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Derivatization of DNAs with selenium at 6-position of guanine for function and crystal structure studies.

Salon J, Jiang J, Sheng J, Gerlits OO, Huang Z - Nucleic Acids Res. (2008)

Bottom Line: We found that the UV absorption of the Se-DNAs red-shifts over 100 nm to 360 nm (epsilon = 2.3 x 10(4) M(-1) cm(-1)), the Se-DNAs are yellow colored, and this Se modification is relatively stable in water and at elevated temperature.Moreover, we successfully crystallized a ternary complex of the Se-G-DNA, RNA and RNase H.Furthermore, this novel selenium modification of nucleic acids can be used to investigate chemogenetics and structure of nucleic acids and their protein complexes.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA.

ABSTRACT
To investigate nucleic acid base pairing and stacking via atom-specific mutagenesis and crystallography, we have synthesized for the first time the 6-Se-deoxyguanosine phosphoramidite and incorporated it into DNAs via solid-phase synthesis with a coupling yield over 97%. We found that the UV absorption of the Se-DNAs red-shifts over 100 nm to 360 nm (epsilon = 2.3 x 10(4) M(-1) cm(-1)), the Se-DNAs are yellow colored, and this Se modification is relatively stable in water and at elevated temperature. Moreover, we successfully crystallized a ternary complex of the Se-G-DNA, RNA and RNase H. The crystal structure determination and analysis reveal that the overall structures of the native and Se-modified nucleic acid duplexes are very similar, the selenium atom participates in a Se-mediated hydrogen bond (Se ... H-N), and the (Se)G and C form a base pair similar to the natural G-C pair though the Se-modification causes the base-pair to shift (approximately 0.3 A). Our biophysical and structural studies provide new insights into the nucleic acid flexibility, duplex recognition and stability. Furthermore, this novel selenium modification of nucleic acids can be used to investigate chemogenetics and structure of nucleic acids and their protein complexes.

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The superimposed global and local structures of the 6-Se-G-modified (2R7Y) and native (2G8U) DNA/RNA duplexes (5′-ATGTCG-p-3′/5′-UCGACA-3′) of the nucleic acid–protein complex; the balls represent selenium atoms in the Se-derivatized DNA (5′-AT-SeG-TC-SeG-p-3′). (A) The structure of the Se-DNA sequence (2R7Y, in yellow) is superimposed over the corresponding native (2G8U, in grey); (B) The structure of the RNA sequence (2R7Y, in green) is superimposed over the corresponding native (2G8U, in grey); (C) The duplex structure of the Se-DNA/RNA hybrid (2R7Y, in green) is superimposed over the corresponding native (2G8U, in cyan); (D) The comparison of the Se-modified (in green) and native (in cyan) G3/C5 base-pair structures; (E) The Se-G3/C5 base pair (2R7Y) with the experimental electron density shows three hydrogen bonds (exo-6-Se/exo-4-NH2, 1-NH/N3, and exo-2-NH2/exo-2-O) with bond lengths in 3.48 Å, 3.16 Å and 2.59 Å, respectively.
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Figure 6: The superimposed global and local structures of the 6-Se-G-modified (2R7Y) and native (2G8U) DNA/RNA duplexes (5′-ATGTCG-p-3′/5′-UCGACA-3′) of the nucleic acid–protein complex; the balls represent selenium atoms in the Se-derivatized DNA (5′-AT-SeG-TC-SeG-p-3′). (A) The structure of the Se-DNA sequence (2R7Y, in yellow) is superimposed over the corresponding native (2G8U, in grey); (B) The structure of the RNA sequence (2R7Y, in green) is superimposed over the corresponding native (2G8U, in grey); (C) The duplex structure of the Se-DNA/RNA hybrid (2R7Y, in green) is superimposed over the corresponding native (2G8U, in cyan); (D) The comparison of the Se-modified (in green) and native (in cyan) G3/C5 base-pair structures; (E) The Se-G3/C5 base pair (2R7Y) with the experimental electron density shows three hydrogen bonds (exo-6-Se/exo-4-NH2, 1-NH/N3, and exo-2-NH2/exo-2-O) with bond lengths in 3.48 Å, 3.16 Å and 2.59 Å, respectively.

