Construction of Pyrenyl Pairs in dsDNA: Fluorescent Properties of Multiple Pyrenyl-attached dsDNAs Through 7-Substituted 8-Aza-7-deaza-2'-deoxyadenosine Analogues†

doi:10.7503/cjcu20180182

Abstract

Abstract:

Pyrenyl excimer is well characterized to be a fluorescent tag suitable for the construction of nucleic acids-based biosensors. dsDNA was used as one of the major motifs for the construction of the pyrenyl pairs in the biosensors. Here, 7-pyrenylethynyl-8-aza-7-deaza-2'-deoxyadenosine(2) and 7-pyrenylethyl-8-aza-7-deaza-2'-deoxyadenosine(3) were used to introduce pyrenyl group to duplex DNA, by which the specific base pairing of 2'-deoxyadenosine was kept, and the pyrenyl group was located at the major groove of the duplex. In the B-duplex DNA formed by 5'-d(TAGGTCAATACT)-3' and 3'-d(ATCCAGTTATGA)-5', the canonical residue 2'-deoxyadenosine(dA) was replaced by residue 2 or 3 at several positions, respectively. All the DNA sequences were synthesized on an ABI 392 DNA/RNA synthesizer and characterized by mass spectrum. The thermal stability of the modified duplexes was significantly affected. It was observed that T_m was dramaticly decreased by residue 2 and dramaticly increased by residue 3. It was supposed that the large hydrophobic pyrenyl group was protruded to the hydrophilic major groove by the rigid ethynyl linkage in residue 2, while the flexible linkage in residue 3 permitted the pyrenyl group to stack into the neighboring basepair. The diffe-rent location of the pyrenyl group from residues 2 and 3 was also confirmed by the circular dichroism(CD), the spectra from 300 nm to 450 nm indicated that more pyrenyl stacking formed in the duplexes with residue 2. Especially, the fluorescence switch-on was observed in the formation of the duplex PY03+PY05 and switch-off in the formation of the duplex PY02+D02, respectively. These results demonstrated that the residue 2 was more sensitive to the conformational changes of duplex DNA, and these two pyrenyl group combinations were worthwhile to be further studied in the context of functional nucleic acids for the construction of the pyrenyl-based sensors.

Key words: Pyrenyl, Deoxyadenosine analogue, Duplex DNA, Fluorescence spectrum, Thermal stability

CLC Number:

O629

TrendMD:

LI Yang, LI Zhiwen, ZHU Junfei, LIU Shihui, HE Junlin. Construction of Pyrenyl Pairs in dsDNA: Fluorescent Properties of Multiple Pyrenyl-attached dsDNAs Through 7-Substituted 8-Aza-7-deaza-2'-deoxyadenosine Analogues^†[J]. Chem. J. Chinese Universities, 2018, 39(10): 2206.

Figures/Tables 5

References 52

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Name	Sequence	MS(calcd.), m/z	Name	Sequence	MS(calcd.), m/z
PY01	5'-d(TAGGTC22TACT)-3'	4092.2(4090.8)	PY06	5'-d(TAGGTC33TACT)-3'	4100.4(4101.0)
PY02	5'-d(TAGGTC2AT2CT)-3'	4092.7(4090.8)	PY07	5'-d(TAGGTC3AT3CT)-3'	4100.1(41010)
PY03	5'-d(TAGGTC2ATACT)-3'	3867.9(3868.7)	PY08	5'-d(TAGGTC3ATACT)-3'	3871.7(3872.7)
PY04	5'-d(TAGGTCA2T2CT)-3'	4092.0(4090.8)	PY09	5'-d(TAGGTCA3T3CT)-3'	4100.2(41010)
PY05	5'-d(AGT2TTGACCTA)-3'	3868.1(3868.7)	PY10	5'-d(AGT3TTGACCTA)-3'	3872.1(3872.7)

Name	Sequence	MS(calcd.), m/z	Name	Sequence	MS(calcd.), m/z
PY01	5'-d(TAGGTC22TACT)-3'	4092.2(4090.8)	PY06	5'-d(TAGGTC33TACT)-3'	4100.4(4101.0)
PY02	5'-d(TAGGTC2AT2CT)-3'	4092.7(4090.8)	PY07	5'-d(TAGGTC3AT3CT)-3'	4100.1(41010)
PY03	5'-d(TAGGTC2ATACT)-3'	3867.9(3868.7)	PY08	5'-d(TAGGTC3ATACT)-3'	3871.7(3872.7)
PY04	5'-d(TAGGTCA2T2CT)-3'	4092.0(4090.8)	PY09	5'-d(TAGGTCA3T3CT)-3'	4100.2(41010)
PY05	5'-d(AGT2TTGACCTA)-3'	3868.1(3868.7)	PY10	5'-d(AGT3TTGACCTA)-3'	3872.1(3872.7)

