But now, by studying DNA extracted from microbes in the blood of almost 10,000 healthy people, this paper shows that there is no such thing. Read Transcription factors bind to DNA and control gene expression. Read Switchable hydrophobic pockets in DNA protocells enhance chemical conversion. Nature Microbiology. Meeussen J.V.W.
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Biology is a Burrito
Codon
FEBRUARY 28, 2023
1 One rarely pauses to ponder how so much DNA — let alone sugar, proteins, and everything else — can fit inside such a small vessel. Students learn the basics through words: DNA is transcribed to RNA, which is translated into proteins. How fast does DNA become RNA, or RNA protein? A typical E.
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Gene-Edited Bananas
Codon
APRIL 19, 2023
In 2016, her team demonstrated that, by adding short snippets of DNA or RNA — which can target and “shut down” the MaMADS regulatory proteins — to bananas, it is possible to slow their ripening. has a genome made of DNA. The idea came from tomatoes, which ripen in much the same way.) From Elitzur T.
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Gene-Edited Bananas
Codon
APRIL 19, 2023
In 2016, her team demonstrated that, by adding short snippets of DNA or RNA — which can target and “shut down” the MaMADS regulatory proteins — to bananas, it is possible to slow their ripening. has a genome made of DNA. The idea came from tomatoes, which ripen in much the same way.) From Elitzur T.
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Codon Digest: Seeing Colors After Gene Therapy
Codon
JULY 27, 2023
They’ve just finished sequencing the patient’s genome, but they don’t have “DNA sorting” software. billion units of DNA code are transcribed into more than a hundred volumes, each a thousand pages long, in type so small as to be barely legible.” LEGO robot to make sucrose gradients.
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Codon Digest: Seeing Colors After Gene Therapy
Codon
JULY 27, 2023
They’ve just finished sequencing the patient’s genome, but they don’t have “DNA sorting” software. billion units of DNA code are transcribed into more than a hundred volumes, each a thousand pages long, in type so small as to be barely legible.” LEGO robot to make sucrose gradients.
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Codon Digest: Vaccine Printer Go Brrrrr!
Codon
APRIL 30, 2023
Yeast die for two reasons: Either their nucleolus (where the DNA is kept) degrades and dies, or their mitochondria whimpers out and they stop making energy. The vaccine printer can make lots of different types of vaccines, including protein, DNA, and mRNA ones, but I’m sure this is all quite expensive right now. From Zhang et al.
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Codon Digest: Vaccine Printer Go Brrrrr!
Codon
APRIL 30, 2023
Yeast die for two reasons: Either their nucleolus (where the DNA is kept) degrades and dies, or their mitochondria whimpers out and they stop making energy. The vaccine printer can make lots of different types of vaccines, including protein, DNA, and mRNA ones, but I’m sure this is all quite expensive right now. From Zhang et al.
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Codon Digest: Hackathon Prize Winners
Codon
JUNE 26, 2023
DNA sequences are designed on a computer, and it takes a dozen or more clicks to change a single nucleotide. DNA sequences are also checked by hand, so it’s easy to make a mistake. The tool outputs a DNA sequence that encodes all the required enzymes. Anyone who has tried to engineer a cell knows how tedious it can be.
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Codon Digest: Hackathon Prize Winners
Codon
JUNE 26, 2023
DNA sequences are designed on a computer, and it takes a dozen or more clicks to change a single nucleotide. DNA sequences are also checked by hand, so it’s easy to make a mistake. The tool outputs a DNA sequence that encodes all the required enzymes. Anyone who has tried to engineer a cell knows how tedious it can be.
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Genomic Sequencing Paves the Way for Better Antiviral Treatments
PerkinElmer
JULY 13, 2020
Sequencing viral genome isolates and creating phylogenetic trees Sequencing a viral genome requires isolating the viral RNA, reverse transcribing it into DNA, and then performing multiple amplification steps using primers. Finally, the DNA library is sequenced, the sequences are aligned, and the full genome annotated.
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Codon Digest: Ghana Approves A Better Malaria Vaccine
Codon
APRIL 23, 2023
Most people would take the two CRISPR gene-editing components (a Cas9 protein and guide RNA), package them up inside of a virus, and then inject the viruses into the skulls of mice. 📎 Papers Strands of DNA can be used to build molecular logic gates. Stahl et al. on bioRxiv. Nature Communications. Nature Communications.
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Codon Digest: Ghana Approves A Better Malaria Vaccine
Codon
APRIL 23, 2023
Most people would take the two CRISPR gene-editing components (a Cas9 protein and guide RNA), package them up inside of a virus, and then inject the viruses into the skulls of mice. 📎 Papers Strands of DNA can be used to build molecular logic gates. Stahl et al. on bioRxiv. Nature Communications. Nature Communications.
