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Partial B-to-A DNA transition upon minor groove binding of protein Sac7d monitored by Raman spectroscopy.
Biochemistry. 2004 Aug 03; 43(30):9600-9.B

Abstract

Members of the Sso7d/Sac7d protein family and other related proteins are believed to play an important role in DNA packaging and maintenance in archeons. Sso7d/Sac7d are small, abundant, basic, and nonspecific DNA-binding proteins of the hyperthermophilic archeon Sulfolobus. Structures of several complexes of Sso7d/Sac7d with DNA octamers are known. These structures are characterized by sequence unspecific minor groove binding of the proteins and sharp kinking of the double helix. Corresponding Raman vibrational signatures have been identified in this study. A Raman spectroscopic analysis of Sac7d binding to the oligonucleotide decamer d(GAGGCGCCTC)(2) reveals large conformational perturbations in the DNA structure upon complex formation. Perturbed Raman bands are associated with the vibrational modes of the sugar phosphate backbone and frequency shifts of bands assigned to nucleoside vibrations. Large changes in the DNA backbone and partial B- to A-form DNA transitions are indicated that are closely associated with C2'-endo/anti to C3'-endo/anti conversion of the deoxyadenosyl moiety upon Sac7d binding. The major spectral feature of Sac7d binding is kinking of the DNA. Raman markers of minor groove binding do not largely contribute to spectral differences; however, clear indications for minor groove binding come from G-N2 and G-N3 signals that are supported by Trp24 features. Trp24 is the only tryptophan present in Sac7d and binds to guanine N3, as has been demonstrated clearly in X-ray structures of Sac7d-DNA complexes. No changes of the Sac7d secondary structure have been detected upon DNA binding.

Authors+Show Affiliations

AG Biopolymerspektroskopie, Max-Delbrück-Centrum für Molekulare Medizin Berlin-Buch, Robert-Rössle-Strabetae 10, D-13092 Berlin, Germany.No affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

15274614

Citation

Dostál, Lubomír, et al. "Partial B-to-A DNA Transition Upon Minor Groove Binding of Protein Sac7d Monitored By Raman Spectroscopy." Biochemistry, vol. 43, no. 30, 2004, pp. 9600-9.
Dostál L, Chen CY, Wang AH, et al. Partial B-to-A DNA transition upon minor groove binding of protein Sac7d monitored by Raman spectroscopy. Biochemistry. 2004;43(30):9600-9.
Dostál, L., Chen, C. Y., Wang, A. H., & Welfle, H. (2004). Partial B-to-A DNA transition upon minor groove binding of protein Sac7d monitored by Raman spectroscopy. Biochemistry, 43(30), 9600-9.
Dostál L, et al. Partial B-to-A DNA Transition Upon Minor Groove Binding of Protein Sac7d Monitored By Raman Spectroscopy. Biochemistry. 2004 Aug 3;43(30):9600-9. PubMed PMID: 15274614.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Partial B-to-A DNA transition upon minor groove binding of protein Sac7d monitored by Raman spectroscopy. AU - Dostál,Lubomír, AU - Chen,Chin-Yu, AU - Wang,Andrew H-J, AU - Welfle,Heinz, PY - 2004/7/28/pubmed PY - 2004/9/25/medline PY - 2004/7/28/entrez SP - 9600 EP - 9 JF - Biochemistry JO - Biochemistry VL - 43 IS - 30 N2 - Members of the Sso7d/Sac7d protein family and other related proteins are believed to play an important role in DNA packaging and maintenance in archeons. Sso7d/Sac7d are small, abundant, basic, and nonspecific DNA-binding proteins of the hyperthermophilic archeon Sulfolobus. Structures of several complexes of Sso7d/Sac7d with DNA octamers are known. These structures are characterized by sequence unspecific minor groove binding of the proteins and sharp kinking of the double helix. Corresponding Raman vibrational signatures have been identified in this study. A Raman spectroscopic analysis of Sac7d binding to the oligonucleotide decamer d(GAGGCGCCTC)(2) reveals large conformational perturbations in the DNA structure upon complex formation. Perturbed Raman bands are associated with the vibrational modes of the sugar phosphate backbone and frequency shifts of bands assigned to nucleoside vibrations. Large changes in the DNA backbone and partial B- to A-form DNA transitions are indicated that are closely associated with C2'-endo/anti to C3'-endo/anti conversion of the deoxyadenosyl moiety upon Sac7d binding. The major spectral feature of Sac7d binding is kinking of the DNA. Raman markers of minor groove binding do not largely contribute to spectral differences; however, clear indications for minor groove binding come from G-N2 and G-N3 signals that are supported by Trp24 features. Trp24 is the only tryptophan present in Sac7d and binds to guanine N3, as has been demonstrated clearly in X-ray structures of Sac7d-DNA complexes. No changes of the Sac7d secondary structure have been detected upon DNA binding. SN - 0006-2960 UR - https://www.unboundmedicine.com/medline/citation/15274614/Partial_B_to_A_DNA_transition_upon_minor_groove_binding_of_protein_Sac7d_monitored_by_Raman_spectroscopy_ L2 - https://doi.org/10.1021/bi049192r DB - PRIME DP - Unbound Medicine ER -