Name	Sequence	T_m/℃	ΔT_m/℃	Name	Sequence	T_m/℃	ΔT_m/℃
D01+D02	5'-d(TAGGTCAATACT)-3'	49.8		PY06+D02	5'-d(TAGGTC33TACT)-3'	45.9	-3.9
	3'-d(ATCCAGTTATGA)-5'				3'-d(ATCCAGTTATGA)-5'
PY03+D02	5'-d(TAGGTC2ATACT)-3'	39.4	-10.4	PY07+D02	5'-d(TAGGTC3AT3CT)-3'	61.7	11.9
	3'-d(ATCCAGTTATGA)-5'				3'-d(ATCCAGTTATGA)-5'
PY08+D02	5'-d(TAGGTC3ATACT)-3'	54.0	4.2	PY09+D02	5'-d(TAGGTCA3T3CT)-3'	59.5	9.7
	3'-d(ATCCAGTTATGA)-5'				3'-d(ATCCAGTTATGA)-5'
D01+PY05	5'-d(TAGGTCAATACT)-3'	41.0	-8.8	PY01+PY05	5'-d(TAGGTC22TACT)-3'	48.8	-1.0
	3'-d(ATCCAGTT2TGA)-5'				3'-d(ATCCAGTT2TGA)-5'
D01+PY10	5'-d(TAGGTCAATACT)-3'	57.0	7.2	PY02+PY05	5'-d(TAGGTC2AT2CT)-3'	54.0	4.2
	3'-d(ATCCAGTT3TGA)-5'				3'-d(ATCCAGTT2TGA)-5'
PY03+PY05	5'-d(TAGGTC2ATACT)-3'	49.8	0	PY04+PY05	5'-d(TAGGTCA2T2CT)-3'	60.0	10.2
	3'-d(ATCCAGTT2TGA)-5'				3'-d(ATCCAGTT2TGA)-5'
PY01+D02	5'-d(TAGGTC22TACT)-3'	44.3	-4.5	PY06+PY10	5'-d(TAGGTC33TACT)-3'	55.2	5.4
	3'-d(ATCCAGTTATGA)-5'				3'-d(ATCCAGTT3TGA)-5'
PY02+D02	5'-d(TAGGTC2AT2CT)-3'	36.5	-13.3	PY09+PY10	5'-d(TAGGTCA3T3CT)-3'	59.4	9.6
	3'-d(ATCCAGTTATGA)-5'				3'-d(ATCCAGTT3TGA)-5'
PY04+D02	5'-d(TAGGTCA2T2CT)-3'	52.1	2.3	PY07+PY10	5'-d(TAGGTC3AT3CT)-3'	58.6	8.8
	3'-d(ATCCAGTTATGA)-5'				3'-d(ATCCAGTT3TGA)-5'
PY08+PY10	5'-d(TAGGTC3ATACT)-3'	64.2	14.4
	3'-d(ATCCAGTT3TGA)-5'

Name	Sequence	T_m/℃	ΔT_m/℃	Name	Sequence	T_m/℃	ΔT_m/℃
D01+D02	5'-d(TAGGTCAATACT)-3'	49.8		PY06+D02	5'-d(TAGGTC33TACT)-3'	45.9	-3.9
	3'-d(ATCCAGTTATGA)-5'				3'-d(ATCCAGTTATGA)-5'
PY03+D02	5'-d(TAGGTC2ATACT)-3'	39.4	-10.4	PY07+D02	5'-d(TAGGTC3AT3CT)-3'	61.7	11.9
	3'-d(ATCCAGTTATGA)-5'				3'-d(ATCCAGTTATGA)-5'
PY08+D02	5'-d(TAGGTC3ATACT)-3'	54.0	4.2	PY09+D02	5'-d(TAGGTCA3T3CT)-3'	59.5	9.7
	3'-d(ATCCAGTTATGA)-5'				3'-d(ATCCAGTTATGA)-5'
D01+PY05	5'-d(TAGGTCAATACT)-3'	41.0	-8.8	PY01+PY05	5'-d(TAGGTC22TACT)-3'	48.8	-1.0
	3'-d(ATCCAGTT2TGA)-5'				3'-d(ATCCAGTT2TGA)-5'
D01+PY10	5'-d(TAGGTCAATACT)-3'	57.0	7.2	PY02+PY05	5'-d(TAGGTC2AT2CT)-3'	54.0	4.2
	3'-d(ATCCAGTT3TGA)-5'				3'-d(ATCCAGTT2TGA)-5'
PY03+PY05	5'-d(TAGGTC2ATACT)-3'	49.8	0	PY04+PY05	5'-d(TAGGTCA2T2CT)-3'	60.0	10.2
	3'-d(ATCCAGTT2TGA)-5'				3'-d(ATCCAGTT2TGA)-5'
PY01+D02	5'-d(TAGGTC22TACT)-3'	44.3	-4.5	PY06+PY10	5'-d(TAGGTC33TACT)-3'	55.2	5.4
	3'-d(ATCCAGTTATGA)-5'				3'-d(ATCCAGTT3TGA)-5'
PY02+D02	5'-d(TAGGTC2AT2CT)-3'	36.5	-13.3	PY09+PY10	5'-d(TAGGTCA3T3CT)-3'	59.4	9.6
	3'-d(ATCCAGTTATGA)-5'				3'-d(ATCCAGTT3TGA)-5'
PY04+D02	5'-d(TAGGTCA2T2CT)-3'	52.1	2.3	PY07+PY10	5'-d(TAGGTC3AT3CT)-3'	58.6	8.8
	3'-d(ATCCAGTTATGA)-5'				3'-d(ATCCAGTT3TGA)-5'
PY08+PY10	5'-d(TAGGTC3ATACT)-3'	64.2	14.4
	3'-d(ATCCAGTT3TGA)-5'