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Codon Digest: CAR-T Therapy for Neuroblastoma
Codon
APRIL 9, 2023
Small snippets of double-stranded RNA were sprayed onto hot pepper plants to control a pest, called Frankliniella occidentalis. The RNA strands shut down a specific gene in the insects, and killed half after 7 days. RNA may offer a safer form of pest control in the future. The new sequences might help de-extinction efforts.
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Discovery Solutions with Alpha, HTRF by Cisbio and Multi-mode Microplate Readers for Viral Therapeutics
PerkinElmer
AUGUST 18, 2020
The technology can be applied to a number of different types of antibody-based assays, which are used to characterize GPCR signaling, activity of various protein kinases and other cytokines, and the interactions of certain singular proteins with each other or DNA and RNA. – [link] Wen et al.
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A Protein Printer
Codon
JULY 11, 2023
That’s because proteins are made, in the laboratory, using synthetic DNA and cells; and DNA is expensive. Our machine would make proteins without using any DNA or cells. All cells make proteins in two steps: DNA is transcribed into messenger RNA, which is then translated into protein.
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Models of Life
Codon
SEPTEMBER 29, 2024
But, regardless of which was first, they all operated with the same core data as their mechanism for understanding life: messenger RNA ( mRNA ). Some emerged from a “DNA is all you need” worldview, investing heavily in better long-read sequencing and chromatin accessibility data.
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Making Eggs Without Ovaries
Codon
SEPTEMBER 22, 2024
Erasing methyl groups on DNA is necessary for normal egg and sperm development. The most important step seems to be erasing DNA methylation. Methyl groups attached to DNA are first artificially erased using a chemical inhibitor to mimic the erasure that happens during germline commitment.
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A Protein Printer
Codon
JULY 11, 2023
That’s because proteins are made, in the laboratory, using synthetic DNA and cells; and DNA is expensive. Our machine would make proteins without using any DNA or cells. All cells make proteins in two steps: DNA is transcribed into messenger RNA, which is then translated into protein.
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Codon: Notes on Progress #2
Codon
MARCH 12, 2023
“The recombinant DNA breakthrough has provided us with a new and powerful approach to the questions that have intrigued and plagued man for centuries. The central dogma is often depicted as DNA→RNA→protein, but it’s much more: A biophysical marvel inside the smallest of vessels. Biology is a Burrito.
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Monkey Embryos Grow to 25 Days — No Womb Required
Codon
MAY 15, 2023
3/ Prime Editing Spree Prime editors can change DNA in ways that Cas9 — and even base editors — cannot. Known as a "search-and-replace" gene-editing tool, prime editors can delete or replace DNA up to 10,000 bases in length, or substitute one base for another. Read more in Cell. ( #1 , #2 ) (Video credit: Gong Y.
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Monkey Embryos Grow to 25 Days — No Womb Required
Codon
MAY 15, 2023
3/ Prime Editing Spree Prime editors can change DNA in ways that Cas9 — and even base editors — cannot. Known as a "search-and-replace" gene-editing tool, prime editors can delete or replace DNA up to 10,000 bases in length, or substitute one base for another. Read more in Cell. ( #1 , #2 ) (Video credit: Gong Y.
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Codon Digest: Discovering Antibiotics with Deep Learning
Codon
MAY 30, 2023
This week: A way to measure a transgene’s expression in the brain using ultrasound, a DNA sequencing method that uses 1000x less reagents, and base editors get even smaller. An engineered version of this protein can convert DNA bases with efficiencies up to 92%. so this Digest will be published more irregularly.
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Codon Digest: Discovering Antibiotics with Deep Learning
Codon
MAY 30, 2023
This week: A way to measure a transgene’s expression in the brain using ultrasound, a DNA sequencing method that uses 1000x less reagents, and base editors get even smaller. An engineered version of this protein can convert DNA bases with efficiencies up to 92%. so this Digest will be published more irregularly.
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Codon Digest: GPT-4 Controls a Robot
Codon
APRIL 16, 2023
Short DNA strands were discovered that can specifically and tightly bind to zinc and cadmium ions. Perhaps there is now a way to use DNA to extract metals: You could fuse the DNA strands to an antibody, coat them onto electronics, and then use a column to isolate the DNA:metal compounds? coli DNA using a Retro-Cascorder.
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Evo 2 Can Design Entire Genomes
Codon
FEBRUARY 19, 2025
The same model can also generate brand-new DNA sequences at the scale of yeast chromosomes or small bacterial genomes. AI Architectures Before explaining how Evo 2 could make bioengineering more predictable, it helps to first understand how AI models actually “learn” the language of DNA.
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The Dangers of “Do Your Own Research” and “Believe in Science”
PLOS: DNA Science
OCTOBER 24, 2024
In those early days, politicians and government officials who’d never heard terms like “cytokine storm” and “RNA virus” were suddenly charged with explaining what was happening. The post The Dangers of “Do Your Own Research” and “Believe in Science” appeared first on DNA Science.
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