TY - JOUR

T1 - How Human H1 Histone Recognizes DNA

AU - Luzhetskaya, Olesya P.

AU - Sedykh, Sergey E.

AU - Nevinsky, Georgy A.

N1 - Funding Information: Funding: This research was maintained by the Russian Foundation for Basic Research (20-04-00281) and Russian State-funded budget project AAAA-A17-117020210023-1. Publisher Copyright: © 2020 by the authors.

PY - 2020/10

Y1 - 2020/10

N2 - Linker H1 histone is one of the five main histone proteins (H1, H2A, H2B, H3, and H4), which are components of chromatin in eukaryotic cells. Here we have analyzed the patterns of DNA recognition by free H1 histone using a stepwise increase of the ligand complexity method; the afinity of H1 histone for various single- and double-stranded oligonucleotides (d(pN)n; n = 1-20) was evaluated using their competition with 12-mer [32P]labeled oligonucleotide and protein-oligonucleotide complex delaying on nitrocellulose membrane filters. It was shown that minimal ligands of H1 histone (like other DNA-dependent proteins and enzymes) are different mononucleotides (dNMPs; Kd = (1.30 ± 0.2) ± 10-2 M). An increase in the length of single-stranded (ss) homo- and hetero-oligonucleotides (d(pA)n, d(pT)n, d(pC)n, and d(pN)n with different bases) by one nucleotide link regardless of their bases, leads to a monotonic increase in their afinity by a factor of f = 3.0 ± 0.2. This factor f corresponds to the Kd value = 1/f characterizing the afinity of one nucleotide of different ss d(pN)n for H1 at n = 2-6 (which are covered by this protein globule) is approximately 0.33 ± 0.02 M. The afinity of five out of six DNA nucleotide units is approximately 25 times lower than for one of the links. The afinity of duplexes of complementary homo- and hetero-d(pN)20 is only 1.3-3.3-fold higher in comparison with corresponding ss oligonucleotides. H1 histone forms mainly weak additive contacts with internucleoside phosphate groups of ssDNAs and one chain of double-stranded DNAs, but not with the bases.

AB - Linker H1 histone is one of the five main histone proteins (H1, H2A, H2B, H3, and H4), which are components of chromatin in eukaryotic cells. Here we have analyzed the patterns of DNA recognition by free H1 histone using a stepwise increase of the ligand complexity method; the afinity of H1 histone for various single- and double-stranded oligonucleotides (d(pN)n; n = 1-20) was evaluated using their competition with 12-mer [32P]labeled oligonucleotide and protein-oligonucleotide complex delaying on nitrocellulose membrane filters. It was shown that minimal ligands of H1 histone (like other DNA-dependent proteins and enzymes) are different mononucleotides (dNMPs; Kd = (1.30 ± 0.2) ± 10-2 M). An increase in the length of single-stranded (ss) homo- and hetero-oligonucleotides (d(pA)n, d(pT)n, d(pC)n, and d(pN)n with different bases) by one nucleotide link regardless of their bases, leads to a monotonic increase in their afinity by a factor of f = 3.0 ± 0.2. This factor f corresponds to the Kd value = 1/f characterizing the afinity of one nucleotide of different ss d(pN)n for H1 at n = 2-6 (which are covered by this protein globule) is approximately 0.33 ± 0.02 M. The afinity of five out of six DNA nucleotide units is approximately 25 times lower than for one of the links. The afinity of duplexes of complementary homo- and hetero-d(pN)20 is only 1.3-3.3-fold higher in comparison with corresponding ss oligonucleotides. H1 histone forms mainly weak additive contacts with internucleoside phosphate groups of ssDNAs and one chain of double-stranded DNAs, but not with the bases.

KW - human H1 histone

KW - oligonucleotides

KW - patterns of DNA recognition

KW - LINKER-HISTONE

KW - KINETIC BASIS

KW - SHORT OLIGONUCLEOTIDES

KW - ENZYME INTERACTION

KW - I TOPOISOMERASES

KW - STRUCTURAL BASIS

KW - FPG PROTEIN

KW - CHROMATIN

KW - REPAIR

KW - SUBFRACTIONS

KW - Oligonucleotides

KW - Human H1 histone

KW - Patterns of DNA recognition

KW - Humans

KW - Oligonucleotides/chemistry

KW - DNA, Single-Stranded/chemistry

KW - Histones/chemistry

UR - http://www.scopus.com/inward/record.url?scp=85092585747&partnerID=8YFLogxK

U2 - 10.3390/molecules25194556

DO - 10.3390/molecules25194556

M3 - Article

C2 - 33028027

VL - 25

JO - Molecules

JF - Molecules

SN - 1420-3049

IS - 19

M1 - 4556

ER -