Binding mode of meso-tetrakis(N-methylpyridinium-4-yl)porphyrin to poly[d(I-C)2]: Effect of amino group at the minor groove of poly[d(G-C)2] on the porphyrin-DNA interaction

Young Ae Lee; Soomin Lee; Tae Sub Cho; Cheal Kim; Sung Wook Han; Seog K. Kim

doi:10.1021/jp025924i

Binding mode of meso-tetrakis(N-methylpyridinium-4-yl)porphyrin to poly[d(I-C)₂]: Effect of amino group at the minor groove of poly[d(G-C)₂] on the porphyrin-DNA interaction

Young Ae Lee, Soomin Lee, Tae Sub Cho, Cheal Kim, Sung Wook Han, Seog K. Kim

Dept. of Fine Chemistry

Research output: Contribution to journal › Article › peer-review

48 Scopus citations

Abstract

The spectral properties of meso-tetrakis(N-methylpyridinium-4-yl)porphyrin (TMPyP) complexed with poly[d(I-C)₂] were compared with that bound to poly[d(G-C)₂] and poly[d(A-T)₂]. At low TMPyP/DNA base ratios, the TMPyP-poly[d(I-C)₂] complex exhibits a similar NaCl dependent absorption and circular dichroism spectrum to that of the TMPyP-poly[d(A-T)₂] complex. The negative CD band in the Sorer absorption region of these complexes disappears as the NaCl concentration reaches around 10 mM. At a NaCl concentration higher than 10 mM, the resulting positive CD band is pronounced. In contrast, the change in negative CD band of the TMPyP-poly[d(G-C)₂] complex, which is believed to be intercalated, is small. The molecular plane of porphyrin in the TMPyP-poly[d(I-C)₂] complex for both species associated with negative and positive CD is perpendicular relative to the polynucleotide helix axis. Therefore, it is indicative that TMPyP (partially) intercalates between the base pairs of poly[d(I-C)₂] at a very low mixing ratio and NaC1 concentration and exhibits an outside binding mode as the NaCl concentration increases. It then follows that the amine group of guanine that protrudes in to the minor groove either helps stabilize the intercalated TMPyP or serves to destabilize the minor groove binding.

Original language	English
Pages (from-to)	11351-11355
Number of pages	5
Journal	Journal of Physical Chemistry B
Volume	106
Issue number	43
DOIs	https://doi.org/10.1021/jp025924i
State	Published - 31 Oct 2002

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@article{d78c5f48d75c4f30a22ba7e041e069b3,

title = "Binding mode of meso-tetrakis(N-methylpyridinium-4-yl)porphyrin to poly[d(I-C)2]: Effect of amino group at the minor groove of poly[d(G-C)2] on the porphyrin-DNA interaction",

abstract = "The spectral properties of meso-tetrakis(N-methylpyridinium-4-yl)porphyrin (TMPyP) complexed with poly[d(I-C)2] were compared with that bound to poly[d(G-C)2] and poly[d(A-T)2]. At low TMPyP/DNA base ratios, the TMPyP-poly[d(I-C)2] complex exhibits a similar NaCl dependent absorption and circular dichroism spectrum to that of the TMPyP-poly[d(A-T)2] complex. The negative CD band in the Sorer absorption region of these complexes disappears as the NaCl concentration reaches around 10 mM. At a NaCl concentration higher than 10 mM, the resulting positive CD band is pronounced. In contrast, the change in negative CD band of the TMPyP-poly[d(G-C)2] complex, which is believed to be intercalated, is small. The molecular plane of porphyrin in the TMPyP-poly[d(I-C)2] complex for both species associated with negative and positive CD is perpendicular relative to the polynucleotide helix axis. Therefore, it is indicative that TMPyP (partially) intercalates between the base pairs of poly[d(I-C)2] at a very low mixing ratio and NaC1 concentration and exhibits an outside binding mode as the NaCl concentration increases. It then follows that the amine group of guanine that protrudes in to the minor groove either helps stabilize the intercalated TMPyP or serves to destabilize the minor groove binding.",

author = "Lee, \{Young Ae\} and Soomin Lee and Cho, \{Tae Sub\} and Cheal Kim and Han, \{Sung Wook\} and Kim, \{Seog K.\}",

year = "2002",

month = oct,

day = "31",

doi = "10.1021/jp025924i",

language = "English",

volume = "106",

pages = "11351--11355",

journal = "Journal of Physical Chemistry B",

issn = "1520-6106",

number = "43",

}

Binding mode of meso-tetrakis(N-methylpyridinium-4-yl)porphyrin to poly[d(I-C)₂]: Effect of amino group at the minor groove of poly[d(G-C)₂] on the porphyrin-DNA interaction. / Lee, Young Ae; Lee, Soomin; Cho, Tae Sub et al.
In: Journal of Physical Chemistry B, Vol. 106, No. 43, 31.10.2002, p. 11351-11355.

