Ancient DNA & Preservation in Amber

by Ben Best

Biological tissues can be preserved through

Cryonics uses low temperature and vitrification for preservation. Mummification is mainly based on dehydration, but involves some chemical preservation. Preservation in amber or other means of isolation from oxygen for preservation of tissues (especially DNA) is the subject of this essay. Isolation from oxygen of a whole human being is described in my essay on St. Bees Man.


In 1984 researchers at the University of California -- notably Allan C. Wilson and Russell Higuchi -- published a preliminary report of isolation of DNA from 40,000 year-old mammoth tissue and from an extinct zebra-like horse (quagga) [FEDERATION PROCEEDINGS; 43:1557 (1984)]. Shortly thereafter they published a paper detailing the sequencing of DNA extracted from 140-year-old salt-preserved quagga tissue -- with a yield of approximately 1% what would be extracted from fresh tissue [NATURE; 312:282-284 (1984)]. The next year Svante Pääbo of Sweden produced a yield of DNA from a 2,400 year-old Egyptian mummy that was nearly 5% of what would be expected from fresh tissue [NATURE; 314:644-645 (1985)]. Skin tissue in direct contact with dehydrating agent (natron) had the best preserved DNA.

Five years later, however, Edward Golenberg of Wayne State University reported extracting DNA from a fossilized 17 million-year-old magnolia leaf found in a deep fresh water lake [NATURE; 344:656-658 (1990)]. Within two years theis record was broken by 25-30 million-year-old DNA from a fossilized termite preserved in amber, extracted by David Grimaldi's team at the American Museum of Natural History [SCIENCE; 257:1933-1936 (1992)]. One year later, even this record was smashed by a report of DNA extracted from a 120-135 million-year-old weevil from Lebanese amber by California scientists Raul Cano and George Poinar [NATURE; 363:536-538 (1993)].

In 1990 -- before scientific reports of success in finding DNA in amber-fossilized insects -- Michael Crichton had published the novel JURASSIC PARK about reconstruction of dinosaurs from DNA cloned from dinosaur cells found in blood-sucking insects preserved in amber. The novel became a smash-hit movie. George and Roberta Poinar published the book THE QUEST FOR LIFE IN AMBER (1994), which popularized the scientific basis for studying life preserved in amber.

In 1997, however, more careful scientific work cast all reports of multi-million-year-old DNA in a more doubtful light. The cornerstone of these DNA studies has been Polymerase Chain Reaction (PCR), an extremely sensitive scientific procedure in which tiny bits of DNA are multiplied ("amplified") millions of times, as with a "genetic photocopier". Contamination of samples has been extremely difficult to avoid. More careful science attempting to reproduce earlier findings resulted in negative results.

Presumed dinosaur DNA from Cretaceous bond fragments was shown to be due to human contamination. And presumed DNA from a dinosaur egg fossil was shown to be from fungi [MOLECULAR BIOLOGY AND EVOLUTION; 14(5):589-591 (1997)]. Other attempts to replicate DNA extracted from insects in amber under the most careful conditions also produced negative results [PROCEEDINGS OF THE ROYAL SOCIETY OF LONDON: BIOLOGICAL SCIENCES; 264:467-474 (1997) and MOLECULAR BIOLOGY AND EVOLUTION; 14(10):1075-1077 (1997)].

Scientists looking for ancient DNA are currently highly sensitized to the dangers of contamination. Following the evidence of contamination in the 1990s it was not believed that DNA older than 100,000 years could be found. Leaves and unfossilized dinosaur remains had been exposed to water & oxygen. There are sound theoretical reasons for believing that DNA could not survive hydrolysis & oxidation under such conditions for more than 50,000 to 100,000 years [NATURE; 365:700 (1993) and NATURE; 366:513 (1993)]. But deep ice cores taken from Greenland permafrost have revealed DNA sequences from plants and insects verified to be between 450,000 and 800,000 years old [SCIENCE; Willerslev,E; 317:111-113 (2007)]. Ice cores taken from Antarctica have the potential to reveal DNA samples that are much older.

Simply extracting ancient DNA and verifying that it is indeed ancient DNA is a less difficult task than attempting to sequence its base pairs. Twenty-eight million base-pairs have been sequenced from DNA extracted from a 28,000 year-old Siberian woolly mammoth sample [SCIENCE; Poinar,HN; 311(5759):392-394 (2006)]. Sequencing of 38,000 year-old Neanderthal genomic DNA led to the identification of 65,250 base-pairs [SCIENCE; Noonan,JP; 311(5802):1113-1118 (2006)]. The entire human genome was sequenced from 4,000-year-old hair recovered from permafrost in Greenland [NATURE; Rasmussen,M; 463:757-762 (2010) and NATURE; Lambert,DM; 463:739-740 (2010)]. Ancient DNA is riddled with interstrand cross-links, but these cross-links protected the DNA from further degradation [MUTATION RESEARCH; Mitchell,D; 571(1-2):265-276 (2005)].

Mass spectrometry of collagen fragments taken from a mastadon (160,000 to 600,000 years old) and a 68-million-year-old dinosaur (Tyrannosaurus Rex) showed the former to be related to modern mammalian collagen and the latter to be related to modern bird collagen [SCIENCE; Schweitzer,MH; 316:227-285 (2007)].


Just as low temperature can extend the period of time that DNA can survive, total isolation from oxygen when trapped in amber is highly protective. Despite problems concerning DNA from insects in amber, there can be no question about the excellent preservation of tissue ultrastructure -- including ribosomes, endoplasmic reticulum and mitochondria -- for tens of millions of years [SCIENCE; 215:1241-1242 (1982) and SCIENTIFIC AMERICAN; 274(4):85-91 (1996)].

Tree sap (resin) contains sugars as well as alcohols & aldehydes (including terpenes), which are dehydrating & antibiotic as well as providing an air-tight seal to prevent further entry of oxygen. Myrrh is a mixture of resin, gum and essential oils from the Commiphora plant that was used by the ancient Egyptians for embalming (by pouring it into the cranial, chest, abdominal and pelvic cavities) and mummification (by soaking the wrapping bandages in it).

Despite the discovery of lucite & epoxy resins, it has not yet been possible to artificially synthesize amber, the hardest natural resin known. A major component of amber, however, is terpene, a class of hydrocarbons of the general formula (C5H8)n -- polymers of isoprene units. Turpentine is a mixture of low molecular weight terpenes (18% of the sap of living pine), whereas the latex of the rubber tree consists of high molecular weight terpene polymers where n=4,000-5,000. Carotenoids (like lycopene and beta-carotene) are built from isoprene units, but have the formula C40H56, rather than C40H64 -- due to unsaturation.

Amber, as a sticky pitch from certain trees, can trap insects when fresh from a tree-wound. The sugars, alcohols & terpene-aldehydes diffuse into the insect to dehydrate & preserve. The amber surrounds the insect, providing an air-tight seal. Further oxidation & polymerization of the terpenes protect the insect from further damage. The continued polymerization of the amber terpenes eventually results in an insoluble gemstone-quality glass that preserves the insect in a strong encasement. Although such fortuituous combination of chemical preservation and oxygen-tight encasement should not be expected for preservation of large specimens (like humans or dinosaurs), the use of some hardened plastic or resin encasement could assist chemical and/or dehydration preservation.