Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

DNA Isolation

DNA Isolation

DNA isolation protocols can be fast and straightforward or complex and time-consuming depending on the type and quality of DNA required for further processing. For example, plasmid DNA extraction is a bit more complicated than genomic DNA extraction because of the need for an appropriate lysis method to separate plasmid DNA from gDNA during isolation. However, for specific applications, such as long-range DNA sequencing that require a good yield of high- quality DNA samples, we need to follow...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

The Vertebrate Genomes Project Phase I: A global reference genome resource.

bioRxiv : the preprint server for biology·2026

Same author

Ancient DNA from shells reveals delayed genomic erosion and rapid immune adaptation in the critically endangered black abalone.

Proceedings of the National Academy of Sciences of the United States of America·2026

Same author

Continuity of eastern Beringian megafauna phylogenetic diversity following deposition of the Late Pleistocene Dawson tephra.

Arctic, antarctic, and alpine research·2026

Same author

Naturally-occurring DNA fragment termini correlate with methylation at CpG sites in hair and blood plasma cell-free DNA.

BMC genomics·2026

Same author

Rootless hair as a reliable source of forensic genetic information.

Genome biology·2026

Same author

Author Correction: Striking convergent selection history of wheat and barley and its potential for breeding.

Nature plants·2025

Same journal

Chromosome-scale genome assembly of the rice stink bug (Hemiptera: Oebalus pugnax) illuminates genome structure and gene family evolution in Pentatomidae.

The Journal of heredity·2026

Same journal

Rapid Derivation of Cloning-Competent Cells from Peripheral Blood Advances Conservation Biobanking.

The Journal of heredity·2026

Same journal

Genomic vulnerability to climate change of a poorly dispersing and threatened fish, the southern pygmy perch (Nannoperca australis).

The Journal of heredity·2026

Same journal

The complete genomes of two hybridizing field crickets, Gryllus pennsylvanicus and Gryllus firmus.

The Journal of heredity·2026

Same journal

Chromosome-level genome assembly and annotation of the transverse lady beetle Coccinella transversoguttata.

The Journal of heredity·2026

Same journal

A Chromosome-Level Assembly of the Pine Processionary Moth (Thaumetopoea pityocampa) genome.

The Journal of heredity·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Nov 11, 2025

Robust DNA Isolation and High-throughput Sequencing Library Construction for Herbarium Specimens

Robust DNA Isolation and High-throughput Sequencing Library Construction for Herbarium Specimens

Published on: March 8, 2018

A Fast and Efficient Single-stranded Genomic Library Preparation Method Optimized for Ancient DNA.

Joshua D Kapp¹, Richard E Green^2,3, Beth Shapiro^1,3,4

¹Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA.

The Journal of Heredity

|March 26, 2021

Summary

This summary is machine-generated.

We developed the Santa Cruz Reaction (SCR) to efficiently prepare ancient and degraded DNA for Illumina sequencing. This method recovers more unique DNA molecules than other protocols, making genomic analysis more accessible.

Keywords:

degraded DNA genomics next generation sequencing

More Related Videos

Ultra-long Read Sequencing for Whole Genomic DNA Analysis

Ultra-long Read Sequencing for Whole Genomic DNA Analysis

Published on: March 15, 2019

Primer Extension Capture: Targeted Sequence Retrieval from Heavily Degraded DNA Sources

Primer Extension Capture: Targeted Sequence Retrieval from Heavily Degraded DNA Sources

Published on: September 3, 2009

Related Experiment Videos

Last Updated: Nov 11, 2025

Robust DNA Isolation and High-throughput Sequencing Library Construction for Herbarium Specimens

Robust DNA Isolation and High-throughput Sequencing Library Construction for Herbarium Specimens

Published on: March 8, 2018

Ultra-long Read Sequencing for Whole Genomic DNA Analysis

Ultra-long Read Sequencing for Whole Genomic DNA Analysis

Published on: March 15, 2019

Primer Extension Capture: Targeted Sequence Retrieval from Heavily Degraded DNA Sources

Primer Extension Capture: Targeted Sequence Retrieval from Heavily Degraded DNA Sources

Published on: September 3, 2009

Area of Science:

Genomics
Molecular Biology
Bioinformatics

Background:

Ancient DNA (aDNA) is often degraded and present in low quantities, posing challenges for genomic sequencing.
Existing library preparation methods for degraded DNA can result in significant loss of unique molecules, limiting downstream analysis.
Optimizing DNA library preparation is crucial for maximizing data recovery from precious and limited ancient samples.

Purpose of the Study:

To introduce a novel protocol, the Santa Cruz Reaction (SCR), for preparing ancient and degraded DNA for Illumina sequencing.
To evaluate the efficiency of SCR in recovering unique DNA molecules compared to established methods.
To demonstrate the cost- and time-efficiency of SCR for broader genomic applications.

Main Methods:

Developed the Santa Cruz Reaction (SCR), a single enzymatic reaction using directional splinted ligation of Illumina P5 and P7 adapters.
Applied SCR, BEST, and ssDNA2.0 protocols to prepare libraries from five ancient DNA extracts.
Quantified library complexity by comparing the recovery of unique molecules across different DNA input amounts.

Main Results:

The SCR protocol consistently outperformed the BEST protocol in recovering unique molecules from degraded DNA.
SCR demonstrated comparable performance to the ssDNA2.0 protocol across various DNA input levels.
SCR proved to be a cost- and time-efficient method with minimal loss of unique molecules.

Conclusions:

The Santa Cruz Reaction (SCR) offers an efficient and accessible method for preparing ancient and degraded DNA for high-throughput sequencing.
SCR enhances library complexity recovery, enabling broader taxonomic, geographic, and temporal sampling of ancient remains.
This protocol facilitates more comprehensive genomic analyses from challenging ancient DNA samples.