Mentions: Both the native and Se-DNA-derivatized complexes were crystallized in C2 space group with similar unit cell dimensions. Our study reveals that the protein structures of both the native (2.70 Å resolution, PDB ID: 2G8U; 37,38) and modified (1.80 Å resolution, PDB ID: 2R7Y) complexes are virtually identical, and that the nucleic acid global structures of the native and Se-modified duplexes are very similar (Figure 6) though the nucleobases shift locally (Figure 6A–D). Probably due to flexibility of the over-hung ends, more structural differences are observed at the DNA and RNA termini. The distance between 1-NH of G3 in the DNA sequence and the N3 of C5 in the RNA sequence, and the distance between exo-2-NH2 of G3 and exo-2-O of C5 are 3.16 Å and 2.59 Å, respectively (the corresponding H-bond lengths of the native G–C pair: 2.99 Å and 2.95 Å). These distances indicate the retention of the two native hydrogen bonds of the G3–C5 base pair. Since the Se atomic radius is 0.43 Å larger than that of O and hydrogen bond length is normally 2.7–3.2 Å, the distance (3.48 Å) between the G3 exo-6-Se and C5 exo-4-NH2 (the native H-bond length: 2.99) indicates a selenium-mediated H-bond (Figure 6E). Thus, the SeG3–C5 base pair consists of three hydrogen bonds (exo-6-Se/exo-4-NH2, 1-NH/N3, and exo-2-NH2/exo-2-O). Interestingly, the hydrogen bond length (2.59 Å) between G3 exo-2-NH2 and C5 exo-2-O is 0.36 Å shorter than the corresponding native bond (2.95 Å).Figure 6.


Derivatization of DNAs with selenium at 6-position of guanine for function and crystal structure studies.

Salon J, Jiang J, Sheng J, Gerlits OO, Huang Z - Nucleic Acids Res. (2008)

