Biomaterial Database

Synthesis of cross-linked DNA containing oxidized abasic site analogues. 2014

Souradyuti Ghosh, and Marc M Greenberg

Department of Chemistry, Johns Hopkins University , 3400 North Charles Street, Baltimore, Maryland 21218, United States.

DNA interstrand cross-links are an important family of DNA damage that block replication and transcription. Recently, it was discovered that oxidized abasic sites react with the opposing strand of DNA to produce interstrand cross-links. Some of the cross-links between 2'-deoxyadenosine and the oxidized abasic sites, 5'-(2-phosphoryl-1,4-dioxobutane) (DOB) and the C4-hydroxylated abasic site (C4-AP), are formed reversibly. Chemical instability hinders biochemical, structural, and physicochemical characterization of these cross-linked duplexes. To overcome these limitations, we developed methods for preparing stabilized analogues of DOB and C4-AP cross-links via solid-phase oligonucleotide synthesis. Oligonucleotides of any sequence are attainable by synthesizing phosphoramidites in which the hydroxyl groups of the cross-linked product were orthogonally protected using photochemically labile and hydrazine labile groups. Selective unmasking of a single hydroxyl group precedes solid-phase synthesis of one arm of the cross-linked DNA. The method is compatible with commercially available phosphoramidites and other oligonucleotide synthesis reagents. Cross-linked duplexes containing as many as 54 nt were synthesized on solid-phase supports. Subsequent enzyme ligation of one cross-link product provided a 60 bp duplex, which is suitable for nucleotide excision repair studies.

UI	MeSH Term	Description	Entries
D009841	Oligonucleotides	Polymers made up of a few (2-20) nucleotides. In molecular genetics, they refer to a short sequence synthesized to match a region where a mutation is known to occur, and then used as a probe (OLIGONUCLEOTIDE PROBES). (Dorland, 28th ed)	Oligonucleotide
D002074	Butanones	Derivatives of butanone, also known as methyl ethyl ketone (with structural formula CH3COC2H5).
D003432	Cross-Linking Reagents	Reagents with two reactive groups, usually at opposite ends of the molecule, that are capable of reacting with and thereby forming bridges between side chains of amino acids in proteins; the locations of naturally reactive areas within proteins can thereby be identified; may also be used for other macromolecules, like glycoproteins, nucleic acids, or other.	Bifunctional Reagent,Bifunctional Reagents,Cross Linking Reagent,Crosslinking Reagent,Cross Linking Reagents,Crosslinking Reagents,Linking Reagent, Cross,Linking Reagents, Cross,Reagent, Bifunctional,Reagent, Cross Linking,Reagent, Crosslinking,Reagents, Bifunctional,Reagents, Cross Linking,Reagents, Cross-Linking,Reagents, Crosslinking
D004247	DNA	A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).	DNA, Double-Stranded,Deoxyribonucleic Acid,ds-DNA,DNA, Double Stranded,Double-Stranded DNA,ds DNA
D004249	DNA Damage	Injuries to DNA that introduce deviations from its normal, intact structure and which may, if left unrepaired, result in a MUTATION or a block of DNA REPLICATION. These deviations may be caused by physical or chemical agents and occur by natural or unnatural, introduced circumstances. They include the introduction of illegitimate bases during replication or by deamination or other modification of bases; the loss of a base from the DNA backbone leaving an abasic site; single-strand breaks; double strand breaks; and intrastrand (PYRIMIDINE DIMERS) or interstrand crosslinking. Damage can often be repaired (DNA REPAIR). If the damage is extensive, it can induce APOPTOSIS.	DNA Injury,DNA Lesion,DNA Lesions,Genotoxic Stress,Stress, Genotoxic,Injury, DNA,DNA Injuries
D001483	Base Sequence	The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.	DNA Sequence,Nucleotide Sequence,RNA Sequence,DNA Sequences,Base Sequences,Nucleotide Sequences,RNA Sequences,Sequence, Base,Sequence, DNA,Sequence, Nucleotide,Sequence, RNA,Sequences, Base,Sequences, DNA,Sequences, Nucleotide,Sequences, RNA
D060327	Solid-Phase Synthesis Techniques	Techniques used to synthesize chemicals using molecular substrates that are bound to a solid surface. Typically a series of reactions are conducted on the bound substrate that results in either the covalent attachment of specific moieties or the modification of existing function groups. These techniques offer an advantage to those involving solution reactions in that the substrate compound does not have to be isolated and purified between the reaction steps.	Solid-Phase Synthesis,Peptide Synthesis, Solid-Phase,Solid-Phase Nucleotide Synthesis,Solid-Phase Nucleotide Synthesis Techniques,Solid-Phase Peptide Synthesis,Solid-Phase Peptide Synthesis Techniques,Solid-Phase Synthesis Methods,Synthesis, Solid-Phase,Method, Solid-Phase Synthesis,Methods, Solid-Phase Synthesis,Nucleotide Syntheses, Solid-Phase,Nucleotide Synthesis, Solid-Phase,Peptide Syntheses, Solid-Phase,Peptide Synthesis, Solid Phase,Solid Phase Nucleotide Synthesis,Solid Phase Nucleotide Synthesis Techniques,Solid Phase Peptide Synthesis,Solid Phase Peptide Synthesis Techniques,Solid Phase Synthesis,Solid Phase Synthesis Methods,Solid Phase Synthesis Techniques,Solid-Phase Nucleotide Syntheses,Solid-Phase Peptide Syntheses,Solid-Phase Syntheses,Solid-Phase Synthesis Method,Solid-Phase Synthesis Technique,Syntheses, Solid-Phase,Syntheses, Solid-Phase Nucleotide,Syntheses, Solid-Phase Peptide,Synthesis Method, Solid-Phase,Synthesis Methods, Solid-Phase,Synthesis Technique, Solid-Phase,Synthesis Techniques, Solid-Phase,Synthesis, Solid Phase,Synthesis, Solid-Phase Nucleotide,Synthesis, Solid-Phase Peptide,Technique, Solid-Phase Synthesis,Techniques, Solid-Phase Synthesis