The interaction of DNA duplexes containing 2-aminopurine with restrictionendonucleases EcoRllandSsoll

Abstract

Oligonucleotides containing 2-aminopurine (2-AP) in place of G or A in the recognition site of EcoRII (CCT/AGG) or SsoII (CCNGG) restriction endonucleases have been synthesized in order to investigate the specific interaction of DNA with these enzymes. Physicochemical properties (CD spectra and melting behaviour) have shown that DNA duplexes containing 2-aminopurine exist largely in a stable B-like form. 2-Aminopurine base paired with cytidine, however, essentially influences the helix structure. The presence of a 2-AP-C mismatch strongly reduces the stability of the duplexes in comparison with the natural double strand, indicated by a biphasic melting behaviour. SsoII restriction endonuclease recognizes and cleaves the modified substrate with a 2-AP-T mismatch in the centre of the recognition site, but it does not cleave the duplexes containing 2-aminopurine in place of inner and outer G, or both. EcoRII restriction endonuclease does not cleave duplexes containing 2-aminopurine at all. The two-substrate mechanism of EcoRII-DNA interaction, however, allows hydrolysis of the duplex containing 2-aminopurine in place of adenine in the presence of the canonical substrate.

Photophysical Characterization of Fluorescent DNA Base Analogue, tC

“…2,5 2-AP has been used for probing structural and dynamic changes in damaged or mismatched DNA, 6,7 and in interactions between DNA and e.g. polymerases, [8][9][10][11][12] restriction endonucleases, [13][14][15] and repair enzymes. [16][17][18][19] However, the sensitivity of its excited state lifetimes to environment makes it rather unreliable as a probe of molecular dynamics using fluorescence anisotropy measurements and energy transfer.…”

Synthesis and Properties of Oligodeoxynucleotides Carrying 2-Aminopurine

“…In the 2-aminopurine: thymine base pair, one of the hydrogen bonds occurs in the minor groove instead of in the major groove. Several groups have taken advantage of this difference to characterize DNA-protein interactions [4,5] and DNA bending [6,7]. Due to the fluorescent properties of 2-aminopurine, this nucleobase is a useful local probe to study enzymes that interact with DNA, such as DNA polymerases [8][9][10][11], helicases [12] and DNA methylases [13,14] as well as in DNA structural studies [15,16].…”

Synthesis and fluorescence study of 7-azaindole in DNA oligonucleotides replacing a purine base

“…There are mainly two groups of 'bases' synthesized and incorporated into DNA oligomers: those made by minor modification of the natural bases or the derivatives of cyclic aromatic compounds. While the former includes 2-aminopurine [1][2][3][4][5][6][7][8], inosine [9] and isoinosine [9][10][11], 3-and 7-deazaadenine [12][13][14][15], and 3-and 7-deazaguanine [14,16], the latter includes analogs of pteridine [17][18][19] and indole [20][21][22][23][24], benzene [23][24][25][26], naphthalene and pyrene derivatives [24], The first group of compounds, when replacing a natural base in duplex DNA, can still form hydrogen bonds with the base in the opposite strand, while the second group of compounds cannot form any hydrogen bonds.…”

“…The fluorescence properties of the above base analogs have been utilized for studying DNA structure and duplex stability [1,2,10,14,15,22,26], protein-DNA interactions [4][5][6][7][8]13,18,25], or simply as universal base analogs [20,27]. Some of the unusual 'bases' are used as anti-HIV or anti-cancer drugs [28][29][30].…”