The superimposed global and local structures of the 6-Se-G-modified (2R7Y) and native (2G8U) DNA/RNA duplexes (5′-ATGTCG-p-3′/5′-UCGACA-3′) of the nucleic acid–protein complex; the balls represent selenium atoms in the Se-derivatized DNA (5′-AT-SeG-TC-SeG-p-3′). (A) The structure of the Se-DNA sequence (2R7Y, in yellow) is superimposed over the corresponding native (2G8U, in grey); (B) The structure of the RNA sequence (2R7Y, in green) is superimposed over the corresponding native (2G8U, in grey); (C) The duplex structure of the Se-DNA/RNA hybrid (2R7Y, in green) is superimposed over the corresponding native (2G8U, in cyan); (D) The comparison of the Se-modified (in green) and native (in cyan) G3/C5 base-pair structures; (E) The Se-G3/C5 base pair (2R7Y) with the experimental electron density shows three hydrogen bonds (exo-6-Se/exo-4-NH2, 1-NH/N3, and exo-2-NH2/exo-2-O) with bond lengths in 3.48 Å, 3.16 Å and 2.59 Å, respectively.
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Figure 6: The superimposed global and local structures of the 6-Se-G-modified (2R7Y) and native (2G8U) DNA/RNA duplexes (5′-ATGTCG-p-3′/5′-UCGACA-3′) of the nucleic acid–protein complex; the balls represent selenium atoms in the Se-derivatized DNA (5′-AT-SeG-TC-SeG-p-3′). (A) The structure of the Se-DNA sequence (2R7Y, in yellow) is superimposed over the corresponding native (2G8U, in grey); (B) The structure of the RNA sequence (2R7Y, in green) is superimposed over the corresponding native (2G8U, in grey); (C) The duplex structure of the Se-DNA/RNA hybrid (2R7Y, in green) is superimposed over the corresponding native (2G8U, in cyan); (D) The comparison of the Se-modified (in green) and native (in cyan) G3/C5 base-pair structures; (E) The Se-G3/C5 base pair (2R7Y) with the experimental electron density shows three hydrogen bonds (exo-6-Se/exo-4-NH2, 1-NH/N3, and exo-2-NH2/exo-2-O) with bond lengths in 3.48 Å, 3.16 Å and 2.59 Å, respectively.
Mentions: Both the native and Se-DNA-derivatized complexes were crystallized in C2 space group with similar unit cell dimensions. Our study reveals that the protein structures of both the native (2.70 Å resolution, PDB ID: 2G8U; 37,38) and modified (1.80 Å resolution, PDB ID: 2R7Y) complexes are virtually identical, and that the nucleic acid global structures of the native and Se-modified duplexes are very similar (Figure 6) though the nucleobases shift locally (Figure 6A–D). Probably due to flexibility of the over-hung ends, more structural differences are observed at the DNA and RNA termini. The distance between 1-NH of G3 in the DNA sequence and the N3 of C5 in the RNA sequence, and the distance between exo-2-NH2 of G3 and exo-2-O of C5 are 3.16 Å and 2.59 Å, respectively (the corresponding H-bond lengths of the native G–C pair: 2.99 Å and 2.95 Å). These distances indicate the retention of the two native hydrogen bonds of the G3–C5 base pair. Since the Se atomic radius is 0.43 Å larger than that of O and hydrogen bond length is normally 2.7–3.2 Å, the distance (3.48 Å) between the G3 exo-6-Se and C5 exo-4-NH2 (the native H-bond length: 2.99) indicates a selenium-mediated H-bond (Figure 6E). Thus, the SeG3–C5 base pair consists of three hydrogen bonds (exo-6-Se/exo-4-NH2, 1-NH/N3, and exo-2-NH2/exo-2-O). Interestingly, the hydrogen bond length (2.59 Å) between G3 exo-2-NH2 and C5 exo-2-O is 0.36 Å shorter than the corresponding native bond (2.95 Å).Figure 6.

Bottom Line: We found that the UV absorption of the Se-DNAs red-shifts over 100 nm to 360 nm (epsilon = 2.3 x 10(4) M(-1) cm(-1)), the Se-DNAs are yellow colored, and this Se modification is relatively stable in water and at elevated temperature.Moreover, we successfully crystallized a ternary complex of the Se-G-DNA, RNA and RNase H.Furthermore, this novel selenium modification of nucleic acids can be used to investigate chemogenetics and structure of nucleic acids and their protein complexes.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA.

ABSTRACT
To investigate nucleic acid base pairing and stacking via atom-specific mutagenesis and crystallography, we have synthesized for the first time the 6-Se-deoxyguanosine phosphoramidite and incorporated it into DNAs via solid-phase synthesis with a coupling yield over 97%. We found that the UV absorption of the Se-DNAs red-shifts over 100 nm to 360 nm (epsilon = 2.3 x 10(4) M(-1) cm(-1)), the Se-DNAs are yellow colored, and this Se modification is relatively stable in water and at elevated temperature. Moreover, we successfully crystallized a ternary complex of the Se-G-DNA, RNA and RNase H. The crystal structure determination and analysis reveal that the overall structures of the native and Se-modified nucleic acid duplexes are very similar, the selenium atom participates in a Se-mediated hydrogen bond (Se ... H-N), and the (Se)G and C form a base pair similar to the natural G-C pair though the Se-modification causes the base-pair to shift (approximately 0.3 A). Our biophysical and structural studies provide new insights into the nucleic acid flexibility, duplex recognition and stability. Furthermore, this novel selenium modification of nucleic acids can be used to investigate chemogenetics and structure of nucleic acids and their protein complexes.

Show MeSH