Research output: Contribution to journal › Article › peer-review

TY - JOUR

T1 - Binding mode of meso-tetrakis(N-methylpyridinium-4-yl)porphyrin to poly[d(I-C)2]

T2 - Effect of amino group at the minor groove of poly[d(G-C)2] on the porphyrin-DNA interaction

AU - Lee, Young Ae

AU - Lee, Soomin

AU - Cho, Tae Sub

AU - Kim, Cheal

AU - Han, Sung Wook

AU - Kim, Seog K.

PY - 2002/10/31

Y1 - 2002/10/31

N2 - The spectral properties of meso-tetrakis(N-methylpyridinium-4-yl)porphyrin (TMPyP) complexed with poly[d(I-C)2] were compared with that bound to poly[d(G-C)2] and poly[d(A-T)2]. At low TMPyP/DNA base ratios, the TMPyP-poly[d(I-C)2] complex exhibits a similar NaCl dependent absorption and circular dichroism spectrum to that of the TMPyP-poly[d(A-T)2] complex. The negative CD band in the Sorer absorption region of these complexes disappears as the NaCl concentration reaches around 10 mM. At a NaCl concentration higher than 10 mM, the resulting positive CD band is pronounced. In contrast, the change in negative CD band of the TMPyP-poly[d(G-C)2] complex, which is believed to be intercalated, is small. The molecular plane of porphyrin in the TMPyP-poly[d(I-C)2] complex for both species associated with negative and positive CD is perpendicular relative to the polynucleotide helix axis. Therefore, it is indicative that TMPyP (partially) intercalates between the base pairs of poly[d(I-C)2] at a very low mixing ratio and NaC1 concentration and exhibits an outside binding mode as the NaCl concentration increases. It then follows that the amine group of guanine that protrudes in to the minor groove either helps stabilize the intercalated TMPyP or serves to destabilize the minor groove binding.

AB - The spectral properties of meso-tetrakis(N-methylpyridinium-4-yl)porphyrin (TMPyP) complexed with poly[d(I-C)2] were compared with that bound to poly[d(G-C)2] and poly[d(A-T)2]. At low TMPyP/DNA base ratios, the TMPyP-poly[d(I-C)2] complex exhibits a similar NaCl dependent absorption and circular dichroism spectrum to that of the TMPyP-poly[d(A-T)2] complex. The negative CD band in the Sorer absorption region of these complexes disappears as the NaCl concentration reaches around 10 mM. At a NaCl concentration higher than 10 mM, the resulting positive CD band is pronounced. In contrast, the change in negative CD band of the TMPyP-poly[d(G-C)2] complex, which is believed to be intercalated, is small. The molecular plane of porphyrin in the TMPyP-poly[d(I-C)2] complex for both species associated with negative and positive CD is perpendicular relative to the polynucleotide helix axis. Therefore, it is indicative that TMPyP (partially) intercalates between the base pairs of poly[d(I-C)2] at a very low mixing ratio and NaC1 concentration and exhibits an outside binding mode as the NaCl concentration increases. It then follows that the amine group of guanine that protrudes in to the minor groove either helps stabilize the intercalated TMPyP or serves to destabilize the minor groove binding.

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U2 - 10.1021/jp025924i

DO - 10.1021/jp025924i

M3 - Article

AN - SCOPUS:0037206702

SN - 1520-6106

VL - 106

SP - 11351

EP - 11355

JO - Journal of Physical Chemistry B

JF - Journal of Physical Chemistry B

IS - 43

ER -

Binding mode of meso-tetrakis(N-methylpyridinium-4-yl)porphyrin to poly[d(I-C)₂]: Effect of amino group at the minor groove of poly[d(G-C)₂] on the porphyrin-DNA